Microbial Genomics

Article	Citations
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification	247
ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes	173
Kaptive 2.0: updated capsule and lipopolysaccharide locus typing for the Klebsiella pneumoniae species complex	72
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history	66
RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12	42
Recovery of small plasmid sequences via Oxford Nanopore sequencing	39
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning	34
Comparison of R9.4.1/Kit10 and R10/Kit12 Oxford Nanopore flowcells and chemistries in bacterial genome reconstruction	33
A comprehensive and high-quality collection of Escherichia coli genomes and their genes	32
ECTyper: in silico Escherichia coli serotype and species prediction from raw and assembled whole-genome sequence data	32
From genotype to phenotype: adaptations of Pseudomonas aeruginosa to the cystic fibrosis environment	28
Comprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery	27
Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains	24
Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction	24
Genomic evolution of the globally disseminated multidrug-resistant Klebsiella pneumoniae clonal group 147	24
Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants	24
Population-level deep sequencing reveals the interplay of clonal and sexual reproduction in the fungal wheat pathogen Zymoseptoria tritici	23
bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands	22
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm	21
Kill and cure: genomic phylogeny and bioactivity of Burkholderia gladioli bacteria capable of pathogenic and beneficial lifestyles	21
Meta-analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology	21
A genomic epidemiological study shows that prevalence of antimicrobial resistance in Enterobacterales is associated with the livestock host, as well as antimicrobial usage	20
Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure	20
Phylogenomics and antimicrobial resistance of Salmonella Typhi and Paratyphi A, B and C in England, 2016–2019	19
Genomic comparisons of Escherichia coli ST131 from Australia	19

Genomic surveillance, characterization and intervention of a polymicrobial multidrug-resistant outbreak in critical care	19
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 locus	19
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data	19
Comparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov.	18
Leviviricetes: expanding and restructuring the taxonomy of bacteria-infecting single-stranded RNA viruses	18
Insights into the acquisition of the pks island and production of colibactin in the Escherichia coli population	18
Comparative genomics of Staphylococcus epidermidis from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence	18
Finding the right fit: evaluation of short-read and long-read sequencing approaches to maximize the utility of clinical microbiome data	18
Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation	18
The genomes of nucleocytoplasmic large DNA viruses: viral evolution writ large	17
Bacterial genomic epidemiology with mixed samples	17
Comprehensive screening of genomic and metagenomic data reveals a large diversity of tetracycline resistance genes	17
Exploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim	17
Large-scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management	16
Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks	16
Phylogenetic structure of Shiga toxin-producing Escherichia coli O157:H7 from sub-lineage to SNPs	16
Optimized use of Oxford Nanopore flowcells for hybrid assemblies	15
Characterization of a pESI-like plasmid and analysis of multidrug-resistant Salmonella enterica Infantis isolates in England and Wales	15
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	15
Validation strategy of a bioinformatics whole genome sequencing workflow for Shiga toxin-producing Escherichia coli using a reference collection extensively characterized with conventional methods	15
Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak	15
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access	14
Host adaptation and microbial competition drive Ralstonia solanacearum phylotype I evolution in the Republic of Korea	14
The promiscuous and highly mobile resistome of Acinetobacter baumannii	14
Plasmids encode niche-specific traits in Lactobacillaceae	14
Early branching arbuscular mycorrhizal fungus Paraglomus occultum carries a small and repeat-poor genome compared to relatives in the Glomeromycotina	14
Rapid molecular evolution of Spiroplasma symbionts of Drosophila	14
Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium	14
Different evolutionary trends form the twilight zone of the bacterial pan-genome	14
Genome evolution drives transcriptomic and phenotypic adaptation in Pseudomonas aeruginosa during 20 years of infection	14
Hogwash: three methods for genome-wide association studies in bacteria	14
Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin	14
Mining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species	13
The structure and diversity of strain-level variation in vaginal bacteria	13
Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC	13
Quantitative analysis of the splice variants expressed by the major hepatitis B virus genotypes	13
Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility	13
Genomic analysis of trimethoprim-resistant extraintestinal pathogenic Escherichia coli and recurrent urinary tract infections	13
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations	13
Whole-genome epidemiology links phage-mediated acquisition of a virulence gene to the clonal expansion of a pandemic Salmonella enterica serovar Typhimurium clone	13
Antimicrobial resistance determinants are associated with Staphylococcus aureus bacteraemia and adaptation to the healthcare environment: a bacterial genome-wide association study	13
Characterization of emergent toxigenic M1UK Streptococcus pyogenes and associated sublineages	13
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 as	13
Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials	13
A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome	13
The open pan-genome architecture and virulence landscape of Mycobacterium bovis	12
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae	12
Multiple evolutionary origins reflect the importance of sialic acid transporters in the colonization potential of bacterial pathogens and commensals	12
Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance	12
Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types	12

Introduction and adaptation of an emerging pathogen to olive trees in Italy	12
Emerging carbapenem-resistant Klebsiella pneumoniae sequence type 16 causing multiple outbreaks in a tertiary hospital in southern Vietnam	12
Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa	12
Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom	12
Genomic epidemiology of Escherichia coli isolates from a tertiary referral center in Lilongwe, Malawi	12
Caution regarding the specificities of pan-cancer microbial structure	12
The virulome of Streptomyces scabiei in response to cello-oligosaccharide elicitors	11
Ongoing evolution of Chlamydia trachomatis lymphogranuloma venereum: exploring the genomic diversity of circulating strains	11
Comprehensive and accurate genetic variant identification from contaminated and low-coverage Mycobacterium tuberculosis whole genome sequencing data	11
Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium	11
Generalizable characteristics of false-positive bacterial variant calls	11
Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC in Escherichia coli K-12	11
Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes	11
Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex	11
Third generation cephalosporin resistance in clinical non-typhoidal Salmonella enterica in Germany and emergence of bla CTX-M-harbouring pESI plasmids	11
A panel of diverse Klebsiella pneumoniae clinical isolates for research and development	11
Translatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes	11
Population genetic structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in children in Argentina	11
Insights into evolution and coexistence of the colibactin- and yersiniabactin secondary metabolite determinants in enterobacterial populations	11
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection	11
Flanker: a tool for comparative genomics of gene flanking regions	11
Clostridioides difficile strain-dependent and strain-independent adaptations to a microaerobic environment	11
Detection of plasmid contigs in draft genome assemblies using customized Kraken databases	11
Genome-wide association study of gastric cancer- and duodenal ulcer-derived Helicobacter pylori strains reveals discriminatory genetic variations and novel oncoprotein candidates	11
Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis	11
Current population structure and pathogenicity patterns of Ascochyta rabiei in Australia	11
Dissemination of novel Tn7 family transposons carrying genes for synthesis and uptake of fimsbactin siderophores among Acinetobacter baumannii isolates	10
Long read genome assemblers struggle with small plasmids	10
A global transcriptomic analysis of Staphylococcus aureus biofilm formation across diverse clonal lineages	10
Genetic diversity of clinical and environmental Mucorales isolates obtained from an investigation of mucormycosis cases among solid organ transplant recipients	10
Analysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing	10
Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity	10
Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts	10
Acinetobacter baumannii from grass: novel but non-resistant clones	10
Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications	10
Genomic epidemiology of nontoxigenic Corynebacterium diphtheriae from King County, Washington State, USA between July 2018 and May 2019	10
Transmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain	10
Revised nomenclature and SNP barcode for Mycobacterium tuberculosis lineage 2	10
Streptococcus suis outbreak caused by an emerging zoonotic strain with acquired multi-drug resistance in Thailand	10
Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail	10
Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1	10
Use of genomics to explore AMR persistence in an outdoor pig farm with low antimicrobial usage	10
The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps?	10
Enhancing genomics-based outbreak detection of endemic Salmonella enterica serovar Typhimurium using dynamic thresholds	10
Curation of the AMRFinderPlus databases: applications, functionality and impact	10
Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis	10
Distribution, organization and expression of genes concerned with anaerobic lactate utilization in human intestinal bacteria	10
Determining the serotype composition of mixed samples of pneumococcus using whole-genome sequencing	10
Monomorphic Trypanozoon: towards reconciling phylogeny and pathologies	10
Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales	10
Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia	9
Sudden emergence of a Neisseria gonorrhoeae clade with reduced susceptibility to extended-spectrum cephalosporins, Norway	9
Colonization with Staphylococcus aureus and Klebsiella pneumoniae causes infections in a Vietnamese intensive care unit	9
Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)	9
Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster connection to an orphan metabolite	9
Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad	9
Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes	9
Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster	9
Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps	9
Diversity of carbapenem-resistant Acinetobacter baumannii and bacteriophage-mediated spread of the Oxa23 carbapenemase	9
Geographical separation and ethnic origin influence the human gut microbial composition: a meta-analysis from a Malaysian perspective	9
Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping	9
Comprehensive in silico survey of the Mycolicibacterium mobilome reveals an as yet underexplored diversity	9
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)	9
Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan	9
The global population structure and evolutionary history of the acquisition of major virulence factor-encoding genetic elements in Shiga toxin-producing Escherichia coli O121:H19	9
Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections	9
Neisseria gonorrhoeae clustering to reveal major European whole-genome-sequencing-based genogroups in association with antimicrobial resistance	9
Phenotypic and genomic characterization of a Vibrio parahaemolyticus strain causing disease in Penaeus vannamei provides insights into its niche adaptation and pathogenic mechanism	9
Genome diversity of domesticated Acinetobacter baumannii ATCC 19606T strains	9
Methods for the targeted sequencing and analysis of integrons and their gene cassettes from complex microbial communities	9
Massively parallel transposon mutagenesis identifies temporally essential genes for biofilm formation in Escherichia coli	9
GBS-SBG - GBS Serotyping by Genome Sequencing	9
Phylogenomic disentangling of the Bifidobacterium longum subsp. infantis taxon	9
Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes	9
Bilateral symmetry of linear streptomycete chromosomes	8
A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile	8
Acquisition and loss of CTX-M plasmids in Shigella species associated with MSM transmission in the UK	8
Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signalling-molecule diversity	8
Characterization of beta-lactam-resistant Escherichia coli from Australian fruit bats indicates anthropogenic origins	8

Carriage prevalence and genomic epidemiology of Staphylococcus aureus among Native American children and adults in the Southwestern USA	8
Unique roles of vaginal Megasphaera phylotypes in reproductive health	8
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae	8
Comparative genomic insights into culturable symbiotic cyanobacteria from the water fern Azolla	8
Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach	8
rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data	8
Epidemiology and population structure of Haemophilus influenzae causing invasive disease	8
A panoramic view of the genomic landscape of the genus Streptomyces	8
Complete microbial genomes for public health in Australia and the Southwest Pacific	8
Association between metabolic status and gut microbiome in obese populations	8
Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing	8
Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive	8
Whole-genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-lactam and carbapenem-resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital	8
SplitStrains, a tool to identify and separate mixed Mycobacterium tuberculosis infections from WGS data	8
GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes	8
A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains	8
wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations	8
Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome	8
Genomic analysis reveals high intra-species diversity of Shewanella algae	7
Read trimming has minimal effect on bacterial SNP-calling accuracy	7
Evaluation of bat adenoviruses suggests co-evolution and host roosting behaviour as drivers for diversity	7
Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations	7
Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils	7
Evolutionary responses to codon usage of horizontally transferred genes in Pseudomonas aeruginosa: gene retention, amelioration and compensatory evolution	7
Cryptic prophages within a Streptococcus pyogenes genotype emm4 lineage	7
Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy	7
The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach	7
Genomic epidemiology of Mycobacterium bovis infection in sympatric badger and cattle populations in Northern Ireland	7
Homologous recombination between tandem paralogues drives evolution of a subset of type VII secretion system immunity genes in firmicute bacteria	7
A critical evaluation of Mycobacterium bovis pangenomics, with reference to its utility in outbreak investigation	7
Characterization of the mitochondrial genomes of three powdery mildew pathogens reveals remarkable variation in size and nucleotide composition	7
Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data	7
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli	7
Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam	7
Exact mapping of Illumina blind spots in the Mycobacterium tuberculosis genome reveals platform-wide and workflow-specific biases	7
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv	7
Phylum barrier and Escherichia coli intra-species phylogeny drive the acquisition of antibiotic-resistance genes	7
Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients	7
Comparative genomics of Rothia species reveals diversity in novel biosynthetic gene clusters and ecological adaptation to different eukaryotic hosts and host niches	7
Molecular characterization of respiratory syncytial viruses circulating in a paediatric cohort in Amman, Jordan	7
Genomic and temporal analyses of Mycobacterium bovis