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List of works by Julian Parkhill

'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs

scientific article published in 2019

'Going wrong with confidence': misleading sequence analyses of CiaB and ClpX

scientific article published on 01 October 1999

16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice

scientific article published on 22 June 2015

A Staphylococcus xylosus isolate with a new mecC allotype

scientific article published on 28 December 2012

A bad combination

scientific article published on 01 July 2003

A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination?

scientific article published on 7 November 2006

A commensal gone bad: complete genome sequence of the prototypical enterotoxigenic Escherichia coli strain H10407.

scientific article published on 27 August 2010

A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria

scientific article

A comprehensive survey of single nucleotide polymorphisms (SNPs) across Mycobacterium bovis strains and M. bovis BCG vaccine strains refines the genealogy and defines a minimal set of SNPs that separate virulent M. bovis strains and M. bovis BCG str

scientific article

A decade of advances in transposon-insertion sequencing

scientific article published on 12 June 2020

A decade of genomic history for healthcare-associated Enterococcus faecium in the United Kingdom and Ireland

scientific article published on 15 August 2016

A dual transacylation mechanism for polyketide synthase chain release in enacyloxin antibiotic biosynthesis

scientific article published on 23 September 2019

A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes

scientific article published on 18 December 2014

A genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria.

scientific article

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

scientific article

A global genomic approach uncovers novel components for twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa

scientific article published in November 2018

A high-resolution view of genome-wide pneumococcal transformation

scientific article

A human gut microbial gene catalogue established by metagenomic sequencing

scientific article

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children

scientific article published on 2 October 2017

A matter of fitness

scientific article published in March 2003

A non-endoscopic device to sample the oesophageal microbiota: a case-control study

scientific article published on 12 November 2016

A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages

scientific article published on 23 September 2019

A novel hybrid SCCmec-mecC region in Staphylococcus sciuri

scientific article published on 02 December 2013

A novel linear plasmid mediates flagellar variation in Salmonella Typhi

scientific article

A novel streptococcal integrative conjugative element involved in iron acquisition.

scientific article published on December 2008

A pilot study of rapid whole-genome sequencing for the investigation of a Legionella outbreak

scientific article (publication date: 9 January 2013)

A shared population of epidemic methicillin-resistant Staphylococcus aureus 15 circulates in humans and companion animals.

scientific article

A simple method for directional transcriptome sequencing using Illumina technology

scientific article

A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus

scientific article

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi

scientific article

A study on the geophylogeny of clinical and environmental Vibrio cholerae in Kenya.

scientific article

A very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin

scientific article

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

scientific article

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads

Accelerated telomere shortening in ataxia telangiectasia

article published in 1996

Acquisition and loss of virulence-associated factors during genome evolution and speciation in three clades of Bordetella species

scientific article

Agricultural intensification and the evolution of host specialism in the enteric pathogen Campylobacter jejuni

scientific article published on 04 May 2020

All walks of life

scientific article published on 01 April 2003

An unusual Burkholderia gladioli double chain-initiating nonribosomal peptide synthetase assembles ‘fungal’ icosalide antibiotics

scientific article published on 25 April 2019

Analysis of Campylobacter jejuni capsular loci reveals multiple mechanisms for the generation of structural diversity and the ability to form complex heptoses

scientific article published on January 2005

Ankyrin repeat domain-encoding genes in the wPip strain of Wolbachia from the Culex pipiens group

scientific article

Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts

scientific article published on 29 June 2009

Antimicrobial exposure in sexual networks drives divergent evolution in modern gonococci

Are commercial providers a viable option for clinical bacterial sequencing?

scientific article published on 5 April 2018

Arginine-deprivation-induced oxidative damage sterilizes

scientific article

Armed to the teeth

scientific article published on 01 April 2002

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

scientific article

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

scientific article

Artemis: sequence visualization and annotation

scientific article (publication date: October 2000)

Assessment of the influence of intrinsic environmental and geographical factors on the bacterial ecology of pit latrines.

scientific article published on 15 February 2016

Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

scientific article published on 27 May 2019

Author Correction: Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

scientific article published on 1 August 2019

Author Correction: Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis.

scientific article published on 19 April 2018

Bacillary dysentery from World War 1 and NCTC1, the first bacterial isolate in the National Collection

scientific article published on 7 November 2014

Bacterial epidemiology and biology - lessons from genome sequencing

scientific article

Bacterial minimalism

scientific article published in 2004

BamView: viewing mapped read alignment data in the context of the reference sequence

scientific article

BamView: visualizing and interpretation of next-generation sequencing read alignments

scientific article (publication date: March 2013)

Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

scientific article published on 15 December 2015

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

scientific article

Candidatus Ornithobacterium hominis sp. nov.: insights gained from draft genomes obtained from nasopharyngeal swabs

scientific article published on 18 May 2018

Capturing the cloud of diversity reveals complexity and heterogeneity of MRSA carriage, infection and transmission

scientific article

Characterisation and distribution of a cryptic Salmonella typhi plasmid pHCM2.

scientific article published on May 2002

Chemokine (C-C Motif) Receptor 2 Mediates Dendritic Cell Recruitment to the Human Colon but Is Not Responsible for Differences Observed in Dendritic Cell Subsets, Phenotype, and Function Between the Proximal and Distal Colon

scientific article

Chlamydia trachomatis: genome sequence analysis of lymphogranuloma venereum isolates

scientific article

Circlator: automated circularization of genome assemblies using long sequencing reads

scientific article

Citrobacter rodentium is an unstable pathogen showing evidence of significant genomic flux

scientific article published in April 2011

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

scientific article published in 2019

Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis

scientific article published on 10 June 2015

Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

scientific article

Cobalamin synthesis in Yersinia enterocolitica 8081. Functional aspects of a putative metabolic island

scientific article published on January 2003

Comment on: characterization of the embB gene in Mycobacterium tuberculosis isolates from Barcelona and rapid detection of main mutations related to ethambutol resistance using a low-density DNA array

scientific article published on 20 April 2014

Community outbreaks of group A Streptococcus revealed by genome sequencing.

scientific article

Comparative Apicomplexan genomics

scientific article published in 2005

Comparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome

scientific article published on 10 August 2015

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica

scientific article

Comparative cell wall core biosynthesis in the mycolated pathogens, Mycobacterium tuberculosis and Corynebacterium diphtheriae

scientific article published on May 2004

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

scientific article

Comparative genome analysis of Wolbachia strain wAu.

