Kat Holt
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Australian biologist
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Biology
Kat Holt's Degrees
- Bachelors Biological Sciences University of Melbourne
Why Is Kat Holt Influential?
(Suggest an Edit or Addition)According to Wikipedia, Kathryn "Kat" Elizabeth Holt is an Australian computational biologist specializing in infectious disease genomics. She is a professor at Monash University's Department of Infectious Diseases and a professor of Microbial Systems Genomics at the London School of Hygiene & Tropical Medicine . Her current research focuses on investigating the evolution and dissemination of antimicrobial resistance. In 2015, Holt received the L'Oréal-UNESCO International Rising Talent Award.
Kat Holt's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016) (3586)
- Bandage: interactive visualization of de novo genome assemblies (2015) (1195)
- Out-of-Africa migration and Neolithic co-expansion of Mycobacterium tuberculosis with modern humans (2013) (866)
- Performance of neural network basecalling tools for Oxford Nanopore sequencing (2019) (840)
- Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health (2015) (810)
- SRST2: Rapid genomic surveillance for public health and hospital microbiology labs (2014) (808)
- The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development (2015) (656)
- Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. (2009) (498)
- Completing bacterial genome assemblies with multiplex MinION sequencing (2017) (484)
- High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi (2008) (477)
- Evolutionary dynamics of Clostridium difficile over short and long time scales (2010) (370)
- Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events (2015) (363)
- Population genomics of Klebsiella pneumoniae (2020) (329)
- Identification of Klebsiella capsule synthesis loci from whole genome data (2016) (325)
- Gastrointestinal Carriage Is a Major Reservoir of Klebsiella pneumoniae Infection in Intensive Care Patients (2017) (288)
- Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe (2012) (272)
- Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. (2018) (242)
- Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations (2018) (206)
- Genome-scale rates of evolutionary change in bacteria (2016) (202)
- Genomic Insights to Control the Emergence of Vancomycin-Resistant Enterococci (2013) (200)
- A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex (2021) (192)
- Genomic history of the seventh pandemic of cholera in Africa (2017) (190)
- Genomic insights into the emergence and spread of antimicrobial-resistant bacterial pathogens (2018) (186)
- Klebsiella pneumoniae Population Genomics and Antimicrobial-Resistant Clones. (2016) (186)
- Kaptive Web: User-Friendly Capsule and Lipopolysaccharide Serotype Prediction for Klebsiella Genomes (2018) (173)
- Typhoid in Kenya Is Associated with a Dominant Multidrug-Resistant Salmonellaenterica Serovar Typhi Haplotype That Is Also Widespread in Southeast Asia (2010) (160)
- Pseudogene accumulation in the evolutionary histories of Salmonella enterica serovars Paratyphi A and Typhi (2009) (159)
- Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination (2017) (158)
- Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae (2018) (153)
- The diversity of Klebsiella pneumoniae surface polysaccharides (2016) (149)
- On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer (2012) (138)
- The genomic signatures of Shigella evolution, adaptation and geographical spread (2016) (134)
- Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for EsxW Beijing variant in Vietnam (2018) (131)
- Deepbinner: Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks (2018) (129)
- Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from South and Southeast Asia (2019) (128)
- FastSpar: rapid and scalable correlation estimation for compositional data (2018) (127)
- An Outpatient, Ambulant-Design, Controlled Human Infection Model Using Escalating Doses of Salmonella Typhi Challenge Delivered in Sodium Bicarbonate Solution (2014) (124)
- Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data (2013) (121)
- Microbial mercury methylation in Antarctic sea ice (2016) (120)
- Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid (2011) (118)
- Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae (2018) (116)
- Combined high-resolution genotyping and geospatial analysis reveals modes of endemic urban typhoid fever transmission (2011) (115)
- Airway Microbiota Dynamics Uncover a Critical Window for Interplay of Pathogenic Bacteria and Allergy in Childhood Respiratory Disease (2018) (114)
- An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid (2016) (112)
- Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing? (2016) (110)
- Tracking the establishment of local endemic populations of an emergent enteric pathogen (2013) (109)
- 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 (2016) (108)
- Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1 (2016) (105)
- Emergence and rapid global dissemination of CTX-M-15-associated Klebsiella pneumoniae strain ST307 (2018) (103)
- Short read sequence typing (SRST): multi-locus sequence types from short reads (2012) (102)
- ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data (2015) (101)
- 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 (2019) (97)
- Evolutionary dynamics and genomic features of the Elizabethkingia anophelis 2015 to 2016 Wisconsin outbreak strain (2017) (97)
- Global expansion of Mycobacterium tuberculosis lineage 4 shaped by colonial migration and local adaptation (2018) (96)
- The sensitivity of real-time PCR amplification targeting invasive Salmonella serovars in biological specimens (2010) (95)
- Benchmarking of long-read assemblers for prokaryote whole genome sequencing. (2019) (90)
- Novel Subclone of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 with Enhanced Virulence and Transmissibility, China (2020) (89)
- Convergent Adaptation in the Dominant Global Hospital Clone ST239 of Methicillin-Resistant Staphylococcus aureus (2015) (89)
- Trycycler: consensus long-read assemblies for bacterial genomes (2021) (88)
- Extensive Capsule Locus Variation and Large-Scale Genomic Recombination within the Klebsiella pneumoniae Clonal Group 258 (2015) (88)
- A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure (2016) (88)
- The Burden and Characteristics of Enteric Fever at a Healthcare Facility in a Densely Populated Area of Kathmandu (2010) (86)
- Multidrug-Resistant Salmonella enterica Serovar Paratyphi A Harbors IncHI1 Plasmids Similar to Those Found in Serovar Typhi (2007) (84)
- Variation in Salmonella enterica Serovar Typhi IncHI1 Plasmids during the Global Spread of Resistant Typhoid Fever (2008) (83)
- Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital (2017) (80)
- Comparative genomics of Crohn's disease-associated adherent-invasive Escherichia coli (2016) (80)
- Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa (2016) (79)
- High-Throughput Genotyping of Salmonella enterica Serovar Typhi Allowing Geographical Assignment of Haplotypes and Pathotypes within an Urban District of Jakarta, Indonesia (2008) (78)
- South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study (2016) (77)
- A Bioinformatic Strategy for the Detection, Classification and Analysis of Bacterial Autotransporters (2012) (74)
- Differential host susceptibility and bacterial virulence factors driving Klebsiella liver abscess in an ethnically diverse population (2016) (74)
- The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa (2018) (72)
- Polypolish: Short-read polishing of long-read bacterial genome assemblies (2021) (72)
- Vitamin D over the first decade and susceptibility to childhood allergy and asthma (2017) (72)
- High-throughput bacterial SNP typing identifies distinct clusters of Salmonella Typhi causing typhoid in Nepalese children (2010) (71)
- Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15 (2019) (67)
- Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198 (2019) (67)
- Global phylogeography and evolutionary history of Shigella dysenteriae type 1 (2016) (65)
- Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate. (2016) (65)
- Navigating the future of bacterial molecular epidemiology (2010) (65)
- Diversity-Generating Machines: Genetics of Bacterial Sugar-Coating (2018) (65)
- A GC1 Acinetobacter baumannii isolate carrying AbaR3 and the aminoglycoside resistance transposon TnaphA6 in a conjugative plasmid (2013) (64)
