Kathryn E Holt

Summary

Affiliation: University of Melbourne
Country: Australia

Publications

  1. pmc Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm
    Jane Hawkey
    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
    BMC Genomics 14:800. 2013
  2. pmc Beginner's guide to comparative bacterial genome analysis using next-generation sequence data
    David J Edwards
    Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria 3010, Australia
    Microb Inform Exp 3:2. 2013
  3. pmc High-resolution genotyping of the endemic Salmonella Typhi population during a Vi (typhoid) vaccination trial in Kolkata
    Kathryn E Holt
    Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
    PLoS Negl Trop Dis 6:e1490. 2012
  4. pmc Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe
    Kathryn E Holt
    Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
    Nat Genet 44:1056-9. 2012
  5. pmc Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    PLoS Negl Trop Dis 5:e1245. 2011
  6. pmc High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    BMC Infect Dis 10:144. 2010
  7. pmc Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam
    Kathryn E Holt
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Negl Trop Dis 5:e929. 2011
  8. pmc Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Genomics 10:36. 2009
  9. pmc High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
    Kathryn E Holt
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Genet 40:987-93. 2008
  10. pmc Evolutionary dynamics of Clostridium difficile over short and long time scales
    Miao He
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Proc Natl Acad Sci U S A 107:7527-32. 2010

Detail Information

Publications30

  1. pmc Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm
    Jane Hawkey
    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
    BMC Genomics 14:800. 2013
    ..We sequenced the genomes of 12 isolates linked to these outbreaks, in order to investigate the microevolution of a pathogenic S. Typhimurium clone in a natural, spatiotemporally restricted population...
  2. pmc Beginner's guide to comparative bacterial genome analysis using next-generation sequence data
    David J Edwards
    Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Victoria 3010, Australia
    Microb Inform Exp 3:2. 2013
    ..Each section includes worked examples using publicly available E. coli data and free software tools, all which can be performed on a desktop computer...
  3. pmc High-resolution genotyping of the endemic Salmonella Typhi population during a Vi (typhoid) vaccination trial in Kolkata
    Kathryn E Holt
    Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
    PLoS Negl Trop Dis 6:e1490. 2012
    ..Typhoid fever, caused by Salmonella enterica serovar Typhi (S. Typhi), is a major health problem especially in developing countries. Vaccines against typhoid are commonly used by travelers but less so by residents of endemic areas...
  4. pmc Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe
    Kathryn E Holt
    Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
    Nat Genet 44:1056-9. 2012
    ....
  5. pmc Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    PLoS Negl Trop Dis 5:e1245. 2011
    ..Typhi host. The PST6 plasmid conferred the ability to grow in high salt medium (4.7% NaCl), which we demonstrate is due to the presence in PST6 of the Tn6062 transposon encoding BetU...
  6. pmc High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
    BMC Infect Dis 10:144. 2010
    ..Kathmandu, the capital of Nepal, is an area of high incidence and the pediatric population appears to be at high risk of exposure and infection...
  7. pmc Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam
    Kathryn E Holt
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Negl Trop Dis 5:e929. 2011
    ..Typhi isolated from 267 typhoid fever patients in the Mekong delta region participating in a randomized trial conducted between 2004 and 2005...
  8. pmc Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
    BMC Genomics 10:36. 2009
    ..The accumulation of pseudogenes is a key feature of these and other host-adapted pathogens, and overlapping pseudogene complements are evident in Paratyphi A and Typhi...
  9. pmc High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi
    Kathryn E Holt
    The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Nat Genet 40:987-93. 2008
    ..The observed patterns of genetic isolation and drift are consistent with the proposed key role of asymptomatic carriers of Typhi as the main reservoir of this pathogen, highlighting the need for identification and treatment of carriers...
  10. pmc Evolutionary dynamics of Clostridium difficile over short and long time scales
    Miao He
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, United Kingdom
    Proc Natl Acad Sci U S A 107:7527-32. 2010
    ..1-85 million years. By contrast, the disease-causing isolates have arisen from multiple lineages, suggesting that virulence evolved independently in the highly epidemic lineages...
  11. pmc Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar
    Robert A Kingsley
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    MBio 4:e00565-13. 2013
    ..Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage...
  12. pmc Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever
    Minh Duy Phan
    The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
    Antimicrob Agents Chemother 53:716-27. 2009
    ..We propose that antibiotic selection acts to maintain resistance genes on the plasmid, but there is also competition between plasmids encoding the same resistance phenotype...
  13. doi request reprint Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
