Microbial Genomics

Papers
(The median citation count of Microbial Genomics is 3. The table below lists those papers that are above that threshold based on CrossRef citation counts [max. 250 papers]. The publications cover those that have been published in the past four years, i.e., from 2020-03-01 to 2024-03-01.)
ArticleCitations
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification149
ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes114
Dynamic linkage of COVID-19 test results between Public Health England’s Second Generation Surveillance System and UK Biobank93
Identification of Acinetobacter baumannii loci for capsular polysaccharide (KL) and lipooligosaccharide outer core (OCL) synthesis in genome assemblies using curated reference databases compatible wit79
Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores74
Metagenomic approaches in microbial ecology: an update on whole-genome and marker gene sequencing analyses65
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history58
Universal whole-sequence-based plasmid typing and its utility to prediction of host range and epidemiological surveillance56
Molecular epidemiology of Salmonella Infantis in Europe: insights into the success of the bacterial host and its parasitic pESI-like megaplasmid53
Metagenome-assembled genome binning methods with short reads disproportionately fail for plasmids and genomic Islands52
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex47
An assessment of genome annotation coverage across the bacterial tree of life43
Recovery of small plasmid sequences via Oxford Nanopore sequencing34
Coinfinder: detecting significant associations and dissociations in pangenomes33
A comprehensive and high-quality collection of Escherichia coli genomes and their genes33
Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes31
Comparison of core-genome MLST, coreSNP and PFGE methods for Klebsiella pneumoniae cluster analysis29
Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors29
Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland29
Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones28
Genomic characterization of Salmonella Uzaramo for human invasive infection27
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-1227
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning26
Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes25
Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery24
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex24
Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains22
From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment22
Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles21
bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands20
Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae20
Trends in Helicobacter pylori resistance to clarithromycin: from phenotypic to genomic approaches20
Comparison of Shiga toxin-encoding bacteriophages in highly pathogenic strains of Shiga toxin-producing Escherichia coli O157:H7 in the UK20
Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants20
Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients20
ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data20
Analysis of the biodegradative and adaptive potential of the novel polychlorinated biphenyl degrader Rhodococcus sp. WAY2 revealed by its complete genome sequence20
Phylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens19
Origin, maintenance and spread of antibiotic resistance genes within plasmids and chromosomes of bloodstream isolates of Escherichia coli19
Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates19
Genomic comparisons of Escherichia coli ST131 from Australia19
Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 14719
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm19
Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici18
Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov.18
Genomic profiling of Escherichia coli isolates from bacteraemia patients: a 3-year cohort study of isolates collected at a Sydney teaching hospital18
A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics18
Microbial genomics amidst the Arctic crisis18
Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care18
Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants17
Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation17
Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes17
Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction17
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data16
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods16
nanoMLST: accurate multilocus sequence typing using Oxford Nanopore Technologies MinION with a dual-barcode approach to multiplex large numbers of samples16
Phylogenomics and antimicrobial resistance of Salmonella Typhi and Paratyphi A, B and C in England, 2016–201916
Bacterial genomic epidemiology with mixed samples16
Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences16
Comparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species16
Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses16
The promiscuous and highly mobile resistome of Acinetobacter baumannii16
A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage16
Genomic epidemiology and population structure of Neisseria gonorrhoeae in Norway, 2016–201715
Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology15
Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim15
Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population15
Microevolution in the major outer membrane protein OmpA of Acinetobacter baumannii15
Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 201815
The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites15
Comparative genomics of Staphylococcus epidermidis from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence15
Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria14
Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction14
Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs14
Community-acquired infection caused by the uncommon hypervirulent Klebsiella pneumoniae ST66-K2 lineage14
Plasmids encode niche-specific traits in Lactobacillaceae14
Mycoparasitism illuminated by genome and transcriptome sequencing of Coniothyrium minitans, an important biocontrol fungus of the plant pathogen Sclerotinia sclerotiorum14
Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data14
Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone14
Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections14
Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management14
Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak13
Optimized use of Oxford Nanopore flowcells for hybrid assemblies13
Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales13
Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital13
An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus13
Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study13
Insertion sequences drive the emergence of a highly adapted human pathogen13
Introduction and adaptation of an emerging pathogen to olive trees in Italy13
Transposable elements contribute to the genome plasticity of Ralstonia solanacearum species complex12
Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins12
Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes12
Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species12
The past, present and future of ancient bacterial DNA12
Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure12
Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection12
Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea12
Different evolutionary trends form the twilight zone of the bacterial pan-genome12
Insights into evolution and coexistence of the colibactin- and yersiniabactin secondary metabolite determinants in enterobacterial populations11
Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis11
Flanker: a tool for comparative genomics of gene flanking regions11
Antibiotic resistance in Pseudomonas aeruginosa and adaptation to complex dynamic environments11
Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin11
Genomic epidemiology of Escherichia coli isolates from a tertiary referral center in Lilongwe, Malawi11
A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages11
Rapid molecular evolution of Spiroplasma symbionts of Drosophila11
Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains11
Forensic genomics of a novel Klebsiella quasipneumoniae type from a neonatal intensive care unit in China reveals patterns of colonization, evolution and epidemiology11
Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds11
Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia11
Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance11
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes11
Genome structure reveals the diversity of mating mechanisms in Saccharomyces cerevisiae x Saccharomyces kudriavzevii hybrids, and the genomic instability that promotes phenotypic diversity11
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access11
Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina10
Emerging carbapenem-resistant Klebsiella pneumoniae sequence type 16 causing multiple outbreaks in a tertiary hospital in southern Vietnam10
The genomes of nucleocytoplasmic large DNA viruses: viral evolution writ large10
Phylogenomics and population genomics of SARS-CoV-2 in Mexico during the pre-vaccination stage reveals variants of interest B.1.1.28.4 and B.1.1.222 or B.1.1.519 and the nucleocapsid mutation S194L as10
Hogwash: three methods for genome-wide association studies in bacteria10
socru: typing of genome-level order and orientation around ribosomal operons in bacteria10
Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 110
Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia10
Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates10
The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps?10
Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain10
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations10
Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium10
A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome10
Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks10
Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective10
Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis10
The structure and diversity of strain-level variation in vaginal bacteria10
Comparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA10
Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa10
Comparative genomic analysis of three intestinal species reveals reductions in secreted pathogenesis determinants in bovine-specific and non-pathogenic Cryptosporidium species10
Defining the transcriptional responses of Aspergillus nidulans to cation/alkaline pH stress and the role of the transcription factor SltA10
Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite9
Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli9
Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps9
Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales9
Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 20199
Current population structure and pathogenicity patterns of Ascochyta rabiei in Australia9
Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing9
Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types9
Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC in Escherichia coli K-129
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection9
Virulence genes and previously unexplored gene clusters in four commensal Neisseria spp. isolated from the human throat expand the neisserial gene repertoire9
Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad9
Detection of plasmid contigs in draft genome assemblies using customized Kraken databases9
Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage9
Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates9
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients9
Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach8
Optimization of sample preparation for culture-independent sequencing of Bordetella pertussis8
Nuclear and mitochondrial genome sequencing of North-African Leishmania infantum isolates from cured and relapsed visceral leishmaniasis patients reveals variations correlating with geography and phen8
Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes8
Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy8
Expanded roles of pyruvate-sensing PdhR in transcription regulation of the Escherichia coli K-12 genome: fatty acid catabolism and cell motility8
Third generation cephalosporin resistance in clinical non-typhoidal Salmonella enterica in Germany and emergence of bla CTX-M-harbouring pESI plasmids8
Differential nasopharyngeal microbiota composition in children according to respiratory health status8
Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts8
Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway8
Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility8
Phylogenetic distribution and evolutionary dynamics of nod and T3SS genes in the genus Bradyrhizobium8
Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing8
Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon8
Population structure and transmission of Mycobacterium bovis in Ethiopia8
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae8
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae8
Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients8
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools8
Comprehensive and accurate genetic variant identification from contaminated and low-coverage Mycobacterium tuberculosis whole genome sequencing data8
Dual transcriptome analysis reveals differential gene expression modulation influenced by Leishmania arginase and host genetic background8
Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity8
Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex8
Monomorphic Trypanozoon: towards reconciling phylogeny and pathologies8
Whole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes8
The open pan-genome architecture and virulence landscape of Mycobacterium bovis8
Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing8
Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium8
Association between metabolic status and gut microbiome in obese populations8
Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance8
Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data7
Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance7
Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand7
Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria7
Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC7
Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity7
Phenotypic and genomic characterization of a Vibrio parahaemolyticus strain causing disease in Penaeus vannamei provides insights into its niche adaptation and pathogenic mechanism7
Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail7
Colonization with Staphylococcus aureus and Klebsiella pneumoniae causes infections in a Vietnamese intensive care unit7
The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach7
Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals7
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes7
Exploring the evolution and epidemiology of European CC1-MRSA-IV: tracking a multidrug-resistant community-associated meticillin-resistant Staphylococcus aureus clone7
Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome7
prewas: data pre-processing for more informative bacterial GWAS7
Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signalling-molecule diversity7
Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 27
Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps)7
Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution7
Complete microbial genomes for public health in Australia and the Southwest Pacific7
Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase7
Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen7
Caution regarding the specificities of pan-cancer microbial structure7
Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes7
Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms7
Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom7
Evaluation of bat adenoviruses suggests co-evolution and host roosting behaviour as drivers for diversity7
Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster7
Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)7
Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam7
Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping7
Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities7
In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes7
The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors7
Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases7
Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials7
Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment7
Transcriptome-wide expression profiling of Sporothrix schenckii yeast and mycelial forms and the establishment of the Sporothrix Genome DataBase7
Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK7
The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H197
Genomic and temporal analyses of Mycobacterium bovis in southern Brazil7
Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections7
Characterization of the mitochondrial genomes of three powdery mildew pathogens reveals remarkable variation in size and nucleotide composition7
Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels7
Curation of the AMRFinderPlus databases: applications, functionality and impact7
Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis6
Chemical biology-whole genome engineering datasets predict new antibacterial combinations6
Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses6
Bilateral symmetry of linear streptomycete chromosomes6
Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia6
A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England6
Acquisition of plasmids conferring carbapenem and aminoglycoside resistance and loss of surface-exposed macromolecule structures as strategies for the adaptation of Acinetobacter baumannii CC104O/CC156
The bacterial biome of ticks and their wildlife hosts at the urban–wildland interface6
GBS-SBG - GBS Serotyping by Genome Sequencing6
Diversity and evolutionary dynamics of spore-coat proteins in spore-forming species of Bacillales6
Comparative genomic insights into culturable symbiotic cyanobacteria from the water fern Azolla6
Evaluation of methods for detecting human reads in microbial sequencing datasets6
Distinct patterns of mutational sensitivity for λ resistance and maltodextrin transport in Escherichia coli LamB6
SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data6
Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products6
Genome structural variation in Escherichia coli O157:H76
A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains6
Centre-specific bacterial pathogen typing affects infection-control decision making6
Unique roles of vaginal Megasphaera phylotypes in reproductive health6
Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive6
Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes6
Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes6
GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes6
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