- Co-circulation of multidrug-resistant Shigella among men who have sex with men, Australia. (2019) (63)
- Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa (2018) (61)
- Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm (2013) (60)
- Evolution of atypical enteropathogenic E. coli by repeated acquisition of LEE pathogenicity island variants (2016) (60)
- Laboratory and molecular surveillance of paediatric typhoidal Salmonella in Nepal: Antimicrobial resistance and implications for vaccine policy (2018) (58)
- A conjugative plasmid carrying the carbapenem resistance gene blaOXA-23 in AbaR4 in an extensively resistant GC1 Acinetobacter baumannii isolate. (2014) (56)
- Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward (2016) (55)
- Temporal Fluctuation of Multidrug Resistant Salmonella Typhi Haplotypes in the Mekong River Delta Region of Vietnam (2011) (54)
- Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar (2013) (54)
- Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection (2017) (53)
- 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 (2017) (50)
- Detecting SNPs and estimating allele frequencies in clonal bacterial populations by sequencing pooled DNA (2009) (49)
- WGS Analysis and Interpretation in Clinical and Public Health Microbiology Laboratories: What Are the Requirements and How Do Existing Tools Compare? (2014) (48)
- A Salmonella Typhimurium-Typhi Genomic Chimera: A Model to Study Vi Polysaccharide Capsule Function In Vivo (2011) (47)
- Informal genomic surveillance of regional distribution of Salmonella Typhi genotypes and antimicrobial resistance via returning travellers (2019) (46)
- A Scalable Permutation Approach Reveals Replication and Preservation Patterns of Network Modules in Large Datasets. (2016) (45)
- Variants of AbGRI3 carrying the armA gene in extensively antibiotic-resistant Acinetobacter baumannii from Singapore (2017) (44)
- Genomic resistance island AGI1 carrying a complex class 1 integron in a multiply antibiotic-resistant ST25 Acinetobacter baumannii isolate. (2015) (42)
- Mercury methylation by metabolically versatile and cosmopolitan marine bacteria (2020) (40)
- Prediction of antibiotic resistance from antibiotic resistance genes detected in antibiotic-resistant commensal Escherichia coli using PCR or WGS (2016) (39)
- The Molecular and Spatial Epidemiology of Typhoid Fever in Rural Cambodia (2016) (39)
- A multiplex single nucleotide polymorphism typing assay for detecting mutations that result in decreased fluoroquinolone susceptibility in Salmonella enterica serovars Typhi and Paratyphi A (2010) (37)
- pCERC3 from a commensal ST95 Escherichia coli: A ColV virulence-multiresistance plasmid carrying a sul3-associated class 1 integron. (2016) (36)
- Empirical ways to identify novel Bedaquiline resistance mutations in AtpE (2019) (36)
- Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1 (2019) (35)
- The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis (2022) (34)
- Benchmarking of long-read assemblers for prokaryote whole genome sequencing (2021) (34)
- Developmental patterns in the nasopharyngeal microbiome during infancy are associated with asthma risk (2020) (34)
- Impact of insertion sequences on convergent evolution of Shigella species (2019) (33)
- A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at pathogenwatch (2020) (33)
- Carbapenem and amikacin resistance on a large conjugative Acinetobacter baumannii plasmid (2014) (32)
- Adaptive Change Inferred from Genomic Population Analysis of the ST93 Epidemic Clone of Community-Associated Methicillin-Resistant Staphylococcus aureus (2014) (32)
- Genomic surveillance framework and global population structure for Klebsiella pneumoniae (2020) (31)
- Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei (2019) (31)
- Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii (2019) (30)
- Gastrointestinal carriage is a major reservoir of K. pneumoniae infection in intensive care patients (2016) (29)
- Genome Sequence of Acinetobacter baumannii Strain A1, an Early Example of Antibiotic-Resistant Global Clone 1 (2015) (29)
- Identification of a marker for two lineages within the GC1 clone of Acinetobacter baumannii (2013) (28)
- A linear plasmid truncation induces unidirectional flagellar phase change in H:z66 positive Salmonella Typhi (2007) (27)
