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Kathryn Holt, Ph.D. - Publications

Affiliations: 
2005 Capella University, Minneapolis, MN, United States 
Area:
Social Psychology, Individual and Family Studies, Medicine and Surgery
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Year Citation  Score
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2019 Hawkey J, Le Hello S, Doublet B, Granier SA, Hendriksen RS, Fricke WF, Ceyssens PJ, Gomart C, Billman-Jacobe H, Holt KE, Weill FX. Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198. Microbial Genomics. PMID 31107206 DOI: 10.1099/mgen.0.000269  0.265
2021 Hawkey J, Paranagama K, Baker KS, Bengtsson RJ, Weill FX, Thomson NR, Baker S, Cerdeira L, Iqbal Z, Hunt M, Ingle DJ, Dallman TJ, Jenkins C, Williamson DA, Holt KE. Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nature Communications. 12: 2684. PMID 33976138 DOI: 10.1038/s41467-021-22700-4  0.262
2016 Schultz MB, Pham Thanh D, Tran Do Hoan N, Wick RR, Ingle DJ, Hawkey J, Edwards DJ, Kenyon JJ, Phu Huong Lan N, Campbell JI, Thwaites G, Thi Khanh Nhu N, Hall RM, Fournier-Level A, Baker S, Holt KE, et al. Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward. Microbial Genomics. 2: e000050. PMID 28348846 DOI: 10.1099/mgen.0.000050  0.259
2019 Wyres KL, Wick RR, Judd LM, Froumine R, Tokolyi A, Gorrie CL, Lam MMC, Duchêne S, Jenney A, Holt KE. Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. Plos Genetics. 15: e1008114. PMID 30986243 DOI: 10.1371/journal.pgen.1008114  0.252
2015 Baines SL, Holt KE, Schultz MB, Seemann T, Howden BO, Jensen SO, van Hal SJ, Coombs GW, Firth N, Powell DR, Stinear TP, Howden BP. Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus. Mbio. 6: e00080. PMID 25736880 DOI: 10.1128/mBio.00080-15  0.252
2023 Zhou K, Xue CX, Xu T, Shen P, Wei S, Wyres KL, Lam MMC, Liu J, Lin H, Chen Y, Holt KE, Xiao Y. A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China. Nature Communications. 14: 2464. PMID 37117217 DOI: 10.1038/s41467-023-38061-z  0.252
2016 Wyres KL, Holt KE. Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones. Trends in Microbiology. PMID 27742466 DOI: 10.1016/j.tim.2016.09.007  0.25
2016 Holt K, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ, Dougan G, Hall R. Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1. Microbial Genomics. 2: e000052. PMID 28348844 DOI: 10.1099/mgen.0.000052  0.249
2018 Ingle DJ, Levine MM, Kotloff KL, Holt KE, Robins-Browne RM. Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa. Nature Microbiology. PMID 30127495 DOI: 10.1038/s41564-018-0217-4  0.247
2009 Kingsley RA, Msefula CL, Thomson NR, Kariuki S, Holt KE, Gordon MA, Harris D, Clarke L, Whitehead S, Sangal V, Marsh K, Achtman M, Molyneux ME, Cormican M, Parkhill J, et al. Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Research. 19: 2279-87. PMID 19901036 DOI: 10.1101/gr.091017.109  0.247
2018 Nigro SJ, Wick R, Holt KE, Hall RM. Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage. Microbiology Resource Announcements. 7. PMID 30533856 DOI: 10.1128/MRA.01199-18  0.241
2014 Stinear TP, Holt KE, Chua K, Stepnell J, Tuck KL, Coombs G, Harrison PF, Seemann T, Howden BP. Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus. Genome Biology and Evolution. 6: 366-78. PMID 24482534 DOI: 10.1093/Gbe/Evu022  0.241
2012 Holt KE, Baker S, Weill FX, Holmes EC, Kitchen A, Yu J, Sangal V, Brown DJ, Coia JE, Kim DW, Choi SY, Kim SH, da Silveira WD, Pickard DJ, Farrar JJ, et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nature Genetics. 44: 1056-9. PMID 22863732 DOI: 10.1038/Ng.2369  0.24
2013 Edwards DJ, Holt KE. Beginner's guide to comparative bacterial genome analysis using next-generation sequence data. Microbial Informatics and Experimentation. 3: 2. PMID 23575213 DOI: 10.1186/2042-5783-3-2  0.238
2014 Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ, Tomita T, Zobel J, Holt KE. SRST2: Rapid genomic surveillance for public health and hospital microbiology labs. Genome Medicine. 6: 90. PMID 25422674 DOI: 10.1186/s13073-014-0090-6  0.238
2023 Hetland MAK, Hawkey J, Bernhoff E, Bakksjø RJ, Kaspersen H, Rettedal SI, Sundsfjord A, Holt KE, Löhr IH. Within-patient and global evolutionary dynamics of ST17. Microbial Genomics. 9. PMID 37200066 DOI: 10.1099/mgen.0.001005  0.238
2018 Lam MMC, Wick RR, Wyres KL, Gorrie CL, Judd LM, Jenney AWJ, Brisse S, Holt KE. Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations. Microbial Genomics. PMID 29985125 DOI: 10.1099/mgen.0.000196  0.235
2018 Baker S, Thomson N, Weill FX, Holt KE. Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens. Science (New York, N.Y.). 360: 733-738. PMID 29773743 DOI: 10.1126/science.aar3777  0.234
2018 Cain AK, Boinett CJ, Barquist L, Dordel J, Fookes M, Mayho M, Ellington MJ, Goulding D, Pickard D, Wick RR, Holt KE, Parkhill J, Thomson NR. Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin. Scientific Reports. 8: 9868. PMID 29959380 DOI: 10.1038/s41598-018-28199-y  0.234
2016 Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, ... Holt KE, et al. Global phylogeography and evolutionary history of Shigella dysenteriae type 1. Nature Microbiology. 1: 16027. PMID 27572446 DOI: 10.1038/Nmicrobiol.2016.27  0.234
2022 Yang L, Shen Y, Jiang J, Wang X, Shao D, Lam MMC, Holt KE, Shao B, Wu C, Shen J, Walsh TR, Schwarz S, Wang Y, Shen Z. Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China. Nature Food. 3: 197-205. PMID 37117646 DOI: 10.1038/s43016-022-00470-6  0.233
2015 Chung The H, Rabaa MA, Thanh DP, Ruekit S, Wangchuk S, Dorji T, Tshering KP, Nguyen TN, Vinh PV, Thanh TH, Minh CN, Turner P, Sar P, Thwaites G, Holt KE, et al. Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan. Microbial Genomics. 1: e000042. PMID 28348825 DOI: 10.1099/mgen.0.000042  0.233
2013 Kingsley RA, Kay S, Connor T, Barquist L, Sait L, Holt KE, Sivaraman K, Wileman T, Goulding D, Clare S, Hale C, Seshasayee A, Harris S, Thomson NR, Gardner P, et al. Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar. Mbio. 4: e00565-13. PMID 23982073 DOI: 10.1128/mBio.00565-13  0.232
2019 Ingle DJ, Nair S, Hartman H, Ashton PM, Dyson ZA, Day M, Freedman J, Chattaway MA, Holt KE, Dallman TJ. Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers. Plos Neglected Tropical Diseases. 13: e0007620. PMID 31513580 DOI: 10.1371/journal.pntd.0007620  0.231
2021 Lam MMC, Wick RR, Watts SC, Cerdeira LT, Wyres KL, Holt KE. A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex. Nature Communications. 12: 4188. PMID 34234121 DOI: 10.1038/s41467-021-24448-3  0.231
2022 Dyson ZA, Malau E, Horwood PF, Ford R, Siba V, Yoannes M, Pomat W, Passey M, Judd LM, Ingle DJ, Williamson DA, Dougan G, Greenhill AR, Holt KE. Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials. Plos Neglected Tropical Diseases. 16: e0010306. PMID 35344544 DOI: 10.1371/journal.pntd.0010306  0.23
2015 Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA, Dance D, Jenney A, Connor TR, Hsu LY, Severin J, Brisse S, Cao H, Wilksch J, Gorrie C, Schultz MB, et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proceedings of the National Academy of Sciences of the United States of America. PMID 26100894 DOI: 10.1073/Pnas.1501049112  0.23
2020 Wyres KL, Cahill SM, Holt KE, Hall RM, Kenyon JJ. Identification of loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with . Microbial Genomics. PMID 32118530 DOI: 10.1099/mgen.0.000339  0.229
2023 Baker KS, Jauneikaite E, Nunn JG, Midega JT, Atun R, Holt KE, Walia K, Howden BP, Tate H, Okeke IN, Carattoli A, Hsu LY, Hopkins KL, Muloi DM, Wheeler NE, et al. Evidence review and recommendations for the implementation of genomics for antimicrobial resistance surveillance: reports from an international expert group. The Lancet. Microbe. PMID 37977164 DOI: 10.1016/S2666-5247(23)00281-1  0.229
2023 Baker KS, Jauneikaite E, Hopkins KL, Lo SW, Sánchez-Busó L, Getino M, Howden BP, Holt KE, Musila LA, Hendriksen RS, Amoako DG, Aanensen DM, Okeke IN, Egyir B, Nunn JG, et al. Genomics for public health and international surveillance of antimicrobial resistance. The Lancet. Microbe. PMID 37977162 DOI: 10.1016/S2666-5247(23)00283-5  0.229
2015 Hamidian M, Hawkey J, Holt KE, Hall RM. Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1. Genome Announcements. 3. PMID 26679588 DOI: 10.1128/genomeA.01478-15  0.228
2021 Argimón S, Yeats CA, Goater RJ, Abudahab K, Taylor B, Underwood A, Sánchez-Busó L, Wong VK, Dyson ZA, Nair S, Park SE, Marks F, Page AJ, Keane JA, Baker S, Holt KE, et al. A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch. Nature Communications. 12: 2879. PMID 34001879 DOI: 10.1038/s41467-021-23091-2  0.228
2008 Holt KE, Parkhill J, Mazzoni CJ, Roumagnac P, Weill FX, Goodhead I, Rance R, Baker S, Maskell DJ, Wain J, Dolecek C, Achtman M, Dougan G. High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nature Genetics. 40: 987-93. PMID 18660809 DOI: 10.1038/ng.195  0.227
2020 Wyres KL, Lam MMC, Holt KE. Population genomics of Klebsiella pneumoniae. Nature Reviews. Microbiology. PMID 32055025 DOI: 10.1038/s41579-019-0315-1  0.226
2021 Viehweger A, Blumenscheit C, Lippmann N, Wyres KL, Brandt C, Hans JB, Hölzer M, Irber L, Gatermann S, Lübbert C, Pletz MW, Holt KE, König B. Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing . Microbial Genomics. 7. PMID 34913861 DOI: 10.1099/mgen.0.000741  0.226
2013 Howden BP, Holt KE, Lam MM, Seemann T, Ballard S, Coombs GW, Tong SY, Grayson ML, Johnson PD, Stinear TP. Genomic insights to control the emergence of vancomycin-resistant enterococci. Mbio. 4. PMID 23943759 DOI: 10.1128/mBio.00412-13  0.224
2010 Kariuki S, Revathi G, Kiiru J, Mengo DM, Mwituria J, Muyodi J, Munyalo A, Teo YY, Holt KE, Kingsley RA, Dougan G. Typhoid in Kenya is associated with a dominant multidrug-resistant Salmonella enterica serovar Typhi haplotype that is also widespread in Southeast Asia. Journal of Clinical Microbiology. 48: 2171-6. PMID 20392916 DOI: 10.1128/JCM.01983-09  0.222
2006 Holt K. What do we tell the children? Contrasting the disclosure choices of two HD families regarding risk status and predictive genetic testing. Journal of Genetic Counseling. 15: 253-65. PMID 16850280 DOI: 10.1007/S10897-006-9021-Z  0.222
2015 Wan Y, Gorrie CL, Jenney A, Mirceta M, Holt KE. Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1. Genome Announcements. 3. PMID 26337895 DOI: 10.1128/genomeA.01007-15  0.222
2016 The HC, Thanh DP, Holt KE, Thomson NR, Baker S. The genomic signatures of Shigella evolution, adaptation and geographical spread. Nature Reviews. Microbiology. PMID 26923111 DOI: 10.1038/nrmicro.2016.10  0.222
2012 Inouye M, Conway TC, Zobel J, Holt KE. Short read sequence typing (SRST): multi-locus sequence types from short reads. Bmc Genomics. 13: 338. PMID 22827703 DOI: 10.1186/1471-2164-13-338  0.221