    Vanessa K Wong
    1 Wellcome Trust Sanger Institute, Hinxton, UK 2 Department of Microbiology, Addenbrooke s Hospital, Cambridge University Hospitals National Health Service NHS Foundation Trust, Cambridge, UK
    Nat Genet 47:632-9. 2015
    ..This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species. ..
  14. pmc Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    Bioinformatics 25:2074-5. 2009
    ....
  15. pmc Tracking the establishment of local endemic populations of an emergent enteric pathogen
    Kathryn E Holt
    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia
    Proc Natl Acad Sci U S A 110:17522-7. 2013
    ..This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population. ..
  16. pmc Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype
    Robert A Kingsley
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Cambridge, United Kingdom
    Genome Res 19:2279-87. 2009
    ..Typhi are either pseudogenes or are absent. Genome analysis of other epidemic ST313 isolates from Malawi and Kenya provided evidence for microevolution and clonal replacement in the field...
  17. pmc A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo
    Angela M Jansen
    The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
    PLoS Pathog 7:e1002131. 2011
    ..The presence of the Vi capsule also correlated with induction of the anti-inflammatory cytokine IL-10 in vivo, a factor that impacted on chemotaxis and the activation of immune cells in vitro...
  18. doi request reprint Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258
    Kelly L Wyres
    IBM Research Australia, Carlton, Victoria, Australia Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
    Genome Biol Evol 7:1267-79. 2015
    ..pneumoniae capsules...
  19. doi request reprint Bandage: interactive visualization of de novo genome assemblies
    Ryan R Wick
    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne and
    Bioinformatics 31:3350-2. 2015
    ..By displaying connections between contigs, Bandage presents new possibilities for analyzing de novo assemblies that are not possible through investigation of contigs alone...
  20. doi request reprint ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data
    Jane Hawkey
    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Vic, 3010, Australia
    BMC Genomics 16:667. 2015
    ..Here we present ISMapper, a mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes, directly from paired-end short read data...
  21. pmc 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
    Karolina Dimovski
    Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Parkville, Victoria, Australia
    J Bacteriol 196:3036-44. 2014
    ....
  22. pmc A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters
    Nermin Celik
    Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
    PLoS ONE 7:e43245. 2012
    ..Another conserved and diagnostic motif maps to the linker region between the passenger domain and barrel-domain, indicating it as an important feature in the assembly of autotransporters...
  23. pmc On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer
    Kenneth D Doig
    Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
    BMC Genomics 13:258. 2012
    ..shinshuense, M. liflandii and M. marinum), however the evolution of M. ulcerans and its relationship to other MPM has not been defined. Here we report the comparative analysis of whole genome sequences from 30 MPM and five M. marinum...
  24. pmc Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi
    Kathryn E Holt
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
    J Bacteriol 189:4257-64. 2007
    ..Our data show that these serovar Typhi and Paratyphi A IncHI1 plasmids share highly conserved core DNA and have acquired similar mobile elements encoding antibiotic resistance genes in past decades...
  25. pmc Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus
    Timothy P Stinear
    Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
    Genome Biol Evol 6:366-78. 2014
    ..The evolution of ST93 S. aureus is thus associated with a reduction in both exotoxin expression and oxacillin MIC, suggesting MRSA ST93 isolates are under pressure for adaptive change. ..
  26. pmc Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium
    Vanessa K Wong
    Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom University of Cambridge Department of Pathology, Addenbrooke s Hospital, Cambridge, United Kingdom
    PLoS ONE 8:e84567. 2013
    ..Typhi and S. Typhimurium) or induce colitis in a murine model (S. Typhimurium only). Growth, metabolic and antimicrobial susceptibility tests identified no obvious influences of yehUT on these phenotypes. ..
  27. pmc Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health
    Kathryn E Holt
    Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia Department of Microbiology and Immunology, The University of Melbourne, Parkville, VIC 3010, Australia
    Proc Natl Acad Sci U S A 112:E3574-81. 2015
    ..pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats. ..
  28. pmc Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus
    Sarah L Baines
    Department of Biochemistry and Molecular Biology, Bio 21, Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
    MBio 6:e00080. 2015
    ....
  29. pmc Short read sequence typing (SRST): multi-locus sequence types from short reads
    Michael Inouye
    Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Australia
    BMC Genomics 13:338. 2012
    ..However given the wealth of data currently available in MLST databases, it is crucial to maintain backwards compatibility with MLST schemes so that new genome analyses can be understood in their proper historical context...