- Recovery of small plasmid sequences via Oxford Nanopore sequencing (2021) (26)
- Persistent circulation of a fluoroquinolone-resistant Salmonella enterica Typhi clone in the Indian subcontinent (2019) (26)
- 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 (2014) (26)
- Correcting index databases improves metagenomic studies (2019) (25)
- Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales (2019) (25)
- Demultiplexing barcoded Oxford Nanopore reads with deep convolutional neural networks (2018) (25)
- Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei (2020) (25)
- Burden of enteric fever at three urban sites in Africa and Asia: a multicentre population-based study. (2021) (24)
- High-Resolution Genotyping of the Endemic Salmonella Typhi Population during a Vi (Typhoid) Vaccination Trial in Kolkata (2012) (24)
- Small IncQ1 and Col-Like Plasmids Harboring blaKPC-2 and Non-Tn4401 Elements (NTEKPC-IId) in High-Risk Lineages of Klebsiella pneumoniae CG258 (2019) (24)
- Insertions in the OCL1 locus of Acinetobacter baumannii lead to shortened lipooligosaccharides (2014) (23)
- Cord blood hemopoietic progenitor profiles predict acute respiratory symptoms in infancy (2008) (23)
- Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch (2021) (23)
- 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 (2012) (22)
- Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immunization Program (2016) (22)
- Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in urban Dhaka, Bangladesh from 2004 to 2016 (2020) (22)
- Azole-resistant Aspergillus fumigatus with the environmental TR46/Y121F/ T289A mutation in India (2014) (22)
- hicap: In Silico Serotyping of the Haemophilus influenzae Capsule Locus (2019) (22)
- Benchmarking of long-read assemblers for prokaryote whole genome sequencing. (2020) (22)
- Multidrug-Resistant Salmonella enterica Serotype Typhi, Gulf of Guinea Region, Africa (2015) (21)
- 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. (2014) (20)
- Silent spread of mobile colistin resistance gene mcr-9.1 on IncHI2 'superplasmids' in clinical carbapenem-resistant Enterobacterales. (2021) (20)
- Trajectories of childhood immune development and respiratory health relevant to asthma and allergy (2018) (19)
- The complete sequence of Salmonella genomic island SGI2. (2015) (19)
- 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. (2020) (19)
- Distinct increase in antimicrobial resistance genes among Escherichia coli during 50 years of antimicrobial use in livestock production in China (2022) (19)
- Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen (2022) (19)
- Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex (2022) (19)
- Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population: a cross-sectional study of risk factors and bacterial genomic diversity (2021) (19)
- Frequent emergence of pathogenic lineages of Klebsiella pneumoniae via mobilisation of yersiniabactin and colibactin (2017) (18)
- Direct Nanopore Sequencing of mRNA Reveals Landscape of Transcript Isoforms in Apicomplexan Parasites (2020) (18)
- Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin (2018) (18)
- Genome Sequence of Acinetobacter baumannii Strain D36, an Antibiotic-Resistant Isolate from Lineage 2 of Global Clone 1 (2015) (18)
- Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium (2021) (18)
- Systems biology and big data in asthma and allergy: recent discoveries and emerging challenges (2019) (18)
- Multiple Genetic Mutations Associated with Polymyxin Resistance in Acinetobacter baumannii (2015) (17)
- Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework (2021) (17)
- The complete sequence of Salmonella genomic island SGI1-K. (2015) (17)
- Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya (2021) (17)
- A small Acinetobacter plasmid carrying the tet39 tetracycline resistance determinant (2015) (17)
- A novel genetic variant of Streptococcus pneumoniae serotype 11A discovered in Fiji (2017) (16)
- The inflated mitochondrial genomes of siphonous green algae reflect processes driving expansion of noncoding DNA and proliferation of introns (2020) (16)
- Elucidation of Pathways Driving Asthma Pathogenesis: Development of a Systems-Level Analytic Strategy (2014) (15)
- Inducible colistin resistance via a disrupted plasmid-borne mcr-1 gene in a 2008 Vietnamese Shigella sonnei isolate (2016) (15)