scientific article

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium

scientific article

Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome

scientific article

Comparative genomic structure of prokaryotes

scientific article

Comparative genomics and proteomics of Helicobacter mustelae, an ulcerogenic and carcinogenic gastric pathogen.

scientific article

Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity

scientific article

Comparative genomics of Mycobacterium africanum Lineage 5 and Lineage 6 from Ghana suggests distinct ecological niches

scientific article published in Scientific Reports

Comparative genomics of prevaccination and modern Bordetella pertussis strains

scientific article

Comparative genomics of the classical Bordetella subspecies: the evolution and exchange of virulence-associated diversity amongst closely related pathogens

scientific article

Comparative genomics of the emerging human pathogen Photorhabdus asymbiotica with the insect pathogen Photorhabdus luminescens

scientific article

Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology

scientific article

Comparison of the genome sequence of the poultry pathogen Bordetella avium with those of B. bronchiseptica, B. pertussis, and B. parapertussis reveals extensive diversity in surface structures associated with host interaction

scientific article published on August 2006

Complete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts

article

Complete DNA sequence of a serogroup A strain of Neisseria meningitidis Z2491

scientific article

Complete Genome Sequence of Bordetella pertussis D420.

scientific article published on 11 June 2015

Complete Genome Sequence of Neisseria weaveri Strain NCTC13585.

scientific article

Complete Genome Sequence of Plesiomonas shigelloides Type Strain NCTC10360.

scientific article published on 22 September 2016

Complete Genome Sequence of Pseudomonas aeruginosa Reference Strain PAK

scientific article published on 10 October 2019

Complete Whole-Genome Sequence of Haemophilus haemolyticus NCTC 10839

scientific article published on 20 June 2019

Complete Whole-Genome Sequence of Salmonella enterica subsp. enterica Serovar Java NCTC5706.

scientific article

Complete Whole-Genome Sequences of Two Raoultella terrigena Strains, NCTC 13097 and NCTC 13098, Isolated from Human Cases

scientific article published on 03 July 2019

Complete assembly of Escherichia coli ST131 genomes using long reads demonstrates antibiotic resistance gene variation within diverse plasmid and chromosomal contexts

article

Complete genome of acute rheumatic fever-associated serotype M5 Streptococcus pyogenes strain manfredo.

scientific article published on 29 September 2006

Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69.

scientific article published on 24 October 2008

Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042

scientific article published on 20 January 2010

Complete genome sequence and lytic phase transcription profile of a Coccolithovirus

scientific article

Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18

scientific article

Complete genome sequence of the plant pathogen Erwinia amylovora strain ATCC 49946.

scientific article published on 29 January 2010

Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility

scientific article published on 28 March 2008

Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance

scientific article

Complete nucleotide sequence of the conjugative tetracycline resistance plasmid pFBAOT6, a member of a group of IncU plasmids with global ubiquity

scientific article published on December 2004

Complete sequence and organization of pBtoxis, the toxin-coding plasmid of Bacillus thuringiensis subsp. israelensis

scientific article published on October 2002

Complex Routes of Nosocomial Vancomycin-Resistant Enterococcus faecium Transmission Revealed by Genome Sequencing

scientific article

Composition, acquisition, and distribution of the Vi exopolysaccharide-encoding Salmonella enterica pathogenicity island SPI-7.

scientific article

Comprehensive assignment of roles for Salmonella typhimurium genes in intestinal colonization of food-producing animals

scientific article

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

scientific article

Comprehensive identification of single nucleotide polymorphisms associated with beta-lactam resistance within pneumococcal mosaic genes

scientific article

Consequences of whiB7 ( Rv3197A ) Mutations in Beijing Genotype Isolates of the Mycobacterium tuberculosis Complex ⬇️

scientific article published on July 1, 2013

Convergent evolution and topologically disruptive polymorphisms among multidrug-resistant tuberculosis in Peru.

scientific article

Correction for Waterfield et al., Rapid Virulence Annotation (RVA): Identification of virulence factors using a bacterial genome library and multiple invertebrate hosts

scholarly article

Correction: Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila

scientific article published in December 2017

Correction: Signatures of Adaptation in Human Invasive Salmonella Typhimurium ST313 Populations from Sub-Saharan Africa

scientific article published on 15 June 2015

Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

scientific article published on September 2017

Corrigendum: Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

scientific article published on 28 January 2015

Cryptic ecology among host generalist Campylobacter jejuni in domestic animals

scientific article

DNAPlotter: circular and linear interactive genome visualization

scientific article

Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence

scientific article

Defining the estimated core genome of bacterial populations using a Bayesian decision model

scientific article

Definition of a major p53 binding site on Ad2E1B58K protein and a possible nuclear localization signal on the Ad12E1B54K protein

scientific article published on January 1999

Dense genomic sampling identifies highways of pneumococcal recombination

scientific article published on 09 February 2014

Description and nomenclature of Neisseria meningitidis capsule locus

scientific article published on April 2013

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

scientific article published on 3 June 2009

Detecting eukaryotic microbiota with single-cell sensitivity in human tissue

scientific article published in 2018

Detection of vancomycin-resistant hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

article

Development of a Multiplex PCR Assay for Rapid Molecular Serotyping of Haemophilus parasuis

scientific article

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

scientific article

Discovery and Biosynthesis of Gladiolin: A Burkholderia gladioli Antibiotic with Promising Activity against Mycobacterium tuberculosis ⬇️

scientific article published on 22 May 2017

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

scientific article published on 22 August 2016

Distinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts

scientific article

Distribution of tetracycline and erythromycin resistance genes among human oral and fecal metagenomic DNA.

scientific article published in September 2009

Diversification of Colonization Factors in a Multidrug-Resistant Escherichia coli Lineage Evolving under Negative Frequency-Dependent Selection

scientific article published on 23 April 2019

Diversity at every level

scientific article published on 01 March 2005

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

scientific article

Dominant role of nucleotide substitution in the diversification of serotype 3 pneumococci over decades and during a single infection

scientific article (publication date: 2013)

Draft Genome Sequence of 24570, the Type Strain of Shigella flexneri

scientific article published on 28 May 2015

Draft Genome Sequence of a Multiresistant Bovine Isolate of Staphylococcus lentus from Tanzania

scientific article published on December 2016

Draft Genome Sequence of the Streptococcus pneumoniae Avery Strain A66.