2022 Qiu S, Liu K, Yang C, Xiang Y, Min K, Zhu K, Liu H, Du X, Yang M, Wang L, Sun Y, Zhou H, Mahe M, Zhao J, Li S, ... ... Holt KE, et al. A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China. Nature Communications. 13: 7365. PMID 36450777 DOI: 10.1038/s41467-022-35136-1  0.221
2016 Ingle DJ, Tauschek M, Edwards DJ, Hocking DM, Pickard DJ, Azzopardi KI, Amarasena T, Bennett-Wood V, Pearson JS, Tamboura B, Antonio M, Ochieng JB, Oundo J, Mandomando I, Qureshi S, ... Holt KE, et al. Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants. Nature Microbiology. 1: 15010. PMID 27571974 DOI: 10.1038/Nmicrobiol.2015.10  0.22
2014 Hamidian M, Holt KE, Pickard D, Dougan G, Hall RM. A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid. The Journal of Antimicrobial Chemotherapy. 69: 955-8. PMID 24235096 DOI: 10.1093/jac/dkt454  0.22
2020 Rahman SIA, Dyson ZA, Klemm EJ, Khanam F, Holt KE, Chowdhury EK, Dougan G, Qadri F. Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016. Plos Neglected Tropical Diseases. 14: e0008036. PMID 32106221 DOI: 10.1371/journal.pntd.0008036  0.22
2018 Ma Q, Huang Y, Wang J, Xu X, Hawkey J, Yang C, Liang B, Hu X, Wu F, Yang X, Wang J, Li R, Li P, Xie J, Jia L, ... Holt KE, et al. Multidrug-resistant Shigella sonnei carrying plasmid-mediated mcr-1 gene in China. International Journal of Antimicrobial Agents. PMID 29501823 DOI: 10.1016/j.ijantimicag.2018.02.019  0.22
2021 Jiang N, Wyres KL, Li J, Feßler AT, Krüger H, Wang Y, Holt KE, Schwarz S, Wu C. Evolution and genomic insight into methicillin-resistant Staphylococcus aureus ST9 in China. The Journal of Antimicrobial Chemotherapy. PMID 33822977 DOI: 10.1093/jac/dkab106  0.22
2019 Hamidian M, Wick RR, Judd LM, Holt KE, Hall RM. Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece. Microbiology Resource Announcements. 8. PMID 31601668 DOI: 10.1128/MRA.00971-19  0.219
2022 Fostervold A, Hetland MAK, Bakksjø R, Bernhoff E, Holt KE, Samuelsen Ø, Simonsen GS, Sundsfjord A, Wyres KL, Löhr IH. A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307. The Journal of Antimicrobial Chemotherapy. 77: 665-674. PMID 34935048 DOI: 10.1093/jac/dkab463  0.219
2021 Argimón S, David S, Underwood A, Abrudan M, Wheeler NE, Kekre M, Abudahab K, Yeats CA, Goater R, Taylor B, Harste H, Muddyman D, Feil EJ, Brisse S, Holt K, et al. Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 73: S325-S335. PMID 34850838 DOI: 10.1093/cid/ciab784  0.219
2018 Park SE, Pham DT, Boinett C, Wong VK, Pak GD, Panzner U, Espinoza LMC, von Kalckreuth V, Im J, Schütt-Gerowitt H, Crump JA, Breiman RF, Adu-Sarkodie Y, Owusu-Dabo E, Rakotozandrindrainy R, ... Holt KE, et al. The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa. Nature Communications. 9: 5094. PMID 30504848 DOI: 10.1038/s41467-018-07370-z  0.218
2018 Hawkey J, Ascher DB, Judd LM, Wick RR, Kostoulias X, Cleland H, Spelman DW, Padiglione A, Peleg AY, Holt KE. Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection. Microbial Genomics. PMID 29547094 DOI: 10.1099/mgen.0.000165  0.217
2007 Holt KE, Thomson NR, Wain J, Phan MD, Nair S, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D, Dougan G, Parkhill J. Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi. Journal of Bacteriology. 189: 4257-64. PMID 17384186 DOI: 10.1128/JB.00232-07  0.217
2019 Boinett CJ, Cain AK, Hawkey J, Do Hoang NT, Khanh NNT, Thanh DP, Dordel J, Campbell JI, Lan NPH, Mayho M, Langridge GC, Hadfield J, Chau NVV, Thwaites GE, Parkhill J, ... Holt KE, et al. Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii. Microbial Genomics. PMID 30720421 DOI: 10.1099/mgen.0.000246  0.217
2023 Jauneikaite E, Baker KS, Nunn JG, Midega JT, Hsu LY, Singh SR, Halpin AL, Hopkins KL, Price JR, Srikantiah P, Egyir B, Okeke IN, Holt KE, Peacock SJ, Feasey NA. Genomics for antimicrobial resistance surveillance to support infection prevention and control in health-care facilities. The Lancet. Microbe. PMID 37977161 DOI: 10.1016/S2666-5247(23)00282-3  0.216
2022 Gorrie CL, Mirčeta M, Wick RR, Judd LM, Lam MMC, Gomi R, Abbott IJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, Pilcher DV, McGloughlin SA, ... ... Holt KE, et al. Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. Nature Communications. 13: 3017. PMID 35641522 DOI: 10.1038/s41467-022-30717-6  0.215
2019 Cerdeira LT, Lam MMC, Wyres KL, Wick RR, Judd LM, Lopes R, Ribas RM, Morais MM, Holt KE, Lincopan N. Small IncQ1 and Col-like Plasmids Harboring and non-Tn Elements (NTE-IId) in High-Risk Lineages of CG258. Antimicrobial Agents and Chemotherapy. PMID 30602517 DOI: 10.1128/AAC.02140-18  0.214
2021 Gomi R, Wyres KL, Holt KE. Detection of plasmid contigs in draft genome assemblies using customized Kraken databases. Microbial Genomics. 7. PMID 33826492 DOI: 10.1099/mgen.0.000550  0.214
2021 Watts SC, Judd LM, Carzino R, Ranganathan S, Holt KE. Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis. Msystems. e0017821. PMID 34463568 DOI: 10.1128/mSystems.00178-21  0.214
2020 Zhou K, Xiao T, David S, Wang Q, Zhou Y, Guo L, Aanensen D, Holt KE, Thomson NR, Grundmann H, Shen P, Xiao Y. Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China. Emerging Infectious Diseases. 26: 289-297. PMID 31961299 DOI: 10.3201/eid2602.190594  0.213
2019 Britto CD, Dyson ZA, Mathias S, Bosco A, Dougan G, Jose S, Nagaraj S, Holt KE, Pollard AJ. Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent. The Journal of Antimicrobial Chemotherapy. PMID 31665304 DOI: 10.1093/jac/dkz435  0.213
2019 Wyrsch ER, Hawkey J, Judd LM, Haites R, Holt KE, Djordjevic SP, Billman-Jacobe H. Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in Typhimurium from Australian Food Animal Production. Microorganisms. 7. PMID 31470501 DOI: 10.3390/microorganisms7090299  0.213
2017 Wick RR, Judd LM, Gorrie CL, Holt KE. Completing bacterial genome assemblies with multiplex MinION sequencing. Microbial Genomics. 3: e000132. PMID 29177090 DOI: 10.1099/mgen.0.000132  0.213
2019 Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen TNT, Ha Thanh T, Voong VP, ... Holt KE, et al. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nature Communications. 10: 4828. PMID 31645551 DOI: 10.1038/s41467-019-12823-0  0.212
2019 Holt KE, Kenyon JJ, Hamidian M, Schultz MB, Pickard DJ, Dougan G, Hall RM. Corrigendum: Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1. Microbial Genomics. 5. PMID 31364967 DOI: 10.1099/mgen.0.000280  0.212
2010 Baker S, Hanage WP, Holt KE. Navigating the future of bacterial molecular epidemiology. Current Opinion in Microbiology. 13: 640-5. PMID 20846899 DOI: 10.1016/j.mib.2010.08.002  0.211
2016 Wyres KL, Wick RR, Gorrie C, Jenney A, Follador R, Thomson NR, Holt KE. Identification of Klebsiella capsule synthesis loci from whole genome data. Microbial Genomics. 2: e000102. PMID 28348840 DOI: 10.1099/mgen.0.000102  0.211
2018 Wick RR, Heinz E, Holt KE, Wyres KL. Kaptive Web: user-friendly capsule and lipopolysaccharide serotype prediction forgenomes. Journal of Clinical Microbiology. PMID 29618504 DOI: 10.1128/JCM.00197-18  0.21
2017 Weill FX, Domman D, Njamkepo E, Tarr C, Rauzier J, Fawal N, Keddy KH, Salje H, Moore S, Mukhopadhyay AK, Bercion R, Luquero FJ, Ngandjio A, Dosso M, Monakhova E, ... Holt KE, et al. Genomic history of the seventh pandemic of cholera in Africa. Science (New York, N.Y.). 358: 785-789. PMID 29123067 DOI: 10.1126/Science.Aad5901  0.21
2023 Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, ... ... Holt KE, et al. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Typhi genomes. Elife. 12. PMID 37697804 DOI: 10.7554/eLife.85867  0.21
2015 Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE. ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data. Bmc Genomics. 16: 667. PMID 26336060 DOI: 10.1186/s12864-015-1860-2  0.209
2013 Hogg G, Dimovski K, Hiley L, Holt KE. Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants. Genome Announcements. 1. PMID 23792739 DOI: 10.1128/genomeA.00293-13  0.208
2016 Moran RA, Holt KE, Hall RM. pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron. Plasmid. PMID 26855083 DOI: 10.1016/j.plasmid.2016.02.002  0.207
2023 Foster-Nyarko E, Cottingham H, Wick RR, Judd LM, Lam MMC, Wyres KL, Stanton TD, Tsang KK, David S, Aanensen DM, Brisse S, Holt KE. Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, . Microbial Genomics. 9. PMID 36752781 DOI: 10.1099/mgen.0.000936  0.204
2016 Moran RA, Anantham S, Holt KE, Hall RM. Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS. The Journal of Antimicrobial Chemotherapy. PMID 28039273 DOI: 10.1093/jac/dkw511  0.204
2023 Miles SL, Torraca V, Dyson ZA, López-Jiménez AT, Foster-Nyarko E, Lobato-Márquez D, Jenkins C, Holt KE, Mostowy S. Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive . Mbio. e0088223. PMID 37255304 DOI: 10.1128/mbio.00882-23  0.203
2020 Okomo U, Senghore M, Darboe S, Bojang E, Zaman SMA, Hossain MJ, Nwakanma D, Le Doare K, Holt KE, Hos NJ, Lawn JE, Bentley SD, Kampmann B. Investigation of sequential outbreaks of Burkholderia cepacia and multidrug-resistant extended spectrum β-lactamase producing Klebsiella species in a West African tertiary hospital neonatal unit: a retrospective genomic analysis. The Lancet. Microbe. 1: e119-e129. PMID 35544262 DOI: 10.1016/S2666-5247(20)30061-6  0.201
2020 Wyres KL, Nguyen TNT, Lam MMC, Judd LM, van Vinh Chau N, Dance DAB, Ip M, Karkey A, Ling CL, Miliya T, Newton PN, Lan NPH, Sengduangphachanh A, Turner P, Veeraraghavan B, ... Holt KE, et al. Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia. Genome Medicine. 12: 11. PMID 31948471 DOI: 10.1186/s13073-019-0706-y  0.201
2013 Pham Thanh D, Tran Vu Thieu N, Tran Thuy C, Lodén M, Tuin K, Campbell JI, Van Minh Hoang N, Voong Vinh P, Farrar JJ, Holt KE, Dougan G, Baker S. Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification. Journal of Clinical Microbiology. 51: 2950-8. PMID 23824765 DOI: 10.1128/JCM.01010-13  0.2
2015 Wyres KL, Gorrie C, Edwards DJ, Wertheim HF, Hsu LY, Van Kinh N, Zadoks R, Baker S, Holt KE. Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258. Genome Biology and Evolution. 7: 1267-79. PMID 25861820 DOI: 10.1093/Gbe/Evv062  0.2
2019 Watts SC, Holt KE. hicap: serotyping of the capsule locus. Journal of Clinical Microbiology. PMID 30944197 DOI: 10.1128/JCM.00190-19  0.2
2018 Britto CD, Dyson ZA, Duchene S, Carter MJ, Gurung M, Kelly DF, Murdoch DR, Ansari I, Thorson S, Shrestha S, Adhikari N, Dougan G, Holt KE, Pollard AJ. Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy. Plos Neglected Tropical Diseases. 12: e0006408. PMID 29684021 DOI: 10.1371/journal.pntd.0006408  0.2