- Cross-validation to select Bayesian hierarchical models in phylogenetics (2016) (15)
- The impact of genomics on precision public health: beyond the pandemic (2021) (14)
- Design of multiple sequence alignment algorithms on parallel, distributed memory supercomputers (2011) (14)
- Genomic adaptations to an endolithic lifestyle in the coral-associated alga Ostreobium (2020) (14)
- Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan (2015) (14)
- Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods (2018) (14)
- Involvement of PatE, a Prophage-Encoded AraC-Like Regulator, in the Transcriptional Activation of Acid Resistance Pathways of Enterohemorrhagic Escherichia coli Strain EDL933 (2012) (12)
- ModuleFinder and CoReg: alternative tools for linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants (2006) (12)
- Multidrug-resistant Shigella sonnei carrying the plasmid-mediated mcr-1 gene in China. (2018) (12)
- Genomic surveillance of antimicrobial resistant bacterial colonisation and infection in intensive care patients (2020) (11)
- Genome-Resolved Metagenomics and Detailed Geochemical Speciation Analyses Yield New Insights into Microbial Mercury Cycling in Geothermal Springs (2020) (11)
- Neonatal genetics of gene expression reveal potential origins of autoimmune and allergic disease risk (2020) (10)
- Species interactions constrain adaptation and preserve ecological stability in an experimental microbial community (2022) (10)
- Insights from the revised complete genome sequences of Acinetobacter baumannii strains AB307-0294 and ACICU belonging to global clones 1 and 2 (2019) (9)
- Evolutionary dynamics and genomic features of the Elizabethkingia anophelis Wisconsin outbreak strain (2017) (9)
- Identification of Salmonella enterica Serovar Typhi Genotypes by Use of Rapid Multiplex Ligation-Dependent Probe Amplification (2013) (9)
- SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments (2020) (8)
- Detection of plasmid contigs in draft genome assemblies using customized Kraken databases (2020) (8)
- A platform for leveraging next generation sequencing for routine microbiology and public health use (2015) (8)
- GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure (2020) (8)
- Characterization of the yehUT Two-Component Regulatory System of Salmonella enterica Serovar Typhi and Typhimurium (2013) (8)
- ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting (2021) (7)
- Z/I1 Hybrid Virulence Plasmids Carrying Antimicrobial Resistance genes in S. Typhimurium from Australian Food Animal Production (2019) (7)
- Shigella sonnei (2020) (7)
- Assembling the perfect bacterial genome using Oxford Nanopore and Illumina sequencing (2023) (7)
- EcOH: In silico serotyping of E. coli from short read data (2015) (7)
- Kaptive 2.0: updated capsule and LPS locus typing for the Klebsiella pneumoniae species complex (2021) (7)
- Dynamics of the upper airway microbiome in the pathogenesis of asthma-associated persistent wheeze in preschool children (2017) (7)
- The infant airway microbiome in health and disease impacts later asthma development (2014) (7)
- Klebsiella MALDI TypeR: a web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry. (2021) (6)
- ModuleFinder and CoReg: linking gene expression modules with promoter sequences motifs to uncover gene regulation mechanisms in plants (2006) (6)
- Benchmarking of long-read assemblers for prokaryote whole genome sequencing. (2020) (6)
- A Bayesian approach for estimating typhoid fever incidence from large‐scale facility‐based passive surveillance data (2020) (6)
- Neonatal genetics of gene expression reveal the origins of autoimmune and allergic disease risk (2019) (5)
- Klebsiella MALDI TypeR: a web-based tool for Klebsiella identification based on MALDI-TOF mass spectrometry (2020) (5)
- ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data (2015) (5)
- Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae (2021) (5)
- Complete Genome Sequence of A388, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 1 Isolate from Greece (2019) (4)
- Evolution and genomic insight into methicillin-resistant Staphylococcus aureus ST9 in China. (2021) (4)