scientific article published on 25 June 2015

Draft genome sequence of a multidrug-resistant caprine isolate of Staphylococcus cohnii subsp. urealyticus from Tanzania encoding ermB, tet(K), dfrG, fusF and fosD

scientific article published on 16 July 2019

Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila

scientific article

Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

scientific article published on 28 July 2015

Elucidating emergence and transmission of multidrug-resistant tuberculosis in treatment experienced patients by whole genome sequencing

scientific article (publication date: 2013)

Emergence and genomic diversification of a virulent serogroup W:ST-2881(CC175) Neisseria meningitidis clone in the African meningitis belt

scientific article published on 21 June 2017

Emergence and global spread of epidemic healthcare-associated Clostridium difficile

scientific article published on 9 December 2012

Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium

scientific article published in November 2016

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

scientific article published in July 2011

Emergence of a new epidemic Neisseria meningitidis serogroup A Clone in the African meningitis belt: high-resolution picture of genomic changes that mediate immune evasion.

scientific article

Emergence of host-adapted Salmonella Enteritidis through rapid evolution in an immunocompromised host

scientific article published on 25 January 2016

Emergence of methicillin resistance predates the clinical use of antibiotics

scientific article published on 05 January 2022

Emergence of the Asian 1 genotype of dengue virus serotype 2 in viet nam: in vivo fitness advantage and lineage replacement in South-East Asia

scientific article

Emergent and evolving antimicrobial resistance cassettes in community-associated fusidic acid and meticillin-resistant Staphylococcus aureus.

scientific article published on 19 February 2015

Engineering bacteriocin-mediated resistance against the plant pathogen Pseudomonas syringae

scientific article published on 03 December 2019

Enterotypes of the human gut microbiome

scientific article

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

scientific article published on 9 November 2009

Erratum for Boinett et al., Complete Genome Sequence of Bordetella pertussis D420.

scientific article published on 16 July 2015

Erratum for Kulohoma et al., Comparative genomic analysis of meningitis- and bacteremia-causing pneumococci identifies a common core genome

scientific article published in December 2015

Erratum: Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

scientific article published in March 2017

Erratum: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

scientific article published on 12 May 2015

Erratum: Global phylogeography and evolutionary history of Shigella dysenteriae type 1

article

Essential roles of methionine and S-adenosylmethionine in the autarkic lifestyle of Mycobacterium tuberculosis

scientific article

Eukaryotes: not beyond compare

scientific article published in 2004

Evaluation of PacBio sequencing for full-length bacterial 16S rRNA gene classification

scientific article

Evaluation of an Optimal Epidemiological Typing Scheme for Legionella pneumophila with Whole-Genome Sequence Data Using Validation Guidelines

scientific article

Evaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.

scientific article

Evidence for Host-Bacterial Co-evolution via Genome Sequence Analysis of 480 Thai Mycobacterium tuberculosis Lineage 1 Isolates

scientific article published in Scientific Reports

Evidence for niche adaptation in the genome of the bovine pathogen Streptococcus uberis

scientific article

Evidence for several waves of global transmission in the seventh cholera pandemic

scientific article

Evidence for soft selective sweeps in the evolution of pneumococcal multidrug resistance and vaccine escape

scientific article

Evidence of antimicrobial resistance-conferring genetic elements among pneumococci isolated prior to 1974

scientific article

Evolution and Epidemiology of Multidrug-Resistant Klebsiella pneumoniae in the United Kingdom and Ireland

scientific article published on 21 February 2017

Evolution and Global Transmission of a Multidrug-Resistant, Community-Associated Methicillin-Resistant Staphylococcus aureus Lineage from the Indian Subcontinent

scientific article published on 26 November 2019

Evolution and transmission of drug-resistant tuberculosis in a Russian population

scientific article published on 26 January 2014

Evolution of mobile genetic element composition in an epidemic methicillin-resistant Staphylococcus aureus: temporal changes correlated with frequent loss and gain events

scientific article published on 4 September 2017

Evolution of the Rhodococcus equi vap pathogenicity island seen through comparison of host-associated vapA and vapB virulence plasmids

scientific article

Evolution of the Staphylococcus argenteus ST2250 Clone in Northeastern Thailand Is Linked with the Acquisition of Livestock-Associated Staphylococcal Genes

scientific article

Evolutionary diversification of an ancient gene family (rhs) through C-terminal displacement

scientific article

Evolutionary dynamics of Clostridium difficile over short and long time scales

scientific article published on 20 April 2010

Evolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.

scientific article

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

scientific article

Expression of cellulosome components and type IV pili within the extracellular proteome of Ruminococcus flavefaciens 007.

scientific article

Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia

scientific article published on 04 May 2020

Fibrinogen-binding and platelet-aggregation activities of aLactobacillus salivariussepticaemia isolate are mediated by a novel fibrinogen-binding protein

article

Fighting Obesity with Bacteria

scientific article published in Science

Fitting the niche by genomic adaptation

scientific article published in November 2003

Fluorescence-Based Flow Sorting in Parallel with Transposon Insertion Site Sequencing Identifies Multidrug Efflux Systems in Acinetobacter baumannii

scientific article

Gene content and diversity of the loci encoding biosynthesis of capsular polysaccharides of the 15 serovar reference strains of Haemophilus parasuis

scientific article published on 19 July 2013

Gene exchange drives the ecological success of a multi-host bacterial pathogen

article

GeneDB--an annotation database for pathogens

scientific article

GeneDB: a resource for prokaryotic and eukaryotic organisms

scientific article published on January 2004

Generating whole bacterial genome sequences of low-abundance species from complex samples with IMS-MDA.

scientific article

Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes

scientific article

Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach

scientific article published on 10 September 2012

Genetic flux over time in the Salmonella lineage

scientific article (publication date: 2007)

Genetic variation associated with infection and the environment in the accidental pathogen Burkholderia pseudomallei

scientific article published on 22 November 2019

Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae

Genetic variation regulates the activation and specificity of Restriction-Modification systems in Neisseria gonorrhoeae

scientific article published on 11 October 2019

Genome analysis of an inducible prophage and prophage remnants integrated in the Streptococcus pyogenes strain SF370.

scientific article

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 evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen

scientific article published on August 2014

Genome evolution of Wolbachia strain wPip from the Culex pipiens group

scientific article published on 12 June 2008

Genome flexibility in Neisseria meningitidis

scientific article published on 27 May 2009

Genome giants

scientific article published on 01 July 2002

Genome mining identifies cepacin as a plant-protective metabolite of the biopesticidal bacterium Burkholderia ambifaria

article

Genome of the actinomycete plant pathogen Clavibacter michiganensis subsp. sepedonicus suggests recent niche adaptation

scientific article (publication date: March 2008)

