Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts
Mickael Orgeur Wafa Frigui Alexandre Pawlik Simon Clark Ann Williams Louis S. Ates Laurence Ma Christiane Bouchier Julian Parkhill Priscille Brodin Roland Brosch
Microbial Genomics, 2021-2-1
https://doi.org/10.1099/mgen.0.000505
Louis Ates
Ates Louis / Louis Simon Ates
ORCID: 0000-0002-2953-8010
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Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts 10.1099/mgen.0.000505
Priscille Brodin
Brodin Priscille
ORCID: 0000-0003-0991-7344
Email: priscille.brodin@inserm.fr
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Christiane Bouchier
Bouchier Christiane
ORCID: 0000-0003-3549-1543
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Genomics ofMycobacterium Tuberculosis and Mycobacterium Leprae 10.1002/9781444311433.ch5
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ESX secretion systems: mycobacterial evolution to counter host immunity 10.1038/nrmicro.2016.131
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Mycobacterium tuberculosis Controls Phagosomal Acidification by Targeting CISH-Mediated Signaling 10.1016/j.celrep.2017.08.101
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The Biology and Epidemiology of Mycobacterium canettii 10.1007/978-3-319-64371-7_2
Targeting Type VII/ESX Secretion Systems for Development of Novel Antimycobacterial Drugs 10.2174/1381612819666131118170717
Taxonomic Diversity of Pseudomonads Revealed by Computer-interpretation of Ribotyping Data 10.1016/s0723-2020(96)80026-9
Comparative genomics of the mycobacteria 10.1016/s1438-4221(00)80083-1
Single Cell Measurements of Vacuolar Rupture Caused by Intracellular Pathogens 10.3791/50116
Type VII Secretion Systems in Gram-Positive Bacteria 10.1007/82_2015_5015
Genomic characterization of Mycobacterium tuberculosis lineage 7 and a proposed name: ‘Aethiops vetus’ 10.1099/mgen.0.000063
Leprosy in red squirrels 10.1126/science.aal0145
CD4+ T Cells Recognizing PE/PPE Antigens Directly or via Cross Reactivity Are Protective against Pulmonary Mycobacterium tuberculosis Infection 10.1371/journal.ppat.1005770
pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence 10.1038/nmicrobiol.2015.19
A unique PE_PGRS protein inhibiting host cell cytosolic defenses and sustaining full virulence ofMycobacterium marinumin multiple hosts 10.1111/cmi.12606
The PE and PPE Protein Families of Mycobacterium tuberculosis 10.1002/9783527611614.ch7
Influence of ESAT-6 Secretion System 1 (RD1) of Mycobacterium tuberculosis on the Interaction between Mycobacteria and the Host Immune System 10.4049/jimmunol.174.6.3570
Multiplexed Quantitation of Intraphagocyte Mycobacterium tuberculosis Secreted Protein Effectors 10.1016/j.celrep.2018.03.125
ESAT-6–dependent cytosolic pattern recognition drives noncognate tuberculosis control in vivo 10.1172/jci84978
Cutting-edge science and the future of tuberculosis control 10.2471/blt.06.035386
ESAT-6 and the Mycobacterial ESX Secretion Systems 10.1128/9781555815783.ch13
RD5-mediated lack of PE_PGRS and PPE-MPTR export in BCG vaccine strains results in strong reduction of antigenic repertoire but little impact on protection 10.1371/journal.ppat.1007139
Unexpected genomic and phenotypic diversity of Mycobacterium africanum Lineage 5 affects drug resistance, protein secretion and immunogenicity 10.1093/gbe/evy145
New substrates and interactors of the mycobacterial Serine/Threonine protein kinase PknG identified by a tailored interactomic approach 10.1016/j.jprot.2018.09.013
Update on the virulence factors of the obligate pathogen Mycobacterium tuberculosis and related tuberculosis-causing mycobacteria 10.1016/j.meegid.2018.12.013
Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis 10.1093/gbe/evz162
Intrinsic Antibacterial Activity of Nanoparticles Made of β-Cyclodextrins Potentiates Their Effect as Drug Nanocarriers against Tuberculosis. 10.1021/acsnano.8b07902
Mycobacterial virulence: impact on immunogenicity and vaccine research 10.12688/f1000research.20572.1
TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages 10.1038/s41467-020-14508-5
Discovery of a novel dehydratase of the fatty acid synthase type II critical for ketomycolic acid biosynthesis and virulence of Mycobacterium tuberculosis 10.1038/s41598-020-58967-8
ESX/Type VII Secretion Systems—An Important Way Out for Mycobacterial Proteins 10.1128/microbiolspec.psib-0029-2019