- Yersiniabactin, Colibactin and Wider Resistome Contribute to Enhanced Virulence and Persistence of KPC-2-Producing Klebsiella pneumoniae CG258 in South America (2018) (4)
- Draft Genome Sequence of a Clinical Isolate of Serratia marcescens, Strain AH0650_Sm1 (2015) (4)
- Population structure and antimicrobial resistance patterns of Salmonella Typhi isolates in Bangladesh from 2004 to 2016 (2019) (4)
- Convergence of virulence and multidrug resistance in a single plasmid vector in multidrug-resistant Klebsiella pneumoniae ST15 (2018) (4)
- wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations (2021) (4)
- Gastrointestinal carriage of Klebsiella pneumoniae in a general adult population in Norway: a cross-sectional study of risk factors and bacterial genomic diversity (2021) (4)
- A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001-2015: Introduction and spread of ESBL facilitated by CG15 and CG307 (2021) (3)
- Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia (2022) (3)
- Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics (2021) (3)
- Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian Fruit Bats (Pteropus poliocephalus) (2021) (3)
- The emergence and intercontinental spread of a multidrug-resistant clade of typhoid agent Salmonella enterica serovar Typhi (2016) (3)
- Complete Genome Sequence of WM99c, an Antibiotic-Resistant Acinetobacter baumannii Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage (2018) (3)
- Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae (2022) (3)
- Genomic analysis of Mycobacterium tuberculosis reveals complex etiology of tuberculosis in Vietnam including frequent introduction and transmission of Beijing lineage and positive selection for EsxW Beijing variant (2016) (3)
- Draft Genome Sequences for Ten Salmonella enterica Serovar Typhimurium Phage Type 135 Variants (2013) (3)
- Typhoid in Kenya is associated with a dominant multidrug resistant Salmonella Typhi 1 haplotype that is also widespread in South East Asia 2 3 4 * (2010) (3)
- Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods (2022) (3)
- Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials (2021) (3)
- Protection conferred by typhoid fever against recurrent typhoid fever in urban Kolkata (2020) (3)
- 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 (2017) (2)
- Corrigendum: Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1 (2019) (2)
- Genomics and Pathogenesis of Salmonella enterica Serovars Typhi and Paratyphi A (2011) (2)
- An Examination of Household Drinking Water Storage and Management Practices in Bonao, Dominican Republic from September 2005-January 2006. (2010) (2)
- Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam (2018) (2)
- Extensive capsule locus variation and large-scale genomic recombination within the Klebsiella pneumoniae clonal complex 258/11 (2014) (2)
- Nasopharyngeal Microbiome During Health and Illness in Early Life (2018) (2)
- A nationwide genomic study of clinical Klebsiella pneumoniae in Norway 2001–15: introduction and spread of ESBLs facilitated by clonal groups CG15 and CG307 (2021) (2)
- On the origin of Mycobacterium ulcerans, the causative agent of Buruli ulcer (2012) (2)
- Rapid Whole Genome Sequencing of Serotype K1 Hypervirulent Klebsiella pneumoniae from an Undocumented Chinese Migrant (2021) (2)
- Genomic dissection of the bacterial population underlying Klebsiella pneumoniae infections in hospital patients: insights into an opportunistic pathogen (2021) (2)
- Genomic diversity and antimicrobial resistance of Haemophilus colonising the airways of young children with cystic fibrosis (2020) (2)
- Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan (2022) (2)
- Novel strains of Klebsiella africana and Klebsiella pneumoniae in Australian Fruit Bats (Pteropus poliocephalus). (2021) (2)
- Transmission of Klebsiella strains and plasmids within and between grey‐headed flying fox colonies (2021) (2)
- Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1 (2016) (2)
- Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination (2018) (2)
- invasive disease in sub-Saharan Africa have a distinct genotype Typhimurium causing Salmonella Epidemic multiple drug resistant Material Supplemental (2009) (2)
- Tracking key virulence loci encoding aerobactin and salmochelin siderophore synthesis in Klebsiella pneumoniae (2018) (2)