Genome plasticity of BCG and impact on vaccine efficacy

scientific article

Genome sequence of Staphylococcus lugdunensis N920143 allows identification of putative colonization and virulence factors

scientific article published on 4 July 2011

Genome sequence of Yersinia pestis, the causative agent of plague

scientific article

Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes

scientific article published on 22 May 2007

Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW).

scientific article published on 30 November 2009

Genome sequence of the enterobacterial phytopathogen Erwinia carotovora subsp. atroseptica and characterization of virulence factors.

scholarly article

Genome sequence of the zoonotic pathogen Chlamydophila psittaci

scientific article published on 23 December 2010

Genome sequencing defines phylogeny and spread of methicillin-resistant Staphylococcus aureus in a high transmission setting

scientific article published on 9 December 2014

Genome specialization and decay of the strangles pathogen, Streptococcus equi, is driven by persistent infection

scientific article

Genome watch: Brothers in arms

article published in 2005

Genome-Based Infection Tracking Reveals Dynamics of Clostridium difficile Transmission and Disease Recurrence

scientific article published on 18 December 2015

Genome-based analysis of Enterococcus faecium bacteremia associated with recurrent and mixed strain infection

scientific article published on 20 December 2017

Genome-based characterization of hospital-adapted Enterococcus faecalis lineages

scientific article published on 8 February 2016

Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

scientific article

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

scientific article

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork

article published in 2016

Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter

scientific article

Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

scientific article

Genome-wide mutational biases fuel transcriptional diversity in the Mycobacterium tuberculosis complex

scientific article published on 05 September 2019

Genomes beyond compare

scientific article published on 01 August 2004

Genomic Analysis and Comparison of Two Gonorrhea Outbreaks

scientific article published on 28 June 2016

Genomic Analysis of Salmonella enterica Serovar Typhimurium from Wild Passerines in England and Wales.

scientific article

Genomic Assemblies of Members of and Related Genera as a Resource for Natural Product Discovery

scientific article published on 15 October 2020

Genomic Assemblies of Members of and Related Genera as a Resource for Natural Product Discovery

Genomic Dissection of an Icelandic Epidemic of Respiratory Disease in Horses and Associated Zoonotic Cases

scientific article

Genomic Surveillance of Enterococcus faecium Reveals Limited Sharing of Strains and Resistance Genes between Livestock and Humans in the United Kingdom

article

Genomic analysis of isolates from the United Kingdom 2012 pertussis outbreak reveals that vaccine antigen genes are unusually fast evolving

scientific article published on 8 December 2014

Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis

scientific article published on 06 January 2013

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

scientific article published on 11 May 2009

Genomic and genetic analysis of Bordetella bacteriophages encoding reverse transcriptase-mediated tropism-switching cassettes

scientific article

Genomic characterization of novel Neisseria species

scientific article published on 24 September 2019

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains

scientific article published in August 2014

Genomic epidemiology of Neisseria gonorrhoeae with reduced susceptibility to cefixime in the USA: a retrospective observational study

scientific article

Genomic epidemiology of Vibrio cholerae O1 associated with floods, Pakistan, 2010.

scientific article

Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil

scientific article published on 3 May 2017

Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study

scientific article published on 26 October 2015

Genomic evidence for the evolution of Streptococcus equi: host restriction, increased virulence, and genetic exchange with human pathogens

scientific article

Genomic history of the seventh pandemic of cholera in Africa.

scientific article published in November 2017

Genomic identification of cryptic susceptibility to penicillins and β-lactamase inhibitors in methicillin-resistant Staphylococcus aureus

scientific article published on 24 June 2019

Genomic information infrastructure after the deluge

scientific article

Genomic perspectives on the evolution and spread of bacterial pathogens

scientific article

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei

scientific article

Genomic pot pourri

scientific article published in 2004

Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis

scientific article

Genomic surveillance of Escherichia coli in municipal wastewater treatment plants as an indicator of clinically relevant pathogens and their resistance genes.

scientific article published on 20 May 2019

Genomic surveillance reveals low prevalence of livestock-associated methicillin-resistant Staphylococcus aureus in the East of England

scientific article published on 07 August 2017

Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages.

scientific article

Genomic variations leading to alterations in cell morphology of Campylobacter spp.

scientific article

Genomics of Mycobacterium bovis

scientific article

Genomics of the Argentinian cholera epidemic elucidate the contrasting dynamics of epidemic and endemic Vibrio cholerae

scientific article published on 01 October 2020

Genomics. Genome project standards in a new era of sequencing

scientific article

Global and regional dissemination and evolution of Burkholderia pseudomallei

scientific article published on 23 January 2017

Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages

scientific article published on 04 December 2014

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 evolution of Bordetella pertussis and their relationship with vaccination

scientific article published on 22 April 2014

Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network

scientific article published on 31 December 2021

Gut microbiota trajectory in early life may predict development of celiac disease

scientific article published on 20 February 2018

High-resolution single nucleotide polymorphism analysis distinguishes recrudescence and reinfection in recurrent invasive nontyphoidal Salmonella typhimurium disease

scientific article published on 7 February 2012

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 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

scientific article

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

scientific article published on 27 July 2008

Homology between a human apoptosis specific protein and the product of APG5, a gene involved in autophagy in yeast

scientific article

Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India

scientific article published on 16 July 2019

Identification and initial characterisation of a protein involved in Campylobacter jejuni cell shape

scientific article

Identification of DNA markers for a transmissible Pseudomonas aeruginosa cystic fibrosis strain

scientific article published on 15 April 2005

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

scientific article published on 19 August 2021

Identification, variation and transcription of pneumococcal repeat sequences

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Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data

scholarly article by Benjamin Sobkowiak et al published 14 August 2018 in BMC Genomics

Implications of multiple freeze-thawing on respiratory samples for culture-independent analyses

scientific article

Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions

scientific article published on 07 July 2020

In defense of complete genomes

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In-depth genetic analysis ofClostridiumdifficilePCR-ribotype 027 strains reveals high genome fluidity including point mutations and inversions ⬇️

scientific article published on March 16, 2010

Incidence and characterisation of methicillin-resistant Staphylococcus aureus (MRSA) from nasal colonisation in participants attending a cattle veterinary conference in the UK

scientific article

Increasing incidence of group B streptococcus neonatal infections in the Netherlands is associated with clonal expansion of CC17 and CC23

scientific article published on 12 June 2020

Independent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06.