2015 Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ, Feasey NA, Kingsley RA, Thomson NR, Keane JA, Weill FX, Edwards DJ, Hawkey J, Harris SR, Mather AE, Cain AK, ... Holt KE, et al. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nature Genetics. 47: 632-9. PMID 25961941 DOI: 10.1038/ng.3281  0.199
2016 Wong VK, Baker S, Connor TR, Pickard D, Page AJ, Dave J, Murphy N, Holliman R, Sefton A, Millar M, Dyson ZA, Dougan G, Holt KE. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nature Communications. 7: 12827. PMID 27703135 DOI: 10.1038/ncomms12827  0.199
2019 Hamidian M, Wick RR, Hartstein RM, Judd LM, Holt KE, Hall RM. Insights from the revised complete genome sequences of strains AB307-0294 and ACICU belonging to global clones 1 and 2. Microbial Genomics. PMID 31556867 DOI: 10.1099/mgen.0.000298  0.199
2014 Kenyon JJ, Holt KE, Pickard D, Dougan G, Hall RM. Insertions in the OCL1 locus of Acinetobacter baumannii lead to shortened lipooligosaccharides. Research in Microbiology. 165: 472-5. PMID 24861001 DOI: 10.1016/j.resmic.2014.05.034  0.198
2013 Hawkey J, Edwards DJ, Dimovski K, Hiley L, Billman-Jacobe H, Hogg G, Holt KE. Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm. Bmc Genomics. 14: 800. PMID 24245509 DOI: 10.1186/1471-2164-14-800  0.198
2015 Holt KE, Hamidian M, Kenyon JJ, Wynn MT, Hawkey J, Pickard D, Hall RM. Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1. Genome Announcements. 3. PMID 25767221 DOI: 10.1128/genomeA.00032-15  0.197
2021 Raffelsberger N, Hetland MAK, Svendsen K, Småbrekke L, Löhr IH, Andreassen LLE, Brisse S, Holt KE, Sundsfjord A, Samuelsen Ø, Gravningen K. Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity. Gut Microbes. 13: 1939599. PMID 34182896 DOI: 10.1080/19490976.2021.1939599  0.197
2023 Hussein M, Sun Z, Hawkey J, Allobawi R, Judd LM, Carbone V, Sharma R, Thombare V, Baker M, Rao GG, Li J, Holt KE, Velkov T. High-level nitrofurantoin resistance in a clinical isolate of a comparative genomics and metabolomics analysis. Msystems. e0097223. PMID 38078757 DOI: 10.1128/msystems.00972-23  0.197
2019 Hamidian M, Hawkey J, Wick R, Holt KE, Hall RM. Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1. Microbial Genomics. PMID 30648939 DOI: 10.1099/mgen.0.000242  0.196
2008 Baker S, Holt K, van de Vosse E, Roumagnac P, Whitehead S, King E, Ewels P, Keniry A, Weill FX, Lightfoot D, van Dissel JT, Sanderson KE, Farrar J, Achtman M, Deloukas P, et al. High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia. Journal of Clinical Microbiology. 46: 1741-6. PMID 18322069 DOI: 10.1128/JCM.02249-07  0.195
2010 He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, Holt KE, Seth-Smith HM, Quail MA, Rance R, Brooks K, Churcher C, Harris D, Bentley SD, Burrows C, et al. Evolutionary dynamics of Clostridium difficile over short and long time scales. Proceedings of the National Academy of Sciences of the United States of America. 107: 7527-32. PMID 20368420 DOI: 10.1073/Pnas.0914322107  0.194
2019 Wyres K, Wick R, Judd L, Froumine R, Tokolyi A, Gorrie C, Lam M, Duchêne S, Jenney A, Holt K. Genomic evolution of Klebsiella pneumoniae clones: the good, the bad and the ugly Access Microbiology. 1. DOI: 10.1099/ACMI.AC2019.PO0306  0.194
2020 Britto CD, Mathias S, Bosco A, Dyson ZA, Dougan G, Raveendran S, Abin VL, Jose S, Nagaraj S, Holt KE, Pollard AJ. Pathogen genomic surveillance of typhoidal infection in adults and children reveals no association between clinical outcomes and infecting genotypes. Tropical Medicine and Health. 48: 58. PMID 32684794 DOI: 10.1186/s41182-020-00247-2  0.193
2023 Foster-Nyarko E, Cottingham H, Wick RR, Judd LM, Lam MMC, Wyres KL, Stanton TD, Tsang KK, David S, Aanensen DM, Brisse S, Holt KE. Corrigendum: 'Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, '. Microbial Genomics. 9. PMID 37555745 DOI: 10.1099/mgen.0.001084  0.192
2011 Holt KE, Phan MD, Baker S, Duy PT, Nga TV, Nair S, Turner AK, Walsh C, Fanning S, Farrell-Ward S, Dutta S, Kariuki S, Weill FX, Parkhill J, Dougan G, et al. Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid. Plos Neglected Tropical Diseases. 5: e1245. PMID 21811646 DOI: 10.1371/journal.pntd.0001245  0.192
2011 Holt KE, Dolecek C, Chau TT, Duy PT, La TT, Hoang NV, Nga TV, Campbell JI, Manh BH, Vinh Chau NV, Hien TT, Farrar J, Dougan G, Baker S. Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam. Plos Neglected Tropical Diseases. 5: e929. PMID 21245916 DOI: 10.1371/journal.pntd.0000929  0.192
2016 Robins-Browne RM, Holt KE, Ingle DJ, Hocking DM, Yang J, Tauschek M. Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing? Frontiers in Cellular and Infection Microbiology. 6: 141. PMID 27917373 DOI: 10.3389/fcimb.2016.00141  0.191
2014 Dimovski K, Cao H, Wijburg OL, Strugnell RA, Mantena RK, Whipp M, Hogg G, Holt KE. Analysis of Salmonella enterica serovar Typhimurium variable-number tandem-repeat data for public health investigation based on measured mutation rates and whole-genome sequence comparisons. Journal of Bacteriology. 196: 3036-44. PMID 24957617 DOI: 10.1128/JB.01820-14  0.191
2015 Hamidian M, Holt KE, Hall RM. Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate. The Journal of Antimicrobial Chemotherapy. 70: 2519-23. PMID 26023211 DOI: 10.1093/jac/dkv137  0.191
2013 Holt KE, Thieu Nga TV, Thanh DP, Vinh H, Kim DW, Vu Tra MP, Campbell JI, Hoang NV, Vinh NT, Minh PV, Thuy CT, Nga TT, Thompson C, Dung TT, Nhu NT, et al. Tracking the establishment of local endemic populations of an emergent enteric pathogen. Proceedings of the National Academy of Sciences of the United States of America. 110: 17522-7. PMID 24082120 DOI: 10.1073/pnas.1308632110  0.19
2021 Macesic N, Blakeway LV, Stewart JD, Hawkey J, Wyres KL, Judd LM, Wick RR, Jenney AW, Holt KE, Peleg AY. Silent spread of mobile colistin resistance gene mcr-9.1 on IncHI2 'superplasmids' in clinical carbapenem-resistant Enterobacterales. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. PMID 33915285 DOI: 10.1016/j.cmi.2021.04.020  0.188
2018 Wyres KL, Hawkey J, Hetland MAK, Fostervold A, Wick RR, Judd LM, Hamidian M, Howden BP, Löhr IH, Holt KE. Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307. The Journal of Antimicrobial Chemotherapy. PMID 30517666 DOI: 10.1093/jac/dky492  0.188
2009 Phan MD, Kidgell C, Nair S, Holt KE, Turner AK, Hinds J, Butcher P, Cooke FJ, Thomson NR, Titball R, Bhutta ZA, Hasan R, Dougan G, Wain J. Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever. Antimicrobial Agents and Chemotherapy. 53: 716-27. PMID 19015365 DOI: 10.1128/AAC.00645-08  0.188
2018 Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Current Opinion in Microbiology. 45: 131-139. PMID 29723841 DOI: 10.1016/j.mib.2018.04.004  0.187
2022 Hawkey J, Vezina B, Monk JM, Judd LM, Harshegyi T, Lopez-Fernandez S, Rodrigues C, Brisse S, Holt K, Wyres KL. A curated collection of metabolic models reveals variable substrate usage and gene essentiality. Genome Research. PMID 35277433 DOI: 10.1101/gr.276289.121  0.186
2021 Dyson ZA, Holt KE. Five years of GenoTyphi: updates to the global Salmonella Typhi genotyping framework. The Journal of Infectious Diseases. PMID 34453548 DOI: 10.1093/infdis/jiab414  0.185
2021 Dainty KR, Hawkey J, Judd LM, Pacidônio EC, Duyvestyn JM, Gonçalves DS, Lin SY, O'Donnell TB, O'Neill SL, Simmons CP, Holt KE, Flores HA. Mel genome remains stable after 7 years in Australian field populations. Microbial Genomics. 7. PMID 34468309 DOI: 10.1099/mgen.0.000641  0.185
2016 Chung The H, Rabaa MA, Pham Thanh D, De Lappe N, Cormican M, Valcanis M, Howden BP, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen Thi Nguyen T, Vu Thuy D, Thompson CN, Phu Huong Lan N, Voong Vinh P, ... Holt KE, et al. South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study. Plos Medicine. 13: e1002055. PMID 27483136 DOI: 10.1371/journal.pmed.1002055  0.184
2018 Brynildsrud OB, Pepperell CS, Suffys P, Grandjean L, Monteserin J, Debech N, Bohlin J, Alfsnes K, Pettersson JO, Kirkeleite I, Fandinho F, da Silva MA, Perdigao J, Portugal I, Viveiros M, ... Holt KE, et al. Global expansion of lineage 4 shaped by colonial migration and local adaptation. Science Advances. 4: eaat5869. PMID 30345355 DOI: 10.1126/Sciadv.Aat5869  0.184
2022 Hawkey J, Cottingham H, Tokolyi A, Wick RR, Judd LM, Cerdeira L, de Oliveira Garcia D, Wyres KL, Holt KE. Linear plasmids in and other . Microbial Genomics. 8. PMID 35416146 DOI: 10.1099/mgen.0.000807  0.183
2018 Lam MMC, Wyres KL, Judd LM, Wick RR, Jenney A, Brisse S, Holt KE. Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae. Genome Medicine. 10: 77. PMID 30371343 DOI: 10.1186/s13073-018-0587-5  0.183
2017 Perrin A, Larsonneur E, Nicholson AC, Edwards DJ, Gundlach KM, Whitney AM, Gulvik CA, Bell ME, Rendueles O, Cury J, Hugon P, Clermont D, Enouf V, Loparev V, Juieng P, ... Holt KE, et al. Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain. Nature Communications. 8: 15483. PMID 28537263 DOI: 10.1038/Ncomms15483  0.182
2021 McDougall FK, Wyres KL, Judd LM, Boardman WSJ, Holt KE, Power ML. Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian Fruit Bats (Pteropus poliocephalus). Research in Microbiology. 103879. PMID 34506927 DOI: 10.1016/j.resmic.2021.103879  0.182
2014 Hamidian M, Kenyon JJ, Holt KE, Pickard D, Hall RM. A conjugative plasmid carrying the carbapenem resistance gene blaOXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate. The Journal of Antimicrobial Chemotherapy. 69: 2625-8. PMID 24907141 DOI: 10.1093/jac/dku188  0.182
2015 Baltazar M, Ngandjio A, Holt KE, Lepillet E, Pardos de la Gandara M, Collard JM, Bercion R, Nzouankeu A, Le Hello S, Dougan G, Fonkoua MC, Weill FX. Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa. Emerging Infectious Diseases. 21: 655-9. PMID 25811307 DOI: 10.3201/eid2104.141355  0.182
2021 Edwards DJ, Duchene S, Pope B, Holt KE. SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments. Microbial Genomics. 7. PMID 34874243 DOI: 10.1099/mgen.0.000694  0.181
2021 Wyres KL, Hawkey J, Mirčeta M, Judd LM, Wick RR, Gorrie CL, Pratt NF, Garlick JS, Watson KM, Pilcher DV, McGloughlin SA, Abbott IJ, Macesic N, Spelman DW, Jenney AWJ, ... Holt KE, et al. Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients. Bmc Infectious Diseases. 21: 683. PMID 34261450 DOI: 10.1186/s12879-021-06386-z  0.181
2019 Karmakar M, Rodrigues CHM, Holt KE, Dunstan SJ, Denholm J, Ascher DB. Empirical ways to identify novel Bedaquiline resistance mutations in AtpE. Plos One. 14: e0217169. PMID 31141524 DOI: 10.1371/journal.pone.0217169  0.181
2018 M C Lam M, Wyres KL, Duchêne S, Wick RR, Judd LM, Gan YH, Hoh CH, Archuleta S, Molton JS, Kalimuddin S, Koh TH, Passet V, Brisse S, Holt KE. Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nature Communications. 9: 2703. PMID 30006589 DOI: 10.1038/s41467-018-05114-7  0.18