ESX-4, un système de sécrétion mycobactérien ancestral, essentiel pour la croissance de Mycobacterium abscessus dans les phagocytes environnementaux et humains 10.1051/medsci/2018196
Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages 10.1371/journal.ppat.1008069
A systematic approach to simultaneously evaluate safety, immunogenicity, and efficacy of novel tuberculosis vaccination strategies 10.1126/sciadv.aaz1767
Live attenuated TB vaccines representing the three modern Mycobacterium tuberculosis lineages reveal that the Euro–American genetic background confers optimal vaccine potential 10.1016/j.ebiom.2020.102761
Mucosal delivery of ESX-1–expressing BCG strains provides superior immunity against tuberculosis in murine type 2 diabetes 10.1073/pnas.2003235117
Le BCG : histoire moléculaire et nouvelles perspectives 10.1016/s0761-8425(08)56032-3
Breaching the phagosome, the case of the tuberculosis agent 10.1111/cmi.13344
Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts 10.1099/mgen.0.000505
The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection 10.7554/elife.55692
IL-1R1-Dependent Signals Improve Control of Cytosolic Virulent Mycobacteria In Vivo 10.1128/mSphere.00153-21
ESX-1-Independent Horizontal Gene Transfer by Mycobacterium tuberculosis Complex Strains 10.1128/mBio.00965-21
Evolution of Mycobacterium tuberculosis : New Insights into Pathogenicity and Drug Resistance 10.1128/microbiolspec.tbtb2-0020-2016
Phthiocerol Dimycocerosates From Mycobacterium tuberculosis Increase the Membrane Activity of Bacterial Effectors and Host Receptors 10.3389/fcimb.2020.00420
Parallel in vivo experimental evolution reveals that increased stress resistance was key for the emergence of persistent tuberculosis bacilli 10.1038/s41564-021-00938-4
Julian Parkhill
Parkhill Julian
ORCID: 0000-0002-7069-5958
Dissemination of Mycobacterium abscessus via global transmission networks 10.1038/s41564-021-00963-3
Description and Nomenclature of Neisseria meningitidis Capsule Locus 10.3201/eid1904.111799
Novel Mycobacterium tuberculosis Complex Isolate from a Wild Chimpanzee 10.3201/eid1906.121012
Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology 10.1001/jamainternmed.2013.7734
A Study on the Geophylogeny of Clinical and Environmental Vibrio cholerae in Kenya 10.1371/journal.pone.0074829
Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts 10.1126/science.1240578
Dominant Role of Nucleotide Substitution in the Diversification of Serotype 3 Pneumococci over Decades and during a Single Infection 10.1371/journal.pgen.1003868
Fighting Obesity with Bacteria 10.1126/science.1243787
Genome and Transcriptome Adaptation Accompanying Emergence of the Definitive Type 2 Host-Restricted Salmonella enterica Serovar Typhimurium Pathovar 10.1128/mBio.00565-13
Survey of Culture, GoldenGate Assay, Universal Biosensor Assay, and 16S rRNA Gene Sequencing as Alternative Methods of Bacterial Pathogen Detection 10.1128/JCM.01342-13
The Distribution and 'In Vivo' Phase Variation Status of Haemoglobin Receptors in Invasive Meningococcal Serogroup B Disease: Genotypic and Phenotypic Analysis 10.1371/journal.pone.0076932
Elucidating Emergence and Transmission of Multidrug-Resistant Tuberculosis in Treatment Experienced Patients by Whole Genome Sequencing 10.1371/journal.pone.0083012
Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA 10.1038/nprot.2013.147
Genomic Epidemiology of Vibrio cholerae O1 Associated with Floods, Pakistan, 2010 10.3201/eid2001.130428
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans 10.1038/ng.2744
Patent Human Infections with the Whipworm, Trichuris trichiura, Are Not Associated with Alterations in the Faecal Microbiota 10.1371/journal.pone.0076573
Tracking the establishment of local endemic populations of an emergent enteric pathogen 10.1073/pnas.1308632110
Transcriptional Regulation of Culex pipiens Mosquitoes by Wolbachia Influences Cytoplasmic Incompatibility 10.1371/journal.ppat.1003647
What has high-throughput sequencing ever done for us? 10.1038/nrmicro3112
A comparison of dense transposon insertion libraries in the Salmonella serovars Typhi and Typhimurium 10.1093/nar/gkt148
A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic 10.1101/gr.147710.112
A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak 10.1136/bmjopen-2012-002175