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Individual-specific changes in the human gut microbiota after challenge with enterotoxigenic Escherichia coli and subsequent ciprofloxacin treatment

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Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data

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Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis

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Integrated chromosomal and plasmid sequence analyses reveal diverse modes of carbapenemase gene spread among Klebsiella pneumoniae

scientific article published on 23 September 2020

Integrated view of Vibrio cholerae in the Americas

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Integration of tools and resources for display and analysis of genomic data for protozoan parasites

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Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

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Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study

scientific article published on 27 April 2015

Interleukin 6 Increases Production of Cytokines by Colonic Innate Lymphoid Cells in Mice and Patients With Chronic Intestinal Inflammation.

scientific article

Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands

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Intra- and interhost evolutionary dynamics of equine influenza virus

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Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa

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Investigating the Campylobacter jejuni Transcriptional Response to Host Intestinal Extracts Reveals the Involvement of a Widely Conserved Iron Uptake System

article published in 2018

Investigation of a Cluster of Sequence Type 22 Methicillin-Resistant Staphylococcus aureus Transmission in a Community Setting

scientific article published on 25 October 2017

Investigations into genome diversity of Haemophilus influenzae using whole genome sequencing of clinical isolates and laboratory transformants

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Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

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Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

scientific article published on 15 May 2019

Kill and cure: genomic phylogeny and bioactivity of a diverse collection of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles

scientific article published on 11 April 2020

Kill and cure: genomic phylogeny and bioactivity of a diverse collection of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles

Kill and cure: genomic phylogeny and bioactivity of bacteria capable of pathogenic and beneficial lifestyles

scientific article published in January 2021

Large scale genomic analysis shows no evidence for pathogen adaptation between the blood and cerebrospinal fluid niches during bacterial meningitis

scientific article published on 31 January 2017

Large scale genomic analysis shows no evidence for repeated pathogen adaptation during the invasive phase of bacterial meningitis in humans

Limited contribution of non-intensive chicken farming to ESBL-producing Escherichia coli colonization in humans in Vietnam: an epidemiological and genomic analysis

scholarly article by Vinh Trung Nguyen et al published 1 March 2019 in Journal of Antimicrobial Chemotherapy

Lineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius

scientific article published in March 2012

Livelihood hazards

scientific article published in 2005

Locally Confined Clonal Complexes of Mycobacterium ulcerans in Two Buruli Ulcer Endemic Regions of Cameroon

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Longitudinal genomic surveillance of MRSA in the UK reveals transmission patterns in hospitals and the community.

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Longitudinal genomic surveillance of multidrug-resistant Escherichia coli carriage in a long-term care facility in the United Kingdom

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Lost and found

scientific article published on 01 November 2001

Massive gene decay in the leprosy bacillus

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Meningococcal genetic variation mechanisms viewed through comparative analysis of serogroup C strain FAM18.

scientific article published on 21 December 2006

Methicillin resistantStaphylococcus aureusemerged long before the introduction of methicillin in to clinical practice

Methicillin-resistant Staphylococcus aureus emerged long before the introduction of methicillin into clinical practice

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Methodology for Whole-Genome Sequencing of Methicillin-Resistant Staphylococcus aureus Isolates in a Routine Hospital Microbiology Laboratory.

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Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study

scientific article published on August 2011

Microbial genomics. Dynamic duos

scientific article published in December 2001

Microbiology in the post-genomic era.

scientific article published on 13 May 2008

Microbiota that affect risk for shigellosis in children in low-income countries

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Microevolution and history of the plague bacillus, Yersinia pestis

scientific article published on 21 December 2004

Microevolution of Burkholderia pseudomallei during an acute infection

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Microevolution of Monophasic Salmonella Typhimurium during Epidemic, United Kingdom, 2005-2010.

scientific article published on April 2016

Microevolution of extensively drug-resistant tuberculosis in Russia

scientific article published on 31 January 2012

Molecular analysis of incHI1 antimicrobial resistance plasmids from Salmonella serovar Typhi strains associated with typhoid fever

scientific article published on September 2003

Molecular epidemiology and whole genome sequencing analysis of clinical Mycobacterium bovis from Ghana

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Molecular tracing of the emergence, adaptation, and transmission of hospital-associated methicillin-resistant Staphylococcus aureus ⬇️

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Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community

scientific article (publication date: 6 May 2014)

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 serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi.

scientific article published on 23 March 2007

Multiple inverted DNA repeats of Bacteroides fragilis that control polysaccharide antigenic variation are similar to the hin region inverted repeats of Salmonella typhimurium

scientific article published in April 2003

Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently

scientific article published on 23 September 2016

Multireplicon genome architecture of Lactobacillus salivarius

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Mutations in the MAB_2299c TetR regulator confer cross-resistance to clofazimine and bedaquiline in

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Mutations in the MAB_2299c TetR regulator confer cross-resistance to clofazimine and bedaquiline in Mycobacterium abscessus

scholarly article by Matthias Richard et al published 15 October 2018 in Antimicrobial Agents and Chemotherapy

Mutations revealed by sequencing the 5' half of the gene for ataxia telangiectasia.

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Mycobacterium abscessus Complex Identification with Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

scientific article published on 6 May 2015

Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv

New Variant of Multidrug-Resistant Serovar Typhimurium Associated with Invasive Disease in Immunocompromised Patients in Vietnam

scholarly article by Alison E Mather et al published 4 September 2018 in mBio

New environments, versatile genomes

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Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa ⬇️

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Novel Mycobacterium tuberculosis complex isolate from a wild chimpanzee

scientific article published on June 2013

Novel determinants of antibiotic resistance: identification of mutated loci in highly methicillin-resistant subpopulations of methicillin-resistant Staphylococcus aureus

scientific article published on 08 April 2014

Novel mutations in penicillin-binding protein genes in clinical Staphylococcus aureus isolates that are methicillin resistant on susceptibility testing, but lack the mec gene

scientific article published on 11 November 2013

Novel staphylococcal species that form part of a Staphylococcus aureus-related complex: the non-pigmented Staphylococcus argenteus sp. nov. and the non-human primate-associated Staphylococcus schweitzeri sp. nov.