2009 Holt KE, Thomson NR, Wain J, Langridge GC, Hasan R, Bhutta ZA, Quail MA, Norbertczak H, Walker D, Simmonds M, White B, Bason N, Mungall K, Dougan G, Parkhill J. Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi. Bmc Genomics. 10: 36. PMID 19159446 DOI: 10.1186/1471-2164-10-36  0.179
2023 Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, ... ... Holt KE, et al. Evolution and transmission of antibiotic resistance is driven by Beijing lineage in Vietnam. Microbiology Spectrum. e0256223. PMID 37971428 DOI: 10.1128/spectrum.02562-23  0.179
2017 Blackwell GA, Holt KE, Bentley SD, Hsu LY, Hall RM. Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore. The Journal of Antimicrobial Chemotherapy. PMID 28073968 DOI: 10.1093/jac/dkw542  0.179
2016 Pham Thanh D, Thompson CN, Rabaa MA, Sona S, Sopheary S, Kumar V, Moore C, Tran Vu Thieu N, Wijedoru L, Holt KE, Wong V, Pickard D, Thwaites GE, Day N, Dougan G, et al. The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia. Plos Neglected Tropical Diseases. 10: e0004785. PMID 27331909 DOI: 10.1371/journal.pntd.0004785  0.179
2022 Vezina B, Judd LM, McDougall FK, Boardman WSJ, Power ML, Hawkey J, Brisse S, Monk JM, Holt KE, Wyres KL. Transmission of Klebsiella strains and plasmids within and between grey-headed flying fox colonies. Environmental Microbiology. PMID 35590448 DOI: 10.1111/1462-2920.16047  0.179
2020 Hawkey J, Monk JM, Billman-Jacobe H, Palsson B, Holt KE. Impact of insertion sequences on convergent evolution of Shigella species. Plos Genetics. 16: e1008931. PMID 32644999 DOI: 10.1371/Journal.Pgen.1008931  0.178
2015 Rusu LI, Wyres KL, Reumann M, Queiroz C, Bojovschi A, Conway T, Garg S, Edwards DJ, Hogg G, Holt KE. A platform for leveraging next generation sequencing for routine microbiology and public health use. Health Information Science and Systems. 3: S7. PMID 25870761 DOI: 10.1186/2047-2501-3-S1-S7  0.178
2018 Holt KE, McAdam P, Thai PVK, Thuong NTT, Ha DTM, Lan NN, Lan NH, Nhu NTQ, Hai HT, Ha VTN, Thwaites G, Edwards DJ, Nath AP, Pham K, Ascher DB, et al. Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nature Genetics. PMID 29785015 DOI: 10.1038/s41588-018-0117-9  0.178
2015 Hamidian M, Holt KE, Hall RM. The complete sequence of Salmonella genomic island SGI2. The Journal of Antimicrobial Chemotherapy. 70: 617-9. PMID 25315365 DOI: 10.1093/jac/dku407  0.177
2020 Okomo U, Senghore M, Darboe S, Bojang E, Zaman SMA, Hossain MJ, Nwakanma D, Le Doare K, Holt KE, Hos NJ, Lawn JE, Bentley SD, Kampmann B. Investigation of sequential outbreaks of Burkholderia cepacia and multidrug-resistant extended spectrum β-lactamase producing Klebsiella species in a West African tertiary hospital neonatal unit: a retrospective genomic analysis The Lancet Microbe. 1: e119-e129. DOI: 10.1016/s2666-5247(20)30061-6  0.177
2023 Carey ME, Dyson ZA, Argimón S, Cerdeira L, Yeats C, Aanensen D, Mboowa G, Baker S, Tessema SK, Smith AM, Okeke IN, Holt KE. Unlocking the Potential of Genomic Data to Inform Typhoid Fever Control Policy: Supportive Resources for Genomic Data Generation, Analysis, and Visualization. Open Forum Infectious Diseases. 10: S38-S46. PMID 37274533 DOI: 10.1093/ofid/ofad044  0.177
2016 Pham Thanh D, Karkey A, Dongol S, Ho Thi N, Thompson CN, Rabaa MA, Arjyal A, Holt KE, Wong V, Tran Vu Thieu N, Voong Vinh P, Ha Thanh T, Pradhan A, Shrestha SK, Gajurel D, et al. A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure. Elife. 5. PMID 26974227 DOI: 10.7554/eLife.14003  0.177
2023 Vezina B, Watts SC, Hawkey J, Cooper HB, Judd LM, Jenney AWJ, Monk JM, Holt KE, Wyres KL. Bactabolize is a tool for high-throughput generation of bacterial strain-specific metabolic models. Elife. 12. PMID 37815531 DOI: 10.7554/eLife.87406  0.176
2016 Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, Levine MM, Robins-Browne RM, Holt KE. In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. Microbial Genomics. 2: e000064. PMID 28348859 DOI: 10.1099/mgen.0.000064  0.175
2015 Hawkey J, Hamidian M, Wick RR, Edwards DJ, Billman-Jacobe H, Hall RM, Holt KE. ISMapper: Identifying transposase insertion sites in bacterial genomes from short read sequence data Bmc Genomics. 16. DOI: 10.1186/s12864-015-1860-2  0.175
2021 Macleod CK, Khokhar FA, Warne B, Wick R, Butcher R, Cassimon B, Hayden P, Holt K, Török ME. Rapid Whole Genome Sequencing of Serotype K1 Hypervirulent from an Undocumented Chinese Migrant. Case Reports in Infectious Diseases. 2021: 6638780. PMID 34007495 DOI: 10.1155/2021/6638780  0.174
2023 Wick RR, Judd LM, Holt KE. Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing. Plos Computational Biology. 19: e1010905. PMID 36862631 DOI: 10.1371/journal.pcbi.1010905  0.174
2015 Lim TP, Ong RT, Hon PY, Hawkey J, Holt KE, Koh TH, Leong ML, Teo JQ, Tan TY, Ng MM, Hsu LY. Multiple genetic mutations associated with polymyxin resistance in Acinetobacter baumannii. Antimicrobial Agents and Chemotherapy. PMID 26438500 DOI: 10.1128/AAC.01884-15  0.173
2021 Wick RR, Judd LM, Wyres KL, Holt KE. Recovery of small plasmid sequences via Oxford Nanopore sequencing. Microbial Genomics. 7. PMID 34431763 DOI: 10.1099/mgen.0.000631  0.17
2015 Harmer CJ, Holt KE, Hall RM. A type 2 A/C2 plasmid carrying the aacC4 apramycin resistance gene and the erm(42) erythromycin resistance gene recovered from two Salmonella enterica serovars. The Journal of Antimicrobial Chemotherapy. 70: 1021-5. PMID 25468903 DOI: 10.1093/jac/dku489  0.168
2022 Le MN, Kayama S, Wyres KL, Yu L, Hisatsune J, Suzuki M, Yahara K, Terachi T, Sawa K, Takahashi S, Okuhara T, Kohama K, Holt KE, Mizutani T, Ohge H, et al. Genomic epidemiology and temperature dependency of hypermucoviscous in Japan. Microbial Genomics. 8. PMID 35622495 DOI: 10.1099/mgen.0.000827  0.166
2022 Lam MMC, Wick RR, Judd LM, Holt KE, Wyres KL. Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the species complex. Microbial Genomics. 8. PMID 35311639 DOI: 10.1099/mgen.0.000800  0.166
2018 Duchene S, Duchene DA, Geoghegan JL, Dyson ZA, Hawkey J, Holt KE. Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods. Bmc Evolutionary Biology. 18: 95. PMID 29914372 DOI: 10.1186/s12862-018-1210-5  0.163
2015 Nigro SJ, Holt KE, Pickard D, Hall RM. Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid. The Journal of Antimicrobial Chemotherapy. 70: 1259-61. PMID 25433005 DOI: 10.1093/jac/dku486  0.163
2015 Hamidian M, Holt KE, Hall RM. The complete sequence of Salmonella genomic island SGI1-K. The Journal of Antimicrobial Chemotherapy. 70: 305-6. PMID 25193084 DOI: 10.1093/jac/dku331  0.163
2021 Iha C, Dougan KE, Varela JA, Avila V, Jackson CJ, Bogaert KA, Chen Y, Judd LM, Wick R, Holt KE, Pasella MM, Ricci F, Repetti SI, Medina M, Marcelino VR, et al. Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium. Current Biology : Cb. PMID 33548192 DOI: 10.1016/j.cub.2021.01.018  0.16
2016 Wong VK, Baker S, Pickard D, Page AJ, Feasey NA, Dougan G, Holt KE. The emergence and intercontinental spread of a multidrug-resistant clade of typhoid agent Salmonella enterica serovar Typhi The Lancet. 387: S10. DOI: 10.1016/S0140-6736(16)00397-4  0.16
2013 Wong VK, Pickard DJ, Barquist L, Sivaraman K, Page AJ, Hart PJ, Arends MJ, Holt KE, Kane L, Mottram LF, Ellison L, Bautista R, McGee CJ, Kay SJ, Wileman TM, et al. Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. Plos One. 8: e84567. PMID 24386394 DOI: 10.1371/Journal.Pone.0084567  0.159
2022 Lam MMC, Koong J, Holt KE, Hall RM, Hamidian M. Detection and Typing of Plasmids in Acinetobacter baumannii Using Genes Encoding Replication Initiation Proteins. Microbiology Spectrum. e0247822. PMID 36472426 DOI: 10.1128/spectrum.02478-22  0.159
2023 Meiring JE, Khanam F, Basnyat B, Charles RC, Crump JA, Debellut F, Holt KE, Kariuki S, Mugisha E, Neuzil KM, Parry CM, Pitzer VE, Pollard AJ, Qadri F, Gordon MA. Typhoid fever. Nature Reviews. Disease Primers. 9: 71. PMID 38097589 DOI: 10.1038/s41572-023-00480-z  0.158
2016 Hamidian M, Holt KE, Pickard D, Hall RM. A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant. The Journal of Antimicrobial Chemotherapy. 71: 269-71. PMID 26416779 DOI: 10.1093/jac/dkv293  0.158
2016 Pham Thanh D, Thanh Tuyen H, Nguyen Thi Nguyen T, Chung The H, Wick RR, Thwaites GE, Baker S, Holt KE. Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate. The Journal of Antimicrobial Chemotherapy. PMID 27246235 DOI: 10.1093/jac/dkw173  0.157
2022 Hawkey J, Wyres KL, Judd LM, Harshegyi T, Blakeway L, Wick RR, Jenney AWJ, Holt KE. ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. Genome Medicine. 14: 97. PMID 35999578 DOI: 10.1186/s13073-022-01103-0  0.157
2010 Holt KE, Baker S, Dongol S, Basnyat B, Adhikari N, Thorson S, Pulickal AS, Song Y, Parkhill J, Farrar JJ, Murdoch DR, Kelly DF, Pollard AJ, Dougan G. High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children. Bmc Infectious Diseases. 10: 144. PMID 20509974 DOI: 10.1186/1471-2334-10-144  0.156
2020 Wan Y, Wick RR, Zobel J, Ingle DJ, Inouye M, Holt KE. GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure. Bmc Genomics. 21: 658. PMID 32972363 DOI: 10.1186/s12864-020-07019-6  0.156
2022 Holt KE, Aanensen DM, Achtman M. Genomic population structures of microbial pathogens. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 377: 20210230. PMID 35989608 DOI: 10.1098/rstb.2021.0230  0.153
2018 Wyres KL, Lam MMC, Holt KE. Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City. The Journal of Antimicrobial Chemotherapy. PMID 30508109 DOI: 10.1093/jac/dky472  0.153
2021 Wyres K, Holt K. Regional differences in carbapenem-resistant Klebsiella pneumoniae. The Lancet. Infectious Diseases. PMID 34767752 DOI: 10.1016/S1473-3099(21)00425-4  0.152
2014 Wyres KL, Conway TC, Garg S, Queiroz C, Reumann M, Holt K, Rusu LI. WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare? Pathogens (Basel, Switzerland). 3: 437-58. PMID 25437808 DOI: 10.3390/Pathogens3020437  0.152
2011 Church PC, Goscinski A, Holt K, Inouye M, Ghoting A, Makarychev K, Reumann M. Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2011: 924-7. PMID 22254462 DOI: 10.1109/IEMBS.2011.6090208  0.152
2016 Duchêne S, Holt KE, Weill FX, Le Hello S, Hawkey J, Edwards DJ, Fourment M, Holmes EC. Genome-scale rates of evolutionary change in bacteria. Microbial Genomics. 2: e000094. PMID 28348834 DOI: 10.1099/mgen.0.000094  0.151
2019 Lam MMC, Wyres KL, Wick RR, Judd LM, Fostervold A, Holt KE, Löhr IH. Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15. The Journal of Antimicrobial Chemotherapy. PMID 30770708 DOI: 10.1093/jac/dkz028  0.149
2020 Repetti SI, Jackson CJ, Judd LM, Wick RR, Holt KE, Verbruggen H. The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns. Peerj. 8: e8273. PMID 31915577 DOI: 10.7717/Peerj.8273  0.148
