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List of works by Kat Holt

A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid.

scientific article

A Salmonella Typhimurium-Typhi genomic chimera: a model to study Vi polysaccharide capsule function in vivo

scientific article

A bioinformatic strategy for the detection, classification and analysis of bacterial autotransporters

scientific article

A conjugative plasmid carrying the carbapenem resistance gene blaOXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate

scientific article published on 6 June 2014

A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex

scientific article published on 07 July 2021

A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi.

scientific article

A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A.

scientific article published on 28 May 2010

A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307

scientific article published on 01 February 2022

A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure

scientific article published on 11 March 2016

A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji

scientific article published on 20 July 2017

A platform for leveraging next generation sequencing for routine microbiology and public health use.

scientific article

A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant

scientific article published on 27 September 2015

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.

scientific article

Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus

scientific article published on February 2014

An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid

scientific article published on 05 October 2016

An outpatient, ambulant-design, controlled human infection model using escalating doses of Salmonella Typhi challenge delivered in sodium bicarbonate solution

scientific article published on 10 February 2014

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

scientific article

Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital

scientific article published on 11 January 2018

Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?

scientific article

Bandage: interactive visualization of de novo genome assemblies

scientific article published on 22 June 2015

Beginner's guide to comparative bacterial genome analysis using next-generation sequence data

scientific article

Burden of enteric fever at three urban sites in Africa and Asia: a multicentre population-based study

scientific article published on 01 December 2021

Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid.

scientific article published on 27 November 2014

Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium.

scientific article

Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii

scientific article published in 2019

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia

article

Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission

scientific article published in October 2011

Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City

scientific article published on 01 March 2019

Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli

scientific article published on 20 April 2016

Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece

scientific article published on 10 October 2019

Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage

article

Completing bacterial genome assemblies with multiplex MinION sequencing.

scientific article published on 14 September 2017

Convergent adaptation in the dominant global hospital clone ST239 of methicillin-resistant Staphylococcus aureus.

scientific article

Cord blood hemopoietic progenitor profiles predict acute respiratory symptoms in infancy

scientific article

Corrigendum: Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1

scientific article published on 01 July 2019

Cross-validation to select Bayesian hierarchical models in phylogenetics

scientific article published on 26 May 2016

Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks

scientific article published on 20 November 2018

Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers.

scientific article published on January 2011

Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA.

scientific article published on 3 June 2009

Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population.

scientific article published on 13 July 2016

Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei

scientific article published on 23 October 2019

Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China

scientific article published in 2022

Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales

scientific article published on 06 April 2020

Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating

article

Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1.

scientific article published on 3 September 2015

Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants ⬇️

scientific article published on June 27, 2013

Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa

article

Elucidation of pathways driving asthma pathogenesis: development of a systems-level analytic strategy

scientific article

Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307

scientific article published on 01 March 2019

Emergence of a globally dominant IncHI1 plasmid type associated with multiple drug resistant typhoid

scientific article published in July 2011

Empirical ways to identify novel Bedaquiline resistance mutations in AtpE

scientific article published on 29 May 2019

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

scientific article published on 9 November 2009

Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm

scientific article

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1

article

Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants

scientific article

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection.

scientific article

Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain

scientific article

Evolutionary dynamics of Clostridium difficile over short and long time scales

scientific article published on 20 April 2010

Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258.

scientific article published on 10 April 2015

FastSpar: rapid and scalable correlation estimation for compositional data

scientific article published on 01 March 2019

Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1.

scientific article published on 23 February 2016

Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam

article

Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients

scientific article

Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations

scientific article published on 09 July 2018

Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1.

scientific article published on 12 March 2015

Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1

scientific article published on 17 December 2015

Genome and transcriptome adaptation accompanying emergence of the definitive type 2 host-restricted Salmonella enterica serovar Typhimurium pathovar

scientific article published on 27 August 2013

Genome-scale rates of evolutionary change in bacteria.

scientific article published on 30 November 2016

Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health

scientific article published on 22 June 2015

Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen

scientific article published on 31 May 2022

Genomic history of the seventh pandemic of cholera in Africa.

scientific article published in November 2017

Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens

scientific article published in Science

Genomic insights to control the emergence of vancomycin-resistant enterococci

scientific article published on 13 August 2013

Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate

scientific article

Global expansion of lineage 4 shaped by colonial migration and local adaptation

article

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198

scientific article published on 20 May 2019

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.

scientific article

Global phylogeography and evolutionary history of Shigella dysenteriae type 1.

scientific article

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

scientific article published on 11 May 2021

High-resolution genotyping of the endemic Salmonella Typhi population during a Vi (typhoid) vaccination trial in Kolkata.

scientific article

High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children

scientific article published on 31 May 2010

High-throughput genotyping of Salmonella enterica serovar Typhi allowing geographical assignment of haplotypes and pathotypes within an urban District of Jakarta, Indonesia

scientific article published on 5 March 2008

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi

scientific article published on 27 July 2008

ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data

scientific article

Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible with Kaptive

scientific article published on 01 March 2020

Identification of Klebsiella capsule synthesis loci from whole genome data

scientific article

Identification of Salmonella enterica serovar Typhi genotypes by use of rapid multiplex ligation-dependent probe amplification

scientific article (publication date: September 2013)

Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii

scientific article published on 29 September 2013

Identifying adaptive differences could provide insight.

scientific article published in March 2009

Impact of insertion sequences on convergent evolution of Shigella species

scientific article published on 09 July 2020

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.

scientific article

Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate

scientific article published on 30 May 2016

Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods.

scientific article published on 19 June 2018

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers

Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers

scientific article published on 12 September 2019

Insertions in the OCL1 locus of Acinetobacter baumannii lead to shortened lipooligosaccharides

scientific article

Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2

scientific article published on 01 October 2019

Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan

scientific article published on 24 December 2015

Involvement of PatE, a prophage-encoded AraC-like regulator, in the transcriptional activation of acid resistance pathways of enterohemorrhagic Escherichia coli strain EDL933.

scientific article

Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes.

scientific article

Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones

scientific article

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

scientific article published on 01 May 2018

Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy

scientific article published on 23 April 2018

Mercury methylation by metabolically versatile and cosmopolitan marine bacteria

scientific article published in 2021

Microbial mercury methylation in Antarctic sea ice.

scientific article published on August 2016

ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants

scientific article published on 11 April 2006

Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa

scientific article published on 22 September 2016

Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin.

scientific article published on 29 June 2018

Multidrug-resistant Salmonella enterica serotype Typhi, Gulf of Guinea Region, Africa.

scientific article

Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.

scientific article published on 23 March 2007

Multidrug-resistant Shigella sonnei carrying plasmid-mediated mcr-1 gene in China

scientific article published on 28 February 2018

Multiple Genetic Mutations Associated with Polymyxin Resistance in Acinetobacter baumannii

scientific article

Navigating the future of bacterial molecular epidemiology.

scientific article published on 16 September 2010

Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk

scientific article published on 28 July 2020

On the origin of mycobacterium ulcerans, the causative agent of buruli ulcer

scientific article

Open-Source Genomic Analysis of Shiga-Toxin–Producing E. coli O104:H4

scientific article

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans

scientific article (publication date: October 2013)

Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events

scientific article published on 11 May 2015

Polypolish: Short-read polishing of long-read bacterial genome assemblies

scientific article published on 24 January 2022

Population genomics of Klebsiella pneumoniae

scientific article published on 13 February 2020

Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination

scientific article published in Nature Communications

Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016

scientific article published on 27 February 2020

Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS.

scientific article published on 30 December 2016

Protection conferred by typhoid fever against recurrent typhoid fever in urban Kolkata

scientific article published on 17 August 2020

Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi

scientific article published on 21 January 2009

Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward

scientific article

Shigella sonnei

scientific article published on 08 April 2020

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe

scientific article published in September 2012

Short read sequence typing (SRST): multi-locus sequence types from short reads

scientific article

Small IncQ1 and Col-Like Plasmids Harboring bla KPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258

scientific article published on 26 February 2019

South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study

scientific article

Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community

scientific article published in 2022

Temporal fluctuation of multidrug resistant salmonella typhi haplotypes in the mekong river delta region of Vietnam

scientific article published on 4 January 2011

The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia

scientific article

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

scientific article published on 2 July 2017

The burden and characteristics of enteric fever at a healthcare facility in a densely populated area of Kathmandu

scientific article published on 15 November 2010

The complete sequence of Salmonella genomic island SGI1-K.

scientific article published on 4 September 2014

The complete sequence of Salmonella genomic island SGI2.

scientific article published on 14 October 2014

The diversity of Klebsiella pneumoniae surface polysaccharides

scientific article published on 25 August 2016

The genomic signatures of Shigella evolution, adaptation and geographical spread

scientific article published on 29 February 2016

The infant nasopharyngeal microbiome impacts severity of lower respiratory infection and risk of asthma development

scientific article published on 9 April 2015

The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa

scientific article published in Nature Communications

The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens

scientific article published on 21 May 2010

Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae

scientific article published on 29 October 2018

Tracking the establishment of local endemic populations of an emergent enteric pathogen

scientific article published on 30 September 2013

Trajectories of childhood immune development and respiratory health relevant to asthma and allergy

scientific article published on 15 October 2018

Typhoid in Kenya is associated with a dominant multidrug-resistant Salmonella enterica serovar Typhi haplotype that is also widespread in Southeast Asia

scientific article

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

scientific article

Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore

scientific article

Variation in Salmonella enterica serovar typhi IncHI1 plasmids during the global spread of resistant typhoid fever

scientific article published on 17 November 2008

Vitamin D over the first decade and susceptibility to childhood allergy and asthma

scientific article published on 7 October 2016

WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare?

scientific article

Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program

scientific article

hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus.

scientific article published on 24 May 2019

pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron.

scientific article published on 5 February 2016

wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations

scientific article published in 2021

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