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O-antigen dependent colicin insensitivity of uropathogenic Escherichia coli

scientific article published on 28 January 2019

Of staphs, streps and other things

scientific article published on 01 July 2001

Old Drugs To Treat Resistant Bugs: Methicillin-Resistant Staphylococcus aureus Isolates with mecC Are Susceptible to a Combination of Penicillin and Clavulanic Acid.

scientific article published on 21 September 2015

One Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock

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

scientific article (publication date: October 2013)

Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic

scientific article published on 31 May 2016

Parallel independent evolution of pathogenicity within the genus Yersinia

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Partitioning core and satellite taxa from within cystic fibrosis lung bacterial communities

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Patent human infections with the whipworm, Trichuris trichiura, are not associated with alterations in the faecal microbiota

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Pathogenomics

scientific article published in December 2003

Pathogenomics of non-pathogens

scientific article published in 2004

Pathogenomics: an updated European Research Agenda.

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Pathogens in decay

scientific article published in October 2004

Patterns of genome evolution that have accompanied host adaptation in Salmonella

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Phase variation of a Type IIG restriction-modification enzyme alters site-specific methylation patterns and gene expression in Campylobacter jejuni strain NCTC11168

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Phenotypic and genomic analysis of hypervirulent human-associated Bordetella bronchiseptica

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Phylogenetic relationships of the Wolbachia of nematodes and arthropods

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Phylogenomic exploration of the relationships between strains of Mycobacterium avium subspecies paratuberculosis

scientific article published on 26 January 2016

Phylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus

scientific article published on 27 December 2012

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

Pilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks

scientific article published on 23 October 2019

Pivotal Roles for pH, Lactate, and Lactate-Utilizing Bacteria in the Stability of a Human Colonic Microbial Ecosystem

scientific article published on 08 September 2020

Pneumococcal capsular switching: a historical perspective

scientific article published on 21 November 2012

PolyTB: a genomic variation map for Mycobacterium tuberculosis

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Population genetic structuring of methicillin-resistant Staphylococcus aureus clone EMRSA-15 within UK reflects patient referral patterns

scientific article published on 4 July 2017

Population genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae

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Population genomics of post-vaccine changes in pneumococcal epidemiology.

scientific article published on 05 May 2013

Population genomics: modeling the new and a renaissance of the old

scientific article published on 14 October 2008

Population structure of multidrug resistant Klebsiella oxytoca within hospitals across the UK and Ireland identifies sharing of virulence and resistance genes with K. pneumoniae

scientific article published on 8 February 2017

Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis

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Prepublication data sharing

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Progressive genome-wide introgression in agricultural Campylobacter coli

scientific article published on 20 December 2012

Prospective genomic surveillance of methicillin-resistant (MRSA) associated with bloodstream infection, England, 1 October 2012 to 30 September 2013

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Proteomic and genomic characterization of highly infectious Clostridium difficile 630 spores

scientific article published on 19 June 2009

Proteomic and microarray characterization of the AggR regulon identifies a pheU pathogenicity island in enteroaggregative Escherichia coli

scientific article published on September 2006

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

scientific article published on 21 January 2009

Public health value of next-generation DNA sequencing of enterohemorrhagic Escherichia coli isolates from an outbreak.

scientific article published on 7 November 2012

Questioning the fetal microbiome illustrates pitfalls of low-biomass microbial studies

scientific article published in 2023

Rapid Pneumococcal Evolution in Response to Clinical Interventions ⬇️

scientific article (publication date: 28 January 2011)

Rapid Virulence Annotation (RVA): identification of virulence factors using a bacterial genome library and multiple invertebrate hosts

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Rapid bacterial whole-genome sequencing to enhance diagnostic and public health microbiology

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Rapid emergence of multidrug resistant, H58-lineage Salmonella typhi in Blantyre, Malawi.

scientific article published on 24 April 2015

Rapid evolution of virulence and drug resistance in the emerging zoonotic pathogen Streptococcus suis

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Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

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Rapid single-colony whole-genome sequencing of bacterial pathogens

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Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak

scientific article published on June 2012

Rapid whole-genome sequencing for investigation of a suspected tuberculosis outbreak

scientific article published on 21 November 2012

Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence

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Read and assembly metrics inconsequential for clinical utility of whole-genome sequencing in mapping outbreaks

scientific article published in July 2013

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

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Reagent contamination can critically impact sequence-based microbiome analyses

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Real-time genomic epidemiological evaluation of human Campylobacter isolates by use of whole-genome multilocus sequence typing

scientific article published on 22 May 2013

Recent independent emergence of multiple multidrug-resistant Serratia marcescens clones within the United Kingdom and Ireland

scientific article published on 18 July 2016

Reclassification of the Specialized Metabolite Producer Pseudomonas mesoacidophila ATCC 31433 as a Member of the Burkholderia cepacia Complex

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Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule

scientific article published on 27 September 2016

Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer

scientific article published on 8 January 2007

Replacement of adenylate cyclase toxin in a lineage of Bordetella bronchiseptica

scientific article published on 13 June 2008

Reply to Dookie et al., "Whole-Genome Sequencing To Guide the Selection of Treatment for Drug-Resistant Tuberculosis"

scientific article published on 27 July 2018

Resolving the structural features of genomic islands: a machine learning approach

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Respiratory microbiota resistance and resilience to pulmonary exacerbation and subsequent antimicrobial intervention

scientific article published on 10 November 2015

Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage

scientific article published in March 2002

Roary: rapid large-scale prokaryote pan genome analysis

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Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data

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Role of alanine racemase mutations in Mycobacterium tuberculosis D-cycloserine resistance

scientific article published on 2 October 2017

Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81

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Routine use of microbial whole genome sequencing in diagnostic and public health microbiology

scientific article (publication date: 2012)

SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2).

scientific article published in March 2004

Salmonella bongori provides insights into the evolution of the Salmonellae

scientific article published in August 2011

Salmonella enterica serovar Typhi possesses a unique repertoire of fimbrial gene sequences.

scientific article published on May 2001

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota

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Searching for clues

scientific article published in August 2002

Seeding and Establishment of Legionella pneumophila in Hospitals: Implications for Genomic Investigations of Nosocomial Legionnaires' Disease

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Selective and genetic constraints on pneumococcal serotype switching

scientific article published on 31 March 2015

Sequence and analysis of a plasmid-encoded mercury resistance operon from Mycobacterium marinum identifies MerH, a new mercuric ion transporter

scientific article

Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

scientific article published on 16 September 2016

Sequence-based analysis of pQBR103; a representative of a unique, transfer-proficient mega plasmid resident in the microbial community of sugar beet

scientific article published on 05 July 2007

Sequence-based analysis uncovers an abundance of non-coding RNA in the total transcriptome of Mycobacterium tuberculosis

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Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions

scientific article published on 17 February 2013

Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei

scientific article (publication date: 22 February 2003)

Sequencing the environment

scientific article published in 2004

Sharing of carbapenemase-encoding plasmids between Enterobacteriaceae in UK sewage uncovered by MinION sequencing

scientific article published on 4 July 2017

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

scientific article published in September 2012

Shrinking genomics

scientific article published in January 2004

Sibling rivalry.