2016 Follador R, Heinz E, Wyres KL, Ellington MJ, Kowarik M, Holt KE, Thomson NR. The diversity of Klebsiella pneumoniae surface polysaccharides. Microbial Genomics. 2: e000073. PMID 28348868 DOI: 10.1099/mgen.0.000073  0.147
2016 Lee IR, Molton JS, Wyres KL, Gorrie C, Wong J, Hoh CH, Teo J, Kalimuddin S, Lye DC, Archuleta S, Holt KE, Gan YH. Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population. Scientific Reports. 6: 29316. PMID 27406977 DOI: 10.1038/srep29316  0.147
2017 Dyson ZA, Thanh DP, Bodhidatta L, Mason CJ, Srijan A, Rabaa MA, Vinh PV, Thanh TH, Thwaites GE, Baker S, Holt KE. Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program. Plos Neglected Tropical Diseases. 11: e0005274. PMID 28060810 DOI: 10.1371/journal.pntd.0005274  0.147
2022 Lindstedt K, Buczek D, Pedersen T, Hjerde E, Raffelsberger N, Suzuki Y, Brisse S, Holt K, Samuelsen Ø, Sundsfjord A. Detection of human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods. Gut Microbes. 14: 2118500. PMID 36045603 DOI: 10.1080/19490976.2022.2118500  0.146
2023 Torraca V, Brokatzky D, Miles SL, Chong CE, De Silva PM, Baker S, Jenkins C, Holt KE, Baker KS, Mostowy S. Shigella serotypes associated with carriage in humans establish persistent infection in zebrafish. The Journal of Infectious Diseases. PMID 37556724 DOI: 10.1093/infdis/jiad326  0.145
2020 Holt KE, Lassalle F, Wyres KL, Wick R, Mostowy RJ. Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. The Isme Journal. PMID 32249276 DOI: 10.1038/s41396-020-0628-0  0.144
2016 O'Brien CL, Bringer MA, Holt KE, Gordon DM, Dubois AL, Barnich N, Darfeuille-Michaud A, Pavli P. Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli. Gut. PMID 27196580 DOI: 10.1136/gutjnl-2015-311059  0.143
2017 Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. Plos Computational Biology. 13: e1005595. PMID 28594827 DOI: 10.1371/journal.pcbi.1005595  0.143
2018 Teo SM, Tang HHF, Mok D, Judd LM, Watts SC, Pham K, Holt BJ, Kusel M, Serralha M, Troy N, Bochkov YA, Grindle K, Lemanske RF, Johnston SL, Gern JE, ... ... Holt KE, et al. Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease. Cell Host & Microbe. 24: 341-352.e5. PMID 30212648 DOI: 10.1016/j.chom.2018.08.005  0.143
2023 Lam MMC, Holt KE, Wyres KL. Comment on: MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009-19. The Journal of Antimicrobial Chemotherapy. PMID 36760082 DOI: 10.1093/jac/dkad028  0.142
2017 Darton TC, Meiring JE, Tonks S, Khan MA, Khanam F, Shakya M, Thindwa D, Baker S, Basnyat B, Clemens JD, Dougan G, Dolecek C, Dunstan SJ, Gordon MA, Heyderman RS, Holt KE, et al. The STRATAA study protocol: a programme to assess the burden of enteric fever in Bangladesh, Malawi and Nepal using prospective population census, passive surveillance, serological studies and healthcare utilisation surveys. Bmj Open. 7: e016283. PMID 28674145 DOI: 10.1136/bmjopen-2017-016283  0.14
2012 Bender JK, Praszkier J, Wakefield MJ, Holt K, Tauschek M, Robins-Browne RM, Yang J. Involvement of PatE, a prophage-encoded AraC-like regulator, in the transcriptional activation of acid resistance pathways of enterohemorrhagic Escherichia coli strain EDL933. Applied and Environmental Microbiology. 78: 5083-92. PMID 22582067 DOI: 10.1128/AEM.00617-12  0.139
2011 Baker S, Holt KE, Clements AC, Karkey A, Arjyal A, Boni MF, Dongol S, Hammond N, Koirala S, Duy PT, Nga TV, Campbell JI, Dolecek C, Basnyat B, Dougan G, et al. Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission. Open Biology. 1: 110008. PMID 22645647 DOI: 10.1098/Rsob.110008  0.138
2022 Stewart J, Judd LM, Jenney A, Holt KE, Wyres KL, Hawkey J. Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia. Bmc Infectious Diseases. 22: 704. PMID 36002802 DOI: 10.1186/s12879-022-07687-7  0.138
2021 Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G, Vezina B, Wyres KL, Holt KE. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biology. 22: 266. PMID 34521459 DOI: 10.1186/s13059-021-02483-z  0.136
2013 Sangal V, Holt KE, Yuan J, Brown DJ, Filliol-Toutain I, Weill FX, Kim DW, da Silveira WD, Pickard D, Thomson NR, Parkhill J, Yu J. Global phylogeny of Shigella sonnei strains from limited single nucleotide polymorphisms (SNPs) and development of a rapid and cost-effective SNP-typing scheme for strain identification by high-resolution melting analysis. Journal of Clinical Microbiology. 51: 303-5. PMID 23115259 DOI: 10.1128/JCM.02238-12  0.136
2016 Wong VK, Holt KE, Okoro C, Baker S, Pickard DJ, Marks F, Page AJ, Olanipekun G, Munir H, Alter R, Fey PD, Feasey NA, Weill FX, Le Hello S, et al. Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa. Plos Neglected Tropical Diseases. 10: e0004781. PMID 27657909 DOI: 10.1371/journal.pntd.0004781  0.135
2022 Azarian T, Sherry NL, Baker K, Holt KE, Okeke IN. Making microbial genomics work for clinical and public health microbiology. Microbial Genomics. 8. PMID 36112024 DOI: 10.1099/mgen.0.000900  0.134
2021 Bridel S, Watts SC, Judd LM, Harshegyi T, Passet V, Rodrigues C, Holt KE, Brisse S. Klebsiella MALDI TypeR: a web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry. Research in Microbiology. 103835. PMID 34004273 DOI: 10.1016/j.resmic.2021.103835  0.134
2021 Vu Thi Ngoc B, Brisse S, Dao Tuyet T, Vu Tien Viet D, Holt KE, Nguyen Vu T, Tran Thi Kieu H, Nguyen Thi Ngoc D, van Doorn HR, Wertheim HFL. Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam F1000research. 10: 454. DOI: 10.12688/F1000RESEARCH.52799.1  0.133
2010 Karkey A, Arjyal A, Anders KL, Boni MF, Dongol S, Koirala S, My PV, Nga TV, Clements AC, Holt KE, Duy PT, Day JN, Campbell JI, Dougan G, Dolecek C, et al. The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu. Plos One. 5: e13988. PMID 21085575 DOI: 10.1371/Journal.Pone.0013988  0.133
2022 Okomo UA, Darboe S, Bah SY, Ayorinde A, Jarju S, Sesay AK, Kebbeh N, Gai A, Dibbasey T, Grey-Johnson M, Le Doare K, Holt KE, Lawn JE, Kampmann B. Maternal colonisation and early-onset neonatal bacterial sepsis in The Gambia, West Africa: a genomic analysis of vertical transmission. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. PMID 36243352 DOI: 10.1016/j.cmi.2022.10.012  0.132
2013 Comas I, Coscolla M, Luo T, Borrell S, Holt KE, Kato-Maeda M, Parkhill J, Malla B, Berg S, Thwaites G, Yeboah-Manu D, Bothamley G, Mei J, Wei L, Bentley S, et al. Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nature Genetics. 45: 1176-82. PMID 23995134 DOI: 10.1038/Ng.2744  0.132
2007 Baker S, Holt K, Whitehead S, Goodhead I, Perkins T, Stocker B, Hardy J, Dougan G. A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi. Molecular Microbiology. 66: 1207-18. PMID 17976161 DOI: 10.1111/j.1365-2958.2007.05995.x  0.132
2018 Gorrie CL, Mirceta M, Wick RR, Judd LM, Wyres KL, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, McGloughlin SA, Spelman DW, Jenney AWJ, Holt KE. Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 29340588 DOI: 10.1093/cid/ciy027  0.131
2021 Jokanovic N, Haines T, Cheng AC, Holt KE, Hilmer SN, Jeon YH, Stewardson AJ, Stuart RL, Spelman T, Peel TN, Peleg AY. Multicentre stepped-wedge cluster randomised controlled trial of an antimicrobial stewardship programme in residential aged care: protocol for the START trial. Bmj Open. 11: e046142. PMID 33653766 DOI: 10.1136/bmjopen-2020-046142  0.131
2021 Kariuki S, Dyson ZA, Mbae C, Ngetich R, Kavai SM, Wairimu C, Anyona S, Gitau N, Onsare RS, Ongandi B, Duchene S, Ali M, Clemens JD, Holt KE, Dougan G. Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya. Elife. 10. PMID 34515028 DOI: 10.7554/eLife.67852  0.131
2019 Wick RR, Holt KE. Benchmarking of long-read assemblers for prokaryote whole genome sequencing. F1000research. 8: 2138. PMID 31984131 DOI: 10.12688/f1000research.21782.4  0.128
2020 Gionfriddo CM, Stott MB, Power JF, Ogorek JM, Krabbenhoft DP, Wick R, Holt K, Chen LX, Thomas BC, Banfield JF, Moreau JW. Genome-resolved metagenomics and detailed geochemical speciation analyses yield new insights into microbial mercury cycling in geothermal springs. Applied and Environmental Microbiology. PMID 32414793 DOI: 10.1128/Aem.00176-20  0.127
2021 Lee VV, Judd LM, Jex AR, Holt KE, Tonkin CJ, Ralph SA. Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites. Msystems. 6. PMID 33688018 DOI: 10.1128/mSystems.01081-20  0.127
2018 Wick RR, Judd LM, Holt KE. Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks. Plos Computational Biology. 14: e1006583. PMID 30458005 DOI: 10.1371/journal.pcbi.1006583  0.126
2014 Hamidian M, Wynn M, Holt KE, Pickard D, Dougan G, Hall RM. Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii. The Journal of Antimicrobial Chemotherapy. 69: 557-8. PMID 24080502 DOI: 10.1093/jac/dkt379  0.126
2018 Mostowy RJ, Holt KE. Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating. Trends in Microbiology. PMID 30037568 DOI: 10.1016/j.tim.2018.06.006  0.124
2021 Khoury MJ, Holt KE. The impact of genomics on precision public health: beyond the pandemic. Genome Medicine. 13: 67. PMID 33892793 DOI: 10.1186/s13073-021-00886-y  0.124
2010 Song Y, Roumagnac P, Weill FX, Wain J, Dolecek C, Mazzoni CJ, Holt KE, Achtman M. A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A. The Journal of Antimicrobial Chemotherapy. 65: 1631-41. PMID 20511368 DOI: 10.1093/jac/dkq175  0.124
2019 Ingle DJ, Easton M, Valcanis M, Seemann T, Kwong JC, Stephens N, Carter GP, Gonçalves da Silva A, Adamopoulos J, Baines SL, Holt KE, Chow EPF, Fairley CK, Chen MY, Kirk M, et al. Co-circulation of multidrug-resistant Shigella among men who have sex with men, Australia. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 30615105 DOI: 10.1093/cid/ciz005  0.123
2024 Miles SL, Holt KE, Mostowy S. Recent advances in modelling Shigella infection. Trends in Microbiology. PMID 38423917 DOI: 10.1016/j.tim.2024.02.004  0.12
2024 Ashton PM, Chunga Chirambo A, Meiring JE, Patel PD, Mbewe M, Silungwe N, Chizani K, Banda H, Heyderman RS, Dyson ZA, MacPherson P, Henrion MYR, Holt KE, Gordon MA. Evaluating the relationship between ciprofloxacin prescription and non-susceptibility in Salmonella Typhi in Blantyre, Malawi: an observational study. The Lancet. Microbe. 5: e226-e234. PMID 38387472 DOI: 10.1016/S2666-5247(23)00327-0  0.12
2024 Cooper HB, Vezina B, Hawkey J, Passet V, López-Fernández S, Monk JM, Brisse S, Holt KE, Wyres KL. A validated pangenome-scale metabolic model for the species complex. Microbial Genomics. 10. PMID 38376382 DOI: 10.1099/mgen.0.001206  0.12
1962 HOLT KS. Librium Developmental Medicine and Child Neurology. 4: 665-666. PMID 13961448  0.12