- A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality (2021) (2)
- ISMapper: Identifying insertion sequences in bacterial genomes from short read sequence data (2015) (1)
- Detection and Typing of Plasmids in Acinetobacter baumannii Using rep Genes Encoding Replication Initiation Proteins (2022) (1)
- SRST2: Rapid genomic surveillance for public health and hospital microbiology labs (2014) (1)
- Drivers of antimicrobial resistance amongst intestinal Escherichia coli isolated from children in South Asia and sub-Saharan Africa (2017) (1)
- Cross-validation to select Bayesian hierarchical models in phylogenetics (2016) (1)
- GeneMates: an R package for detecting horizontal gene co-transfer between bacteria using gene-gene associations controlled for population structure (2020) (1)
- Klebsiella pneumoniae with capsule type K64 is overrepresented among invasive disease in Vietnam (2021) (1)
- Cohort-wide characterization of the nasopharyngeal microbiome across year 1 in "high risk" infants by PCR and 16S rRNA gene deep sequencing: elucidation of viral-bacterial-host interactions driving early atopic asthma pathogenesis (2015) (1)
- Comment on: MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009–19 (2023) (1)
- Inferring demographic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods (2018) (1)
- Maternal colonisation and early-onset neonatal bacterial sepsis in The Gambia, West Africa: a genomic analysis of vertical transmission. (2022) (1)
- Genomic Diversity and Antimicrobial Resistance of Haemophilus Colonizing the Airways of Young Children with Cystic Fibrosis (2021) (1)
- Eosinophil Progenitors at Birth: Intimations of Future Atopy and Inflammation. Cellular and Molecular Targets in Allergy and Clinical Immunology (2007) (1)
- THE EARLY-LIFE NASOPHARYNGEAL MICROBIOME INTERACTS WITH ALLERGIC AND NON-ALLERGIC MECHANISMS OF CHILDHOOD WHEEZE (2019) (1)
- Genomic epidemiology and antimicrobial resistance transmission of Salmonella Typhi and Paratyphi A at three urban sites in Africa and Asia (2023) (1)
- A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China (2022) (1)
- Author response: A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure (2016) (1)
- The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa (2018) (1)
- Identifying adaptive differences could provide insight. (2009) (1)
- Comment on: CG258 Klebsiella pneumoniae isolates without β-lactam resistance at the onset of the carbapenem-resistant Enterobacteriaceae epidemic in New York City (2018) (1)
- Short read sequence typing (SRST): multi-locus sequence types from short reads (2012) (1)
- Performance of neural network basecalling tools for Oxford Nanopore sequencing (2019) (1)
- A platform for leveraging next generation sequencing for routine microbiology and public health use (2015) (1)
- Dynamics of antimicrobial resistance in intestinal Escherichia coli from children in community settings in South Asia and sub-Saharan Africa (2018) (1)
- Author ' s response to reviews Title : The Limitations of Real-Time PCR Amplification for the Detection of Invasive Salmonella serovars in Blood and Bone Marrow Specimens from Enteric fever Patients (0)
- Genomic analysis reveals fifty years of antimicrobial resistance evolution in husbandry Escherichia coli from China (2021) (0)
- Bacteria genomic rates data: First release (2016) (0)
- Non-parametric mixture models identify trajectories of childhood immune development relevant to asthma and allergy (2017) (0)
- Pathogen genomic surveillance of typhoidal Salmonella infection in adults and children reveals no association between clinical outcomes and infecting genotypes (2020) (0)
- DOP089 Comparative genome analysis of Crohn's Disease-associated adherent, invasive Escherichia coli fails to detect a common molecular property (2015) (0)
- Morphological, genomic and transcriptomic responses of Klebsiella pneumoniae to the last-line antibiotic colistin (2018) (0)
- OP-JANM180472 831..834 (2019) (0)
- Kaptive 0.2 (2016) (0)
- Genomic population structures of microbial pathogens (2022) (0)
- Science meets Parliament in Canberra: 2014 (2014) (0)
- Use of Anti-O 12 Monoclonal Antibody in Tubex Test to Identify Salmonella Bacteria from Blood Culture (2013) (0)
- Linear plasmids in Klebsiella and other Enterobacteriaceae (2021) (0)