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Signatures of adaptation in human invasive Salmonella Typhimurium ST313 populations from sub-Saharan Africa.

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Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants

scientific article published on 13 October 2009

Single-cell genomics

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Single-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus

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Size matters?

scientific article published in August 2001

Some Synonymous and Nonsynonymous gyrA Mutations in Mycobacterium tuberculosis Lead to Systematic False-Positive Fluoroquinolone Resistance Results with the Hain GenoType MTBDRsl Assays

scientific article published on 30 January 2017

Spatiotemporal Co-existence of Two Mycobacterium ulcerans Clonal Complexes in the Offin River Valley of Ghana

scientific article

SpeS: A Novel Superantigen and Its Potential as a Vaccine Adjuvant against Strangles

scientific article published on 23 June 2020

Species-wide whole genome sequencing reveals historical global spread and recent local persistence in Shigella flexneri

scientific article published on 4 August 2015

Split personalities

scientific article published on 01 March 2002

SpolPred: rapid and accurate prediction of Mycobacterium tuberculosis spoligotypes from short genomic sequences

scientific article published on 26 September 2012

Spot the difference…

scientific article published on 01 November 2002

Staphylococcus aureus adapts to oxidative stress by producing H2O2-resistant small-colony variants via the SOS response.

scientific article published on 17 February 2015

Strength in diversity

scientific article published in 2004

Streptococcus agalactiae clones infecting humans were selected and fixed through the extensive use of tetracycline

scientific article

Streptococcus bovimastitidis sp. nov., isolated from a dairy cow with mastitis

scientific article

Streptococcus suis contains multiple phase-variable methyltransferases that show a discrete lineage distribution

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Structure, diversity, and mobility of the Salmonella pathogenicity island 7 family of integrative and conjugative elements within Enterobacteriaceae

scientific article published on 13 January 2012

Surveillance and Epidemiology of Drug Resistant Infections Consortium (SEDRIC): Supporting the transition from strategy to action.

scientific article

Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England

scientific article published on 27 April 2016

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131.

scientific article published on 18 July 2017

TLR signaling modulates side effects of anticancer therapy in the small intestine

scientific article

Tales of the unexpected

scientific article published on 01 June 2002

Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice

scientific article

Temporal population structure of invasive Group B Streptococcus during a period of rising disease incidence shows expansion of a CC17 clone

The Burkholderia cepacia epidemic strain marker is part of a novel genomic island encoding both virulence and metabolism-associated genes in Burkholderia cenocepacia

scientific article published on March 2004

The Capsule Regulatory Network of Defined by density-TraDISort

article published in 2018

The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation

scientific article

The Citrobacter rodentium genome sequence reveals convergent evolution with human pathogenic Escherichia coli

scientific article published on 6 November 2009

The Ecological Dynamics of Fecal Contamination and Salmonella Typhi and Salmonella Paratyphi A in Municipal Kathmandu Drinking Water

scientific article

The Ess/Type VII secretion system of Staphylococcus aureus shows unexpected genetic diversity

scientific article

The First population structure and comparative genomics analysis of Mycobacterium africanum strains from Ghana reveals higher diversity of Lineage 5.

scientific article published on 11 November 2016

The Flag-2 locus, an ancestral gene cluster, is potentially associated with a novel flagellar system from Escherichia coli

scientific article

The Full Monty

scientific article published on 01 September 2001

The Genome Sequences of Three Paraburkholderia sp. Strains Isolated from Wood-Decay Fungi Reveal Them as Novel Species with Antimicrobial Biosynthetic Potential

scientific article published on 22 August 2019

The Impact of NOD2 Variants on Fecal Microbiota in Crohn's Disease and Controls Without Gastrointestinal Disease

scholarly article by Nicholas A Kennedy et al published 15 February 2018 in Inflammatory Bowel Diseases

The Impact of NOD2 Variants on Fecal Microbiota in Crohn’s Disease and Controls Without Gastrointestinal Disease

scholarly article by Nicholas A. Kennedy et al published 16 February 2018 in Inflammatory Bowel Diseases

The Influence of HIV on the Evolution of Mycobacterium tuberculosis

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The Microevolution and Epidemiology of Staphylococcus aureus Colonization during Atopic Eczema Disease Flare.

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The Murray collection of pre-antibiotic era Enterobacteriacae: a unique research resource

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The TraDIS toolkit: sequencing and analysis for dense transposon mutant libraries

scientific article published on 21 January 2016

The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing

scientific article published on July 2010

The bordetellae: lessons from genomics

scientific article published on May 2004

The building blocks of pathogenicity

scientific article published on 01 February 2003

The capsule regulatory network of Klebsiella pneumoniae defined by density-TraDISort

The complete genome sequence and analysis of Corynebacterium diphtheriae NCTC13129

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The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081.

scientific article published in December 2006

The complete genome sequence of Mycobacterium bovis

scientific article

The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants

scientific article

The complete nucleotide sequence of the resistance plasmid R478: defining the backbone components of incompatibility group H conjugative plasmids through comparative genomics

scientific article published on November 2004

The devil is in the detail

scientific article published on 01 June 2003

The dissemination of multidrug-resistant Enterobacter cloacae throughout the UK and Ireland

scientific article published on 26 September 2016

The distribution and 'in vivo' phase variation status of haemoglobin receptors in invasive meningococcal serogroup B disease: genotypic and phenotypic analysis

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The extant World War 1 dysentery bacillus NCTC1: a genomic analysis

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The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients

scientific article published on 17 October 2008

The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex

scientific article published on 28 February 2012

The genome of Rhizobium leguminosarum has recognizable core and accessory components

scientific article

The genome of a pathogenic rhodococcus: cooptive virulence underpinned by key gene acquisitions

scientific article (publication date: 30 September 2010)