2021 Meiring JE, Shakya M, Khanam F, Voysey M, Phillips MT, Tonks S, Thindwa D, Darton TC, Dongol S, Karkey A, Zaman K, Baker S, Dolecek C, Dunstan SJ, Dougan G, ... Holt KE, et al. Burden of enteric fever at three urban sites in Africa and Asia: a multicentre population-based study. The Lancet. Global Health. 9: e1688-e1696. PMID 34798028 DOI: 10.1016/S2214-109X(21)00370-3  0.119
2012 Doig KD, Holt KE, Fyfe JA, Lavender CJ, Eddyani M, Portaels F, Yeboah-Manu D, Pluschke G, Seemann T, Stinear TP. On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Bmc Genomics. 13: 258. PMID 22712622 DOI: 10.1186/1471-2164-13-258  0.118
2023 Fachrul M, Karkey A, Shakya M, Judd LM, Harshegyi T, Sim KS, Tonks S, Dongol S, Shrestha R, Salim A, Baker S, Pollard AJ, Khor CC, Dolecek C, Basnyat B, ... ... Holt KE, et al. Direct inference and control of genetic population structure from RNA sequencing data. Communications Biology. 6: 804. PMID 37532769 DOI: 10.1038/s42003-023-05171-9  0.115
2017 Manna S, Ortika B, Dunne EM, Holt KE, Kama M, Russell FM, Hinds J, Satzke C. A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji. Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases. PMID 28736074 DOI: 10.1016/j.cmi.2017.06.031  0.114
2009 Holt KE, Teo YY, Li H, Nair S, Dougan G, Wain J, Parkhill J. Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA. Bioinformatics (Oxford, England). 25: 2074-5. PMID 19497932 DOI: 10.1093/bioinformatics/btp344  0.113
2010 Nga TV, Karkey A, Dongol S, Thuy HN, Dunstan S, Holt K, Tu le TP, Campbell JI, Chau TT, Chau NV, Arjyal A, Koirala S, Basnyat B, Dolecek C, Farrar J, et al. The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens. Bmc Infectious Diseases. 10: 125. PMID 20492644 DOI: 10.1186/1471-2334-10-125  0.112
2022 Wick RR, Holt KE. Polypolish: Short-read polishing of long-read bacterial genome assemblies. Plos Computational Biology. 18: e1009802. PMID 35073327 DOI: 10.1371/journal.pcbi.1009802  0.107
2014 Waddington CS, Darton TC, Jones C, Haworth K, Peters A, John T, Thompson BA, Kerridge SA, Kingsley RA, Zhou L, Holt KE, Yu LM, Lockhart S, Farrar JJ, Sztein MB, et al. An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. 58: 1230-40. PMID 24519873 DOI: 10.1093/cid/ciu078  0.107
2019 Wick RR, Judd LM, Holt KE. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biology. 20: 129. PMID 31234903 DOI: 10.1186/s13059-019-1727-y  0.106
2017 Gorrie CL, Mirceta M, Wick RR, Edwards DJ, Thomson NR, Strugnell RA, Pratt N, Garlick J, Watson K, Pilcher D, McGloughlin S, Spelman DW, Jenney AW, Holt KE. Gastrointestinal carriage is a major reservoir of K. pneumoniae infection in intensive care patients. Clinical Infectious Diseases : An Official Publication of the Infectious Diseases Society of America. PMID 28369261 DOI: 10.1093/cid/cix270  0.106
2011 Jansen AM, Hall LJ, Clare S, Goulding D, Holt KE, Grant AJ, Mastroeni P, Dougan G, Kingsley RA. A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo. Plos Pathogens. 7: e1002131. PMID 21829346 DOI: 10.1371/journal.ppat.1002131  0.105
1976 Holt KS. Some key points in planning services for handicapped children Child: Care, Health and Development. 2: 387-394.  0.1
2017 Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, Levine MM, Robins-Browne RM, Holt KE. Corrigendum: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. Microbial Genomics. 3: e000109. PMID 29026653 DOI: 10.1099/mgen.0.000109  0.098
2022 Barber JN, Nicholson LC, Woods LC, Judd LM, Sezmis AL, Hawkey J, Holt KE, McDonald MJ. Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community. The Isme Journal. PMID 35066567 DOI: 10.1038/s41396-022-01191-1  0.098
2015 Teo SM, Mok D, Pham K, Kusel M, Serralha M, Troy N, Holt BJ, Hales BJ, Walker ML, Hollams E, Bochkov YA, Grindle K, Johnston SL, Gern JE, Sly PD, ... ... Holt KE, et al. The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development. Cell Host & Microbe. 17: 704-15. PMID 25865368 DOI: 10.1016/j.chom.2015.03.008  0.095
2021 Phillips MT, Meiring JE, Voysey M, Warren JL, Baker S, Basnyat B, Clemens JD, Dolecek C, Dunstan SJ, Dougan G, Gordon MA, Thindwa D, Heyderman RS, Holt KE, Qadri F, et al. A Bayesian approach for estimating typhoid fever incidence from large-scale facility-based passive surveillance data. Statistics in Medicine. PMID 34428309 DOI: 10.1002/sim.9159  0.091
2012 Holt KE, Dutta S, Manna B, Bhattacharya SK, Bhaduri B, Pickard DJ, Ochiai RL, Ali M, Clemens JD, Dougan G. High-resolution genotyping of the endemic Salmonella Typhi population during a Vi (typhoid) vaccination trial in Kolkata. Plos Neglected Tropical Diseases. 6: e1490. PMID 22303491 DOI: 10.1371/journal.pntd.0001490  0.09
2021 Lin H, Ascher DB, Myung Y, Lamborg CH, Hallam SJ, Gionfriddo CM, Holt KE, Moreau JW. Mercury methylation by metabolically versatile and cosmopolitan marine bacteria. The Isme Journal. PMID 33504941 DOI: 10.1038/s41396-020-00889-4  0.089
1984 Holt KS. Clinical approach to young disabled children: discussion paper Journal of the Royal Society of Medicine. 77: 125-130. PMID 6234392 DOI: 10.1177/014107688407700211  0.088
1956 Holt KS. The rebound phenomenon in acute rheumatic fever Archives of Disease in Childhood. 31: 444-451. PMID 13395571 DOI: 10.1136/adc.31.160.444  0.088
2009 Holt K. Identifying adaptive differences could provide insight. Nature. 458: 145. PMID 19279608 DOI: 10.1038/458145b  0.087
2016 Duchêne S, Duchêne DA, Di Giallonardo F, Eden JS, Geoghegan JL, Holt KE, Ho SY, Holmes EC. Cross-validation to select Bayesian hierarchical models in phylogenetics. Bmc Evolutionary Biology. 16: 115. PMID 27230264 DOI: 10.1186/S12862-016-0688-Y  0.087
2009 Holt K. Developing a triage tool for paediatric care Emergency Nurse. 17: 12-17. PMID 19552327  0.087
1957 Holt KS. A suggested medical classification of handicapped children Archives of Disease in Childhood. 32: 226-229. PMID 13445304 DOI: 10.1136/adc.32.163.226  0.087
2020 Huang QQ, Tang HHF, Teo SM, Mok D, Ritchie SC, Nath AP, Brozynska M, Salim A, Bakshi A, Holt BJ, Khor CC, Sly PD, Holt PG, Holt KE, Inouye M. Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk. Nature Communications. 11: 3761. PMID 32724101 DOI: 10.1038/s41467-020-17477-x  0.085
2012 Celik N, Webb CT, Leyton DL, Holt KE, Heinz E, Gorrell R, Kwok T, Naderer T, Strugnell RA, Speed TP, Teasdale RD, Likić VA, Lithgow T. A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters. Plos One. 7: e43245. PMID 22905239 DOI: 10.1371/journal.pone.0043245  0.085
2006 Holt KE, Millar AH, Whelan J. ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants. Plant Methods. 2: 8. PMID 16606469 DOI: 10.1186/1746-4811-2-8  0.085
2020 Torraca V, Holt K, Mostowy S. Shigella sonnei. Trends in Microbiology. 28: 696-697. PMID 32663462 DOI: 10.1016/j.tim.2020.02.011  0.085
1966 Holt K. Symposium: The Handicapped Child [Abridged]: Principles of Child Health as Seen in the Care of Handicapped Children Journal of the Royal Society of Medicine. 59: 135-139. DOI: 10.1177/003591576605900236  0.081
1981 Holt KS. Review: The assessment of walking in children with particular reference to cerebral palsy Child: Care, Health and Development. 7: 281-297. PMID 7307240  0.078
2019 Tang HHF, Sly PD, Holt PG, Holt KE, Inouye M. Systems biology and big data in asthma and allergy - recent discoveries and emerging challenges. The European Respiratory Journal. PMID 31619470 DOI: 10.1183/13993003.00844-2019  0.078
2005 Holt K. Wireless LAN: Past, present, and future Proceedings -Design, Automation and Test in Europe, Date '05. 2005: 92-93. DOI: 10.1109/DATE.2005.329  0.077
2020 Im J, Islam MT, Kim DR, Ahmmed F, Chon Y, Zaman K, Khan AI, Ali M, Sur D, Kanungo S, Dutta S, Bhattacharya SK, Dougan G, Holt KE, Marks F, et al. Protection conferred by typhoid fever against recurrent typhoid fever in urban Kolkata. Plos Neglected Tropical Diseases. 14: e0008530. PMID 32804950 DOI: 10.1371/journal.pntd.0008530  0.076
1973 Holt KS. Assessment of multiply handicapped children: Functional assessment of handicapped children: An introduction Journal of the Royal Society of Medicine. 66: 611-612. DOI: 10.1177/003591577306600703  0.076
1960 HOLT KS. Doctors and children Medical World. 92: 171-175. PMID 14402853  0.076
1973 Holt KS. Functional assessment of handicapped children: an introduction Proceedings of the Royal Society of Medicine. 66: 611-612. PMID 4741384  0.076
1958 HOLT KS. The welfare of young children Medical World. 89: 249-252. PMID 13577228  0.076
1963 HOLT KS. Subdural haematoma in children The British Journal of Clinical Practice. 17: 299-303. PMID 13961449  0.075
1991 Holt KS. Everyday aids and appliances. Mobility aids and appliances for disabled children British Medical Journal. 302: 105-107. PMID 1995105 DOI: 10.1136/BMJ.302.6768.105  0.074
1985 Holt K. User-oriented product innovation - Some research findings Technovation. 3: 199-208. DOI: 10.1016/0166-4972(85)90014-8  0.072
1987 Holt K. User-oriented product innovation in theory and practice Technovation. 6: 37-45. DOI: 10.1016/0166-4972(87)90037-X  0.072
1978 Holt K. Information inputs to new product planning and development Research Policy. 7: 342-360. DOI: 10.1016/0048-7333(78)90011-2  0.072
1970 Holt KS. The problems of deformity and disability in cerebral palsy Psychiatrie, Neurologie Und Medizinische Psychologie. Beihefte. 13: 109-112. PMID 4283589  0.071
1972 Holt KS. The treatment of spasticity in children Postgraduate Medical Journal. 48. PMID 4585730  0.071
1958 HOLT KS. The home care of severely retarded children Pediatrics. 22: 744-755. PMID 13590852  0.071
1954 Holt KS. SALICYLATES IN RHEUMATIC FEVER DIFFICULTIES EXPERIENCED IN TREATING CHILDREN WITH LARGE DOSES The Lancet. 264: 1197-1199. PMID 13213159  0.071
2016 Njamkepo E, Fawal N, Tran-Dien A, Hawkey J, Strockbine N, Jenkins C, Talukder KA, Bercion R, Kuleshov K, Kolínská R, Russell JE, Kaftyreva L, Accou-Demartin M, Karas A, Vandenberg O, ... ... Holt KE, et al. Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1. Nature Microbiology. 1: 16209. PMID 27694821 DOI: 10.1038/nmicrobiol.2016.209  0.071
1991 Holt K. Technology strategy—is there a need for it? Journal of Engineering Design. 2: 105-112. DOI: 10.1080/09544829108901674  0.071
1962 HOLT KS. The calf blood flow in normal children and in children with cerebral palsy Clinical Science. 22: 363-372. PMID 13908568  0.07
2014 Walker ML, Holt KE, Anderson GP, Teo SM, Sly PD, Holt PG, Inouye M. Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy. Frontiers in Immunology. 5: 447. PMID 25295037 DOI: 10.3389/fimmu.2014.00447  0.07
1991 Holt K. The impact of technology strategy on the engineering design process Design Studies. 12: 90-95. DOI: 10.1016/0142-694X(91)90050-7  0.068
1969 Holt KS. Developmental Pædiatrics: Neurological Aspects Journal of the Royal Society of Medicine. 62: 997-998. DOI: 10.1177/003591576906201007  0.067