A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus 10.1038/ismej.2012.90
A Staphylococcus xylosus Isolate with a New mecC Allotype 10.1128/AAC.01882-12
BamView: visualizing and interpretation of next-generation sequencing read alignments 10.1093/bib/bbr073
Comprehensive Assignment of Roles for Salmonella Typhimurium Genes in Intestinal Colonization of Food-Producing Animals 10.1371/journal.pgen.1003456
Consequences of whiB7 (Rv3197A) Mutations in Beijing Genotype Isolates of the Mycobacterium tuberculosis Complex 10.1128/AAC.00626-13
Emergence and global spread of epidemic healthcare-associated Clostridium difficile 10.1038/ng.2478
Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974 10.1186/1471-2164-14-500
Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007 10.1371/journal.pone.0065333
Gene Content and Diversity of the Loci Encoding Biosynthesis of Capsular Polysaccharides of the 15 Serovar Reference Strains of Haemophilus parasuis 10.1128/JB.00471-13
Genome-wide association study identifies vitamin B-5 biosynthesis as a host specificity factor in Campylobacter 10.1073/pnas.1305559110
Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis 10.1038/ng.2517
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 10.1128/JCM.02238-12
Incidence and Characterisation of Methicillin-Resistant Staphylococcus aureus (MRSA) from Nasal Colonisation in Participants Attending a Cattle Veterinary Conference in the UK 10.1371/journal.pone.0068463
Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data 10.1186/1471-2334-13-110
Pneumococcal Capsular Switching: A Historical Perspective 10.1093/infdis/jis703
Population genomics of post-vaccine changes in pneumococcal epidemiology 10.1038/ng.2625
Progressive genome-wide introgression in agricultural Campylobacter coli 10.1111/mec.12162
Public Health Value of Next-Generation DNA Sequencing of Enterohemorrhagic Escherichia coli Isolates from an Outbreak 10.1128/JCM.01696-12
Rapid Whole-Genome Sequencing for Investigation of a Suspected Tuberculosis Outbreak 10.1128/JCM.02279-12
Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks 10.1038/nbt.2616
Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing 10.1128/JCM.00066-13
Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions 10.1038/ng.2536
Unusual features in organisation of capsular polysaccharide-related genes of C-jejuni strain X 10.1016/j.gene.2013.03.087
Use of Vitek 2 Antimicrobial Susceptibility Profile To Identify mecC in Methicillin-Resistant Staphylococcus aureus 10.1128/JCM.00847-13
Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC 10.1002/emmm.201202413
Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture 10.1101/gr.150037.112
Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study 10.1016/S1473-3099(12)70268-2
Whole-Genome Sequencing for Rapid Susceptibility Testing of M-tuberculosis 10.1056/NEJMc1215305
Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study 10.1016/S1473-3099(12)70277-3
Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study 10.1016/S0140-6736(13)60632-7
A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria 10.1099/mic.0.056077-0
A High-Resolution View of Genome-Wide Pneumococcal Transformation 10.1371/journal.ppat.1002745
Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data 10.1093/bioinformatics/btr703
Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity 10.1186/1471-2164-13-454
Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens 10.1186/1471-2164-13-545
Fibrinogen-binding and platelet-aggregation activities of a Lactobacillus salivarius septicaemia isolate are mediated by a novel fibrinogen-binding protein 10.1111/j.1365-2958.2012.08148.x
GeneDB-an annotation database for pathogens 10.1093/nar/gkr1032
Genetic Characterisation of Malawian Pneumococci Prior to the Roll-Out of the PCV13 Vaccine Using a High-Throughput Whole Genome Sequencing Approach 10.1371/journal.pone.0044250
High-Resolution Single Nucleotide Polymorphism Analysis Distinguishes Recrudescence and Reinfection in Recurrent Invasive Nontyphoidal Salmonella Typhimurium Disease 10.1093/cid/cir1032
Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa 10.1038/ng.2423
Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants 10.1186/1471-2180-12-273
Lineage-specific Virulence Determinants of Haemophilus influenzae Biogroup aegyptius 10.3201/eid1803.110728
Microevolution of extensively drug-resistant tuberculosis in Russia 10.1101/gr.128678.111
Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus 10.1073/pnas.1202869109
Phenotypic and Genomic Analysis of Hypervirulent Human-associated Bordetella bronchiseptica 10.1186/1471-2180-12-167
Resolution of a Meningococcal Disease Outbreak from Whole-Genome Sequence Data with Rapid Web-Based Analysis Methods 10.1128/JCM.01312-12
Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology 10.1371/journal.ppat.1002824
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe 10.1038/ng.2369
SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences 10.1093/bioinformatics/bts544
Structure, Diversity, and Mobility of the Salmonella Pathogenicity Island 7 Family of Integrative and Conjugative Elements within Enterobacteriaceae 10.1128/JB.06403-11
Targeted Restoration of the Intestinal Microbiota with a Simple, Defined Bacteriotherapy Resolves Relapsing Clostridium difficile Disease in Mice 10.1371/journal.ppat.1002995
The Genome of Mycobacterium Africanum West African 2 Reveals a Lineage-Specific Locus and Genome Erosion Common to the M. tuberculosis Complex 10.1371/journal.pntd.0001552
The newly described mecA homologue, mecA LGA251, is present in methicillin-resistant Staphylococcus aureus isolates from a diverse range of host species 10.1093/jac/dks329
The Transcription Factor T-bet Regulates Intestinal Inflammation Mediated by Interleukin-7 Receptor + Innate Lymphoid Cells 10.1016/j.immuni.2012.09.008
Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing 10.1038/ng.2214
A Very Early-Branching Staphylococcus aureus Lineage Lacking the Carotenoid Pigment Staphyloxanthin 10.1093/gbe/evr078
Citrobacter rodentium is an Unstable Pathogen Showing Evidence of Significant Genomic Flux 10.1371/journal.ppat.1002018
Dominant and diet-responsive groups of bacteria within the human colonic microbiota 10.1038/ismej.2010.118
Emergence of a Globally Dominant IncHI1 Plasmid Type Associated with Multiple Drug Resistant Typhoid 10.1371/journal.pntd.0001245
Evidence for several waves of global transmission in the seventh cholera pandemic 10.1038/nature10392
Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors 10.1111/j.1574-6968.2011.02339.x
Genome Sequence of the Zoonotic Pathogen Chlamydophila psittaci 10.1128/JB.01435-10
High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease 10.1186/1471-2180-11-7
Identification, variation and transcription of pneumococcal repeat sequences 10.1186/1471-2164-12-120
Ileal Pouch Microbial Diversity Reply 10.1097/SLA.0b013e318230669c
Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study 10.1016/S1473-3099(11)70126-8
Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities 10.1038/ismej.2010.175
Rapid Pneumococcal Evolution in Response to Clinical Interventions 10.1126/science.1198545
Salmonella bongori Provides Insights into the Evolution of the Salmonellae 10.1371/journal.ppat.1002191
Sequence-Based Analysis Uncovers an Abundance of Non-Coding RNA in the Total Transcriptome of Mycobacterium tuberculosis 10.1371/journal.ppat.1002342
The Impact of Recombination on dN/dS within Recently Emerged Bacterial Clones 10.1371/journal.ppat.1002129
A Commensal Gone Bad: Complete Genome Sequence of the Prototypical Enterotoxigenic Escherichia coli Strain H10407 10.1128/JB.00710-10
A human gut microbial gene catalogue established by metagenomic sequencing 10.1038/nature08821
Evolution and transmission of drug-resistant tuberculosis in a Russian population 10.1038/ng.2878
Microevolution of Burkholderia pseudomallei during an Acute Infection 10.1128/JCM.01219-14
Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses 10.1016/j.jcf.2014.10.004
Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy 10.1128/JCM.02574-14
Staphylococcus aureus Adapts to Oxidative Stress by Producing H 2 O 2 -Resistant Small-Colony Variants via the SOS Response 10.1128/IAI.03016-14
Mycobacterium abscessus Complex Identification with Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry 10.1128/JCM.00494-15
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events 10.1038/ng.3281
Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri 10.1128/genomeA.00393-15
Complete Genome Sequence of Bordetella pertussis D420 10.1128/genomeA.00657-15
Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66 10.1128/genomeA.00697-15
Erratum for Boinett et al., Complete Genome Sequence of Bordetella pertussis D420 10.1128/genomeA.00842-15
Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome 10.1128/IAI.00814-15
Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates withmecCAre Susceptible to a Combination of Penicillin and Clavulanic Acid 10.1128/AAC.01469-15
Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae 10.1038/sdata.2015.58
Genomic perspectives on the evolution and spread of bacterial pathogens 10.1098/rspb.2015.0488
Genome-based characterization of hospital-adapted Enterococcus faecalis lineages 10.1038/nmicrobiol.2015.33
Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines 10.1128/JCM.00432-16
Wild-Type and Non-Wild-Type Mycobacterium tuberculosis MIC Distributions for the Novel Fluoroquinolone Antofloxacin Compared with Those for Ofloxacin, Levofloxacin, and Moxifloxacin 10.1128/AAC.00393-16
Genomic Analysis and Comparison of Two Gonorrhea Outbreaks 10.1128/mBio.00525-16
Complete Genome Sequence of Neisseria weaveri Strain NCTC13585 10.1128/genomeA.00815-16
Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales 10.1128/AEM.01660-16
Complete Genome Sequence of Plesiomonas shigelloides Type Strain NCTC10360 10.1128/genomeA.01031-16
The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland 10.1038/nmicrobiol.2016.173
Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule 10.1128/mBio.01053-16
Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study 10.1371/journal.pmed.1002137
Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706 10.1128/genomeA.01219-16
Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania 10.1128/genomeA.01345-16
Evolution and Epidemiology of Multidrug-Resistant Klebsiella pneumoniae in the United Kingdom and Ireland 10.1128/mBio.01976-16
Within-Host Sampling of a Natural Population Shows Signs of Selection on Pde1 during Bacterial Meningitis 10.1128/IAI.01061-16
ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads 10.1101/118000
Methicillin resistant Staphylococcus aureus emerged long before the introduction of methicillin in to clinical practice 10.1101/122408
Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila 10.1371/journal.pgen.1006855
Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131 10.1101/gr.216606.116
Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England 10.1038/s41598-017-07662-2
Community outbreaks of group A Streptococcus revealed by genome sequencing 10.1038/s41598-017-08914-x
The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare 10.1016/j.jid.2017.09.023
A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children 10.1371/journal.pntd.0005975
Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community 10.1126/scitranslmed.aak9745
What is resistance? Impact of phenotypic versus molecular drug resistance testing on multi- and extensively drug-resistant tuberculosis therapy 10.1128/AAC.01550-17
Genome-based analysis of Enterococcus faecium bacteremia associated with recurrent and mixed strain infection 10.1128/JCM.01520-17
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study 10.12688/wellcomeopenres.14265.1
Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC): Supporting the transition from strategy to action 10.12688/wellcomeopenres.14586.1
Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study 10.12688/wellcomeopenres.14265.2
Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC): Supporting the transition from strategy to action 10.12688/wellcomeopenres.14586.2
Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157 10.1128/mBio.00705-18
The widespread use of topical antimicrobials enriches for resistance in Staphylococcus aureus isolated from patients with atopic dermatitis 10.1111/bjd.16722
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The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential 10.1128/MRA.00778-19
Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks 10.1128/JCM.00858-19
Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex 10.1038/s41467-019-11948-6
A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis 10.1038/s41557-019-0309-7
Genomic characterization of novel Neisseria species 10.1038/s41598-019-50203-2
Complete Genome Sequence of Pseudomonas aeruginosa Reference Strain PAK 10.1128/MRA.00865-19
Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae 10.1038/s41598-019-51102-2
Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones 10.1101/814731
Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure 10.1128/mBio.01755-19
Whole-Genome Sequences of Five Strains of Kocuria rosea, NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511 10.1128/MRA.00256-19
Engineering bacteriocin‐mediated resistance against the plant pathogen Pseudomonas syringae 10.1111/pbi.13294
Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones 10.1099/mgen.0.000352
Defining metrics for whole-genome sequence analysis of MRSA in clinical practice 10.1099/mgen.0.000354
Kill and cure: genomic phylogeny and bioactivity of a diverse collection of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles 10.1101/2020.04.09.033878
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence 10.1101/2020.05.26.116038
Increasing incidence of group B streptococcus neonatal infections in the Netherlands is associated with clonal expansion of CC17 and CC23 10.1038/s41598-020-66214-3
A decade of advances in transposon-insertion sequencing 10.1038/s41576-020-0244-x
A Novel Inducible Prophage from Burkholderia vietnamiensis G4 Is Widely Distributed across the Species and Has Lytic Activity against Pathogenic Burkholderia 10.3390/v12060601
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv 10.1101/2020.06.22.164186
SpeS: A Novel Superantigen and Its Potential as a Vaccine Adjuvant against Strangles 10.3390/ijms21124467
Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions 10.1128/mBio.01344-20
Genomic Profiling Reveals Distinct Routes To Complement Resistance in Klebsiella pneumoniae 10.1128/IAI.00043-20
Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial Ecosystem 10.1128/mSystems.00645-20
Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae 10.1073/pnas.2003407117
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Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project 10.12688/wellcomeopenres.16291.1
Genomic Assemblies of Members of Burkholderia and Related Genera as a Resource for Natural Product Discovery 10.1128/MRA.00485-20
Screening for highly transduced genes in Staphylococcus aureus reveals both lateral and specialized transduction 10.1101/2020.10.28.360172
Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella 10.1101/2020.10.30.362657
A global data-driven census of Salmonella small proteins and their potential functions in bacterial virulence 10.1093/femsml/uqaa002
Fundamental differences in physiology of Bordetella pertussis dependent on the two-component system Bvg revealed by gene essentiality studies 10.1099/mgen.0.000496
Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles 10.1099/mgen.0.000515
Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts 10.1099/mgen.0.000505
Genomic fitness profiling of Acinetobacter baumannii reveals modes of action for common biocides and mechanisms of biocide-antibiotic antagonism 10.21203/rs.3.rs-157820/v1
Genome Sequencing of a Historic Staphylococcus aureus Collection Reveals New Enterotoxin Genes and Sheds Light on the Evolution and Genomic Organization of This Key Virulence Gene Family 10.1128/JB.00587-20
The gut microbiome of 7-37 month old children from The Gambia shows the development of a distinct non-industrial Prevotella-based trophic network 10.21203/rs.3.rs-220931/v1
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DksA is a central regulatory switch for stress protection and virulence in Acinetobacter baumannii 10.21203/rs.3.rs-449513/v1
Genomic and temporal analyses of Mycobacterium bovis in southern Brazil 10.1099/mgen.0.000569
Bacterial genotypic and patient risk factors for adverse outcomes in Escherichia coli bloodstream infections: a prospective molecular-epidemiological study 10.1101/2021.06.18.21258557
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv 10.1099/mgen.0.000437
Identification of Tse8 as a Type VI secretion system toxin from Pseudomonas aeruginosa that targets the bacterial transamidosome to inhibit protein synthesis in prey cells 10.1038/s41564-021-00950-8
Summary of the Sussex-Huawei locomotion-transportation recognition challenge
Observation of a manifold in the chaotic phase space of an asymmetric optical microcavity
Localized temporal variation of Earth's inner-core boundary from high-quality waveform doublets
Off-axis multi-wavelength dispersion controlling metalens for multi-color imaging
Impact of United States political sanctions on international collaborations and research in Iran