- Novel type IV CRISPR-Cas system element on plasmids carried by KPC-2-producing Klebsiella pneumoniae belonging to CG258 (2019) (0)
- Multicentre stepped-wedge cluster randomised controlled trial of an antimicrobial stewardship programme in residential aged care: protocol for the START trial (2021) (0)
- Acquisition of a large virulence plasmid (pINV) promoted temperature-dependent virulence and global dispersal of O96:H19 enteroinvasive Escherichia coli (2022) (0)
- Author response: Trajectories of childhood immune development and respiratory health relevant to asthma and allergy (2018) (0)
- Properties of genes encoding transfer RNAs as integration sites for genomic islands and prophages in Klebsiella pneumoniae (2020) (0)
- Mercury Methylation and Detoxification by Novel Microorganisms in Mercury Enriched Mesothermal Springs (2015) (0)
- Resource The Infant Nasopharyngeal Microbiome Impacts Severity of Lower Respiratory Infection and Risk of Asthma Development Graphical (2015) (0)
- Correction to: Diversity and evolution of surface polysaccharide synthesis loci in Enterobacteriales (2020) (0)
- Inferring phylodynamic parameters in bacterial genomic data using Bayesian and hybrid phylogenetic methods (2017) (0)
- Precision Medicine: Dawn of Supercomputing in ‘omics Research (2011) (0)
- Rapid Acquisition and Transmission of Drug Resistance Amongst Beijing Lineage Mycobacterium tuberculosis in Vietnam (2022) (0)
- Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models (2023) (0)
- Shigella serotypes associated with carriage in humans establish persistent infection in zebrafish (2022) (0)
- Whole Genome Sequence Analysis of Salmonella Typhi Isolated in Thailand before and after the Introduction of a National Immuniza- (2018) (0)
- Genomic evolution of Klebsiella pneumoniae clones: the good, the bad and the ugly (2019) (0)
- Making microbial genomics work for clinical and public health microbiology (2022) (0)
- Trycycler: consensus long-read assemblies for bacterial genomes (2021) (0)
- ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting (2022) (0)
- Pathovar Serovar Typhimurium Salmonella enterica Host-Restricted Accompanying Emergence of the Definitive Type 2 Genome and Transcriptome Adaptation 2013 (2013) (0)
- Evolutionary History and Spread of Multidrug Resistant IncHI1 Plasmids in Salmonella Typhi (2011) (0)
- A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China (2023) (0)
- 1 Identification of Salmonella enterica serovar Typhi genotypes using rapid Multiplex Ligation-1 dependent Probe Amplification ( MLPA ) 2 3 (2013) (0)
- 1 Shigella sonnei genome sequencing and phylogenetic analysis indicate recent 1 global dissemination from Europe 2 (2018) (0)
- Within-patient and global evolutionary dynamics of Klebsiella pneumoniae ST17 (2022) (0)
- Evidence of microevolution of Salmonella Typhimurium during a series of egg-associated outbreaks linked to a single chicken farm (2013) (0)
- The rapid emergence of Salmonella Typhi with decreased ciprofloxacin susceptibility following an increase in ciprofloxacin prescriptions in Blantyre, Malawi (2023) (0)
- Vancomycin-Resistant Enterococci Genomic Insights to Control the Emergence of 2013 (2013) (0)
- Complete Genome Sequence of WM99c, an Antibiotic-Resistant <named-content content-type='genus-species'>Acinetobacter baumannii</named-content> Global Clone 2 (GC2) Strain Representing an Australian GC2 Lineage (2018) (0)
- Implementation Guide for Modernizing Conservatorship Monitoring Basic Strategies and Technology Enhancements (2021) (0)
- Genome-Resolved Investigation of Potential New Mercury-Methylating Marine Bacterial Phyla (2020) (0)
- hicap validation assembly set (2019) (0)
- Kleborate v2.0.0 (2020) (0)
- Supplementary text for Kleborate paper (2020) (0)
- Direct inference and control of genetic population structure from RNA sequencing data (2022) (0)
- The impact of genomics on precision public health: beyond the pandemic (2021) (0)
- SPATIAL AND TEMPORAL RELATIONSHIP OF CIRCULATING SALMONELLA TYPHI IN KATHMANDU, NEPAL (2010) (0)
- Rapid Whole Genome Sequencing of Serotype K1 Hypervirulent Klebsiella pneumoniae from an Undocumented Chinese Migrant. (2021) (0)
- Running title: Multidrug resistance plasmid in Salmonella Paratyphi A (2007) (0)
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