2012 Holt K. Authentic Journalism? A Critical Discussion about Existential Authenticity in Journalism Ethics Journal of Mass Media Ethics: Exploring Questions of Media Morality. 27: 2-14. DOI: 10.1080/08900523.2012.636244  0.067
2016 Ritchie SC, Watts S, Fearnley LG, Holt KE, Abraham G, Inouye M. A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets. Cell Systems. 3: 71-82. PMID 27467248 DOI: 10.1016/j.cels.2016.06.012  0.067
2018 Tang HH, Teo SM, Belgrave DC, Evans MD, Jackson DJ, Brozynska M, Kusel MM, Johnston SL, Gern JE, Lemanske RF, Simpson A, Custovic A, Sly PD, Holt PG, Holt KE, et al. Trajectories of childhood immune development and respiratory health relevant to asthma and allergy. Elife. 7. PMID 30320550 DOI: 10.7554/eLife.35856  0.066
1988 Holt K. Market-oriented product innovation at Høyang Polaris and Jøtul Technovation. 8: 249-254.  0.064
1965 Holt KS. Mentally Subnormal Children British Medical Journal. 1: 1233-1235. DOI: 10.1136/bmj.1.5444.1233  0.063
1990 Holt KS. Understanding child development Indian Pediatrics. 27: 9-13. PMID 2361751  0.063
1990 Fetters L, Holt K. Efficiency of movement: Biomechanical and metabolic aspects Pediatric Physical Therapy. 2: 155-159.  0.063
1979 Holt KS. Assessment of handicap in childhood Child: Care, Health and Development. 5: 151-162. PMID 156603  0.063
2013 Holt K. Collective authorship and Platonov's socialist realism Russian Literature. 73: 57-83. DOI: 10.1016/j.ruslit.2013.01.005  0.063
2008 Fernandes R, Kusel M, Cyr M, Sehmi R, Holt K, Holt B, Kebadze T, Johnston SL, Sly P, Denburg JA, Holt P. Cord blood hemopoietic progenitor profiles predict acute respiratory symptoms in infancy. Pediatric Allergy and Immunology : Official Publication of the European Society of Pediatric Allergy and Immunology. 19: 239-47. PMID 18397408 DOI: 10.1111/j.1399-3038.2007.00615.x  0.063
1964 Holt KS. The use of diazepam in childhood cerebral palsy. Report of a small study including electromyographic observations Annals of Physical Medicine. 16-24. PMID 5317889  0.061
1975 Holt K. Industrial engineering: a dynamic response to change? Omega. 3: 523-540. DOI: 10.1016/0305-0483(75)90026-2  0.06
1966 Holt KS. Education of Handicapped Children British Medical Journal. 2: 587. DOI: 10.1136/bmj.2.5513.587-b  0.059
2015 Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics (Oxford, England). 31: 3350-2. PMID 26099265 DOI: 10.1093/bioinformatics/btv383  0.058
1980 Holt KS. Evaluation of motor development Motricite Cerebrale Readaptation Neurologie Du Developpement. 1: 5-17.  0.058
1993 Holt K. Computer-Aided creativity in engineering design Journal of Engineering Design. 4: 371-376. DOI: 10.1080/09544829308914792  0.058
1994 Holt K. The user in focus - the development of a market-oriented corporate culture Technovation. 14: 573-584. DOI: 10.1016/0166-4972(94)90040-X  0.057
2005 Holt K, Kraft K. Oral health and learning: when children's oral health suffers, so does their ability to learn Journal - Oklahoma Dental Association. 97: 24-25. PMID 16268273  0.057
1985 Holt KS. A developmental approach to physical disability in childhood Disability and Rehabilitation. 7: 18-26. DOI: 10.3109/03790798509165974  0.057
1960 Holt KS. Early motor development. Posturally induced variations The Journal of Pediatrics. 57: 571-575. PMID 13715540  0.056
2006 Holt K. Strategic issue diagnosis identifies risks, opportunities Hotel and Motel Management. 221: 23-24.  0.056
2022 Holt KE, Lassalle F, Wyres KL, Wick R, Mostowy RJ. Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales. The Isme Journal. PMID 35046560 DOI: 10.1038/s41396-021-01181-9  0.056
1973 Holt KS. Developmental paediatrics in other countries: Israel Community Health. 5: 124-130. PMID 4765217  0.056
2014 Holt K. Total Nuclear Variation and Jacobian Extensions of Total Variation for Vector Fields. Ieee Transactions On Image Processing : a Publication of the Ieee Signal Processing Society. PMID 24968168 DOI: 10.1109/TIP.2014.2332397  0.053
1996 Holt K. Brainstorming - From classics to electronics Journal of Engineering Design. 7: 77-82.  0.053
1989 Holt K. Does the engineer forget the user? Design Studies. 10: 163-168. DOI: 10.1016/0142-694X(89)90034-3  0.052
2010 Holt KE. A View from the Inside: A Practitioner's Encounter with Patient Privacy Breast Diseases. 21: 25-27. DOI: 10.1016/S1043-321X(10)79505-9  0.052
2011 Holt KM. Angular regularization of vector-valued signals Icassp, Ieee International Conference On Acoustics, Speech and Signal Processing - Proceedings. 1105-1108. DOI: 10.1109/ICASSP.2011.5946601  0.051
2011 Holt K. 'All parts of the union i considered my home': The federal imagination of the algerine captive Early American Literature. 46: 481-515.  0.051
1999 Crutcher M, Holt K. From the Oklahoma State Department of Health. CDC recommendations for diagnosis and initial management of hepatitis C virus infection The Journal of the Oklahoma State Medical Association. 92: 93-95. PMID 10024789  0.05
1985 Holt KS. Introduction Disability and Rehabilitation. 7: 9-10. DOI: 10.3109/03790798509165972  0.05
2005 Holt KC. Frazier's Cold mountain Explicator. 63: 118-121.  0.049
1977 Holt K. Creativity—a new challenge to the industrial engineer International Journal of Production Research. 15: 411-421. DOI: 10.1080/00207547708943140  0.049
1975 Holt K, Seetzen J. Innovation research at the international institute for the management of technology Omega. 3: 219-227.  0.049
2005 Holt KG. Biomechanical models, motor control theory, and development Infant and Child Development. 14: 523-527. DOI: 10.1002/icd.424  0.049
2009 Holt KM. Geometric calibration and Distortion Calibration for CT from Scans of Unknown Objects Using Complementary Rays Progress in Biomedical Optics and Imaging - Proceedings of Spie. 7258. DOI: 10.1117/12.811652  0.048
2020 Tang HHF, Lang A, Teo SM, Judd LM, Gangnon R, Evans MD, Lee KE, Vrtis R, Holt PG, Lemanske RF, Jackson DJ, Holt KE, Inouye M, Gern JE. Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk. The Journal of Allergy and Clinical Immunology. PMID 33091409 DOI: 10.1016/j.jaci.2020.10.009  0.048
1990 Holt K. Consulting in innovation through intercompany study groups Technovation. 10: 347-354. DOI: 10.1016/0166-4972(90)90018-F  0.048
2007 Holt KB. Diamond at the nanoscale: Applications of diamond nanoparticles from cellular biomarkers to quantum computing Philosophical Transactions of the Royal Society a: Mathematical, Physical and Engineering Sciences. 365: 2845-2861. DOI: 10.1098/rsta.2007.0005  0.048
2018 Watts SC, Ritchie SC, Inouye M, Holt KE. FastSpar: Rapid and scalable correlation estimation for compositional data. Bioinformatics (Oxford, England). PMID 30169561 DOI: 10.1093/bioinformatics/bty734  0.045
1975 Holt KS. A single nurse teacher therapist? Child Care, Hlth Dev.. 1: 45-50.  0.045
2018 Lang A, Holt KE, Inouye M, Holt PG, Teo SM, Tang HH, Judd LM, Lemanske RF, Evans MD, Jackson DJ, Gern JE. Nasopharyngeal Microbiome During Health and Illness in Early Life Journal of Allergy and Clinical Immunology. 141: AB109. DOI: 10.1016/J.JACI.2017.12.348  0.045
1964 Holt KS. The use of diazepam in childhood cerebral palsy Rheumatology (United Kingdom). 7: 16-24. DOI: 10.1093/rheumatology/VII.suppl_1.16  0.045
2006 Holt KM. Geometric calibration of third-generation computed tomography scanners from scans of unknown objects using complementary rays Proceedings - International Conference On Image Processing, Icip. 4. DOI: 10.1109/ICIP.2007.4379971  0.045
1974 Holt KS. Rehabilitation today. IX. The handicapped child Update. 9: 425-442.  0.044
1999 Holt K. Management and organization through 100 years Technovation. 19: 135-140.  0.044
2016 Holt K. Blacklisted: Boundaries, Violations, and Retaliatory Behavior in the BDSM Community Deviant Behavior. 1-14. DOI: 10.1080/01639625.2016.1156982  0.044
2009 Holt KM. Geometric calibration of detectors with discrete irregularities for computed tomography Progress in Biomedical Optics and Imaging - Proceedings of Spie. 7258. DOI: 10.1117/12.811643  0.044
2015 Suggs S, Holt K. The use of tranexamic acid in joint replacement surgery. Orthopedic Nursing. 34: 89-92; quiz 93-4. PMID 25785617 DOI: 10.1097/NOR.0000000000000125  0.044
2016 Gionfriddo CM, Tate MT, Wick RR, Schultz MB, Zemla A, Thelen MP, Schofield R, Krabbenhoft DP, Holt KE, Moreau JW. Microbial mercury methylation in Antarctic sea ice. Nature Microbiology. 1: 16127. PMID 27670112 DOI: 10.1038/Nmicrobiol.2016.127  0.043
2004 Listrom C, Holt K. Inflammatory bowel disease Emergency Medicine. 36: 24-28.  0.042
2004 Holt K. Improving early detection of COPD: the role of spirometry screening assessment Professional Nurse (London, England). 20: 31-33. PMID 15552437  0.042
2018 Holt KM, Thompson AN. Implementation of a Medication Reconciliation Process in an Internal Medicine Clinic at an Academic Medical Center. Pharmacy (Basel, Switzerland). 6. PMID 29587353 DOI: 10.3390/pharmacy6020026  0.041
1974 Holt KS. INFANCY AND CHILDHOOD The Lancet. 304: 1057-1061. PMID 4138625 DOI: 10.1016/S0140-6736(74)92162-X  0.041
1973 Holt K. An integrated child health service British Medical Journal. 1: 352. PMID 4685630 DOI: 10.1136/bmj.1.5849.352  0.041
2010 Holt K. Graves' disease: clinical pathophysiology, presentation and treatment options The Journal of Practical Nursing. 60: 13-18. PMID 21175104  0.041
1987 Holt K, Morris J. Developments in Central Government Internal Audit Managerial Auditing Journal. 2: 3-6. DOI: 10.1108/eb017588  0.04
1979 Holt KS. Medical examination of the child with cerebral palsy Pediatric Annals. 8: 581-588. PMID 91154  0.04
1969 Holt KS. Postgraduate Training in Epidemiology and Community Medicine [Abridged]: Postgraduate Training in Child Health Journal of the Royal Society of Medicine. 62: 677-679. DOI: 10.1177/003591576906200718  0.04
1969 Holt KS. Postgraduate training in child health Proceedings of the Royal Society of Medicine. 62: 677-679. PMID 5803505  0.04
2013 Lounsbery MA, McKenzie TL, Morrow JR, Monnat SM, Holt KA. District and school physical education policies: implications for physical education and recess time. Annals of Behavioral Medicine : a Publication of the Society of Behavioral Medicine. 45: S131-41. PMID 23334759 DOI: 10.1007/s12160-012-9427-9  0.04
1975 Holt KS. The handicapped child Child Care, Hlth. Dev.. 1: 185-189. PMID 130996  0.039
2010 Holt KB. Undoped diamond nanoparticles: Origins of surface redox chemistry Physical Chemistry Chemical Physics. 12: 2048-2058. DOI: 10.1039/b920075d  0.039
2013 Holt K. Assessor's expertise valued Kai Tiaki Nursing New Zealand. 19: 4.  0.039
1958 HOLT KS. The influence of a retarded child upon family limitation Journal of Mental Deficiency Research. 2: 28-36. PMID 13576051  0.039