The genome of the blood fluke Schistosoma mansoni

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The genome sequence of the fish pathogen Aliivibrio salmonicida strain LFI1238 shows extensive evidence of gene decay

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The genome sequence of the food-borne pathogen Campylobacter jejuni reveals hypervariable sequences

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The good, the bad and the ugly?

scientific article published on 01 May 2003

The hospital microbiome project: meeting report for the UK science and innovation network UK-USA workshop ‘beating the superbugs: hospital microbiome studies for tackling antimicrobial resistance’, October 14th 2013

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The impact of antimicrobials on gonococcal evolution

scientific article published on 29 July 2019

The impact of recombination on dN/dS within recently emerged bacterial clones

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The importance of complete genome sequences

scientific article published in May 2002

The magnificent seven

scientific article published on 01 January 2003

The minimum information about a genome sequence (MIGS) specification

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The multidrug-resistant PMEN1 pneumococcus is a paradigm for genetic success

scientific article published on 16 November 2012

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome

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The newly described mecA homologue, mecALGA251, is present in methicillin-resistant Staphylococcus aureus isolates from a diverse range of host species.

scientific article published on 31 August 2012

The pCoo plasmid of enterotoxigenic Escherichia coli is a mosaic cointegrate

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The role of prophage-like elements in the diversity of Salmonella enterica serovars

scientific article published in May 2004

The secondary resistome of multidrug-resistant Klebsiella pneumoniae

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The speciation and hybridization history of the genus Salmonella

scientific article published on 26 July 2019

The transcription factor T-bet regulates intestinal inflammation mediated by interleukin-7 receptor+ innate lymphoid cells.

scientific article published on 11 October 2012

The use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis

scientific article published on 24 December 2014

The value of comparison

scientific article published in 2003

The widespread use of topical antimicrobials enriches for resistance in Staphylococcus aureus isolated from Atopic Dermatitis patients.

scientific article published on 5 May 2018

Time between collection and storage significantly influences bacterial sequence composition in sputum samples from cystic fibrosis respiratory infections

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Time to remove the model organism blinkers

scientific article published on 29 September 2008

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

scientific article published on 30 September 2013

Transcriptional regulation of Culex pipiens mosquitoes by Wolbachia influences cytoplasmic incompatibility

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Transient Silencing of Antibiotic Resistance by Mutation Represents a Significant Potential Source of Unanticipated Therapeutic Failure

scientific article published on 29 October 2019

Transmission of M abscessus in patients with cystic fibrosis - Authors' reply

scientific article published in August 2013

Transmission of methicillin-resistant Staphylococcus aureus in long-term care facilities and their related healthcare networks

scientific article published on 03 October 2016

Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in O157

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Twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of Bacteroides fragilis

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Tyrosine site-specific recombinases mediate DNA inversions affecting the expression of outer surface proteins of Bacteroides fragilis

scientific article published in September 2004

Understanding pneumococcal serotype 1 biology through population genomic analysis

scientific article published on 8 November 2016

Unlocking the genome of the human typhoid bacillus

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Unusual features in organisation of capsular polysaccharide-related genes of C. jejuni strain X

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Use of Vitek 2 antimicrobial susceptibility profile to identify mecC in methicillin-resistant Staphylococcus aureus

scientific article published on 29 May 2013

Variable recombination dynamics during the emergence, transmission and 'disarming' of a multidrug-resistant pneumococcal clone

scientific article published on 23 June 2014

Variation in the effectors of the type III secretion system among Photorhabdus species as revealed by genomic analysis

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What Is Resistance? Impact of Phenotypic versus Molecular Drug Resistance Testing on Therapy for Multi- and Extensively Drug-Resistant Tuberculosis.

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What has high-throughput sequencing ever done for us?

scientific article published on 27 August 2013

What's in a Name? Species-Wide Whole-Genome Sequencing Resolves Invasive and Noninvasive Lineages of Salmonella enterica Serotype Paratyphi B ⬇️

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Wheat bran promotes enrichment within the human colonic microbiota of butyrate-producing bacteria that release ferulic acid

scientific article published on 04 December 2015

Whole Genome Sequence Analysis of a Large Isoniazid-Resistant Tuberculosis Outbreak in London: A Retrospective Observational Study

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Whole Genome Sequencing Shows a Low Proportion of Tuberculosis Disease Is Attributable to Known Close Contacts in Rural Malawi

scientific article published on 16 July 2015

Whole genome comparison of Campylobacter jejuni human isolates using a low-cost microarray reveals extensive genetic diversity.

scientific article

Whole genome investigation of a divergent clade of the pathogen Streptococcus suis

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Whole genome sequencing identifies zoonotic transmission of MRSA isolates with the novel mecA homologue mecC

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Whole genome sequencing of ESBL-producing Escherichia coli isolated from patients, farm waste and canals in Thailand

scientific article published on 6 September 2017

Whole genome sequencing reveals high-resolution epidemiological links between clinical and environmental Klebsiella pneumoniae

scientific article published on 24 January 2017

Whole-Genome Sequences of Five Strains of Kocuria rosea, NCTC2676, NCTC7514, NCTC7512, NCTC7528, and NCTC7511

scientific article published on 31 October 2019

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe

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Whole-genome analysis of diverse Chlamydia trachomatis strains identifies phylogenetic relationships masked by current clinical typing

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Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

scientific article published on 22 March 2013

Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy

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Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study.

scientific article published on 14 November 2012

Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study

scientific article published on 23 June 2015

Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis

scientific article published on July 2013

Whole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals

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Whole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network

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Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study

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Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study

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Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study

scientific article published on 29 March 2013

Wild-Type and Non-Wild-Type Mycobacterium tuberculosis MIC Distributions for the Novel Fluoroquinolone Antofloxacin Compared with Those for Ofloxacin, Levofloxacin, and Moxifloxacin

scientific article published on 20 June 2016

Within-Host Sampling of a Natural Population Shows Signs of Selection on Pde1 during Bacterial Meningitis

scientific article published on 23 February 2017

Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients

scientific article published on 27 December 2017

Wolbachia variability and host effects on crossing type in Culex mosquitoes.

scientific article published in July 2005

Yersinia pestis pFra shows biovar-specific differences and recent common ancestry with a Salmonella enterica serovar Typhi plasmid

scientific article

Zero tolerance for healthcare-associated MRSA bacteraemia: is it realistic?

scientific article

complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv

scientific article published in 2021

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