1966 Holt KS. Facts and fallacies about neuromuscular function in cerebral palsy as revealed by electromyography Developmental Medicine and Child Neurology. 8: 255-268. PMID 5926429  0.038
1967 Holt KS. Communication difficulties in childhood Midwife and Health Visitor. 3: 30-32. PMID 5180505  0.038
1957 Holt KS. Idiopathic hyperlipaemia: Report of a case studied with radioactive iodine-labelled fat Archives of Disease in Childhood. 32: 142-145. PMID 13425664 DOI: 10.1136/adc.32.162.142  0.038
2010 Holt K. Author's response Nursing For Women's Health. 14: 270-270. DOI: 10.1111/j.1751-486X.2010.01556_1.x  0.038
1969 Holt KS. Care of the handicapped child Nursing Mirror and Midwives Journal. 128: 19-21. PMID 4238920  0.037
1977 Holt KS. Child development: normal and abnormal Nursing Mirror. 145. PMID 73171  0.037
1979 Holt KS. Development guidance Child: Care, Health and Development. 5: 249-266. PMID 158443  0.037
1970 Holt KS. The training of therapists engaged in the child health and rehabilitation services Developmental Medicine and Child Neurology. 12: 680-681. PMID 4249072  0.037
1997 Holt KE. VNA of Washington is a forward-moving, family-friendly home care career option Nursing Spectrum (D.C./Baltimore Metro Ed.). 7: 11. PMID 9431191  0.036
2016 Hollams EM, Teo SM, Kusel M, Holt BJ, Holt KE, Inouye M, De Klerk NH, Zhang G, Sly PD, Hart PH, Holt PG. Vitamin D over the first decade and susceptibility to childhood allergy and asthma. The Journal of Allergy and Clinical Immunology. PMID 27726947 DOI: 10.1016/j.jaci.2016.07.032  0.036
2011 Holt K. Response to correspondence on great ormond street hospital The Lancet. 378: 223. PMID 21737134 DOI: 10.1016/S0140-6736(11)61066-0  0.036
1973 Holt KS. "Physiotherapy for the spastic child: an evaluation" Developmental Medicine and Child Neurology. 15: 537-540. PMID 4732907  0.035
1978 Holt KS. Obituary. Mary Sheridan 1899-1978 Child: Care, Health and Development. 4: 421-423. PMID 367628  0.035
2014 Lounsbery MA, Holt KA, Monnat SM, Funk B, McKenzie TL. JROTC as a substitute for PE: really? Research Quarterly For Exercise and Sport. 85: 414-9. PMID 25141093 DOI: 10.1080/02701367.2014.930408  0.033
1966 Holt KS. Community developmental centres Developmental Medicine and Child Neurology. 8: 770-771. PMID 5972747  0.032
1994 Holt KM. Myopathy presenting as developmental delay and short stature Journal of the Royal Society of Medicine. 87: 45-46. PMID 7508511  0.032
2013 Holt K. "The speak out safely campaign empowers those who whistleblow". Nursing Times. 109: 7. PMID 23560339  0.032
2017 Kelly KM, Holt KT, Neshewat GM, Skolarus LE. Community Interventions to Increase Stroke Preparedness and Acute Stroke Treatment Rates. Current Atherosclerosis Reports. 19: 64. PMID 29147858 DOI: 10.1007/s11883-017-0695-5  0.031
2012 Holt K. "Neither a Saint, a hero, nor a tyrant": Teaching Equiano comparatively Project Muse 4. 2147483647: 215-238.  0.031
1972 Holt KS. The care of the chronic sick. The problem of the young Proceedings of the Royal Society of Medicine. 65: 204-206. PMID 4263807  0.031
1988 Holt K. The role of the user in product innovation Technovation. 7: 249-258. DOI: 10.1016/0166-4972(88)90023-5  0.03
2012 Holt K. Frenchifying the frontier: Transnational federalism in the early west Studies in American Fiction. 39: 1-22. DOI: 10.1353/saf.2012.0005  0.03
1978 Holt K. The damaged child Update. 17: 629-636.  0.029
2006 Holt KB. Using scanning electrochemical microscopy (SECM) to measure the electron-transfer kinetics of cytochrome c immobilized on a COOH-terminated alkanethiol monolayer on a gold electrode Langmuir. 22: 4298-4304. PMID 16618178 DOI: 10.1021/la0529916  0.029
2013 Lounsbery MA, McKenzie TL, Morrow JR, Holt KA, Budnar RG. School physical activity policy assessment. Journal of Physical Activity & Health. 10: 496-503. PMID 22975809  0.029
1994 Holt KG. Assisted Suicide: Sheer Cliff or Clinical Reality? Jama: the Journal of the American Medical Association. 271: 23. PMID 8258877 DOI: 10.1001/jama.1994.03510250039016  0.028
2009 Ellis AW, Ferreira R, Cathles-Hagan P, Holt K, Jarvis L, Barca L. Word learning and the cerebral hemispheres: from serial to parallel processing of written words. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 364: 3675-96. PMID 19933140 DOI: 10.1098/rstb.2009.0187  0.028
2013 Holt K, Johnstone D. A new commission can clean up the NHS. The Health Service Journal. 123: 18-9. PMID 24044260  0.028
1966 Holt KS. The physiological classification of cerebral palsy Developmental Medicine and Child Neurology. 8: 337-339. PMID 5926434  0.026
1961 Holt KE. Third Interim Report of the A.O.C.S.-A.O.A.C. Crude Fiber Liaison Committee, 1959–1960 Journal of the American Oil Chemists Society. 38: 150-151. DOI: 10.1007/BF02641239  0.026
2006 Holt KA. Ultrasonic plastic welding: Weld processing modes, their descriptions, functions and applications Annual Technical Conference - Antec, Conference Proceedings. 1: 433-435.  0.024
1967 Holt KS. Undergraduate Teaching in Paediatrics British Medical Journal. 2: 308. DOI: 10.1136/bmj.2.5547.308  0.024
1948 HOLT KS. The care of the patient Manchester University Medical School Gazette. 27: 73. PMID 18862459  0.024
2017 Stahnke AM, Holt KM. Ocrelizumab: A New B-cell Therapy for Relapsing Remitting and Primary Progressive Multiple Sclerosis. The Annals of Pharmacotherapy. 1060028017747635. PMID 29232960 DOI: 10.1177/1060028017747635  0.024
2010 Holt K. Calcium imbalance, resulting disorders and the available prevention and treatment options The Journal of Practical Nursing. 60: 13-21. PMID 21534441  0.023
1963 HOLT KS. DEFORMITY AND DISABILITY IN CEREBRAL PALSY Developmental Medicine and Child Neurology. 5: 629-631. PMID 14090623  0.023
2007 Holt KB. Clarke oxygen microelectrode Handbook of Electrochemistry. 243-249. DOI: 10.1016/B978-044451958-0.50017-3  0.021
2011 Holt K. Common side effects and interactions of colorectal cancer therapeutic agents The Journal of Practical Nursing. 61: 7-20. PMID 21751717  0.021
2021 Heinz E, Holt KE, Meehan CJ, Sheppard SK. Addressing parachute research and removing barriers for LMIC researchers in . Microbial Genomics. 7. PMID 34704921 DOI: 10.1099/mgen.0.000722  0.021
1956 Holt KS. DRUG TREATMENT OF ENURESIS. CONTROLLED TRIALS WITH PROPANTHELINE, AMPHETAMINE, AND PITUITARY SNUFF The Lancet. 268: 1334-1336. PMID 13386254  0.02
1972 Holt KS. The Problem: The Problem in the Young Journal of the Royal Society of Medicine. 65: 204-206. DOI: 10.1177/003591577206500249  0.02
1983 Holt KJ. FLIGHT TEST AIRSPACE - A VITAL PART OF THE PLAN Aiaa Paper.  0.019
1998 Holt KD. Changing lives, one smile at a time: an operation smile mission to Machala, Ecuador Journal of Biological Photography. 66: 21-22. PMID 9700934  0.019
2009 Holt K. Double-crossings: The trans-American patriotism of Francis Berrian Western American Literature. 44: 313-341.  0.019
1969 Holt KS. The handicapped in society Journal of the Royal College of General Practitioners. 17. PMID 4238322  0.018
1987 Holt K. Schistosomus reflexus--a cluster of cases Veterinary Record. 121: 155. PMID 3660553  0.017
1984 Holt K. Do we spend our research money wisely? Omega. 12: 327-331.  0.017
1977 Holt KS. Some thoughts on developmental screening Child: Care, Health and Development. 3: 275-282. PMID 74299  0.017
1966 Holt KE. Report of AOCS Industrial Oils and Derivatives Committee Journal of the American Oil Chemists Society. 43: 358A-359A. DOI: 10.1007/BF02641289  0.016
1985 Holt KS. Paediatric rehabilitation International Rehabilitation Medicine. 7: 9-10. PMID 3157657  0.016
1963 HOLT KS. Difficulties and dangers in the management of phenylketonuria Acta Paediatrica. 52: 417-423. PMID 13961450  0.016
1961 HOLT K. Record-keeping--a Canadian solution Cerebral Palsy Bulletin. 3: 107-109. PMID 13715539  0.015
2006 Holt K. Workforce plan critical to survival during labor deficit Hotel and Motel Management. 221: 27.  0.015
1982 Holt KS. Diets and development Child: Care, Health and Development. 8: 183-201. PMID 6754124 DOI: 10.1111/J.1365-2214.1982.TB00281.X  0.014
1973 Holt K. Tasteful city named for smelly vegetable Nutrition Today. 8: 36.  0.014
1969 Holt KS. Neurological aspects Proceedings of the Royal Society of Medicine. 62: 997-998. PMID 5346177  0.013
1967 Holt K. Teaching the Behavioural Sciences British Medical Journal. 4: 420. DOI: 10.1136/bmj.4.5576.420-a  0.01
2015 Holt K. Whistleblowing in the NHS. Bmj (Clinical Research Ed.). 350: h2300. PMID 25934650 DOI: 10.1136/bmj.h2300  0.01
2014 Holt K. Kim Holt: Pet hate is bullying. Bmj (Clinical Research Ed.). 349: g7093. PMID 25428211 DOI: 10.1136/bmj.g7093  0.01
2014 Holt K, Manefield M. Science meets Parliament in Canberra: 2014 Microbiology Australia. 35: 110. DOI: 10.1071/MA14036  0.01
2014 Holt KB. Electrochemistry of nanodiamond particles Rsc Nanoscience and Nanotechnology. 2014: 128-150.  0.01
2011 Holt KB. Diamond Ultramicroelectrodes and Nanostructured Electrodes Synthetic Diamond Films: Preparation, Electrochemistry, Characterization, and Applications. 133-152. DOI: 10.1002/9781118062364.ch6  0.01
2010 Holt K. It does matter Nursing For Women's Health. 14: 34-41. PMID 20137041 DOI: 10.1111/j.1751-486X.2010.01505.x  0.01
2010 Holt KA. Evaluation of ultrasonic welding results using microscopy Spe Decorating and Assembly Division 2010 Topical Conference - Tune Into Innovation: Advancements in Decorating and Assembly, Topcon 2010.  0.01
2005 Holt KA. Troubleshooting the ultrasonic welding process: The interpretation of welding graphs in a thermoplastic plunge welding process Annual Technical Conference - Antec, Conference Proceedings. 7: 368-372.  0.01
1992 Holt KG. Growth deficits and desipramine Journal of the American Academy of Child and Adolescent Psychiatry. 31: 1167.  0.01
1969 Holt KS. The Lesch-Nyhan syndrome Developmental Medicine and Child Neurology. 11: 382-384. PMID 5794174  0.01
1969 Holt KS. Language Disorder Journal of the Royal Society of Medicine. 62: 1094. PMID 5356857 DOI: 10.1177/003591576906211P108  0.01
1965 Holt KS. Feeding the Phenylketonuric Infant British Medical Journal. 1: 447. PMID 14237934 DOI: 10.1136/bmj.1.5432.447-b  0.01
1964 HOLT KS. EPILEPSY AND LUPUS ERYTHEMATOSUS Proceedings of the Royal Society of Medicine. 57: 115. PMID 14116024 DOI: 10.1177/003591576405700216  0.01
1946 HOLT KE. The separation of acetylsalicylic acid, acetophenetidin, and caffeine Journal of the American Pharmaceutical Association. American Pharmaceutical Association. 35: 71. PMID 21018234  0.01
1946 HOLT KE. The extraction of caffeine from pharmaceutical preparations Journal of the American Pharmaceutical Association. American Pharmaceutical Association. 35: 313-315. PMID 21002918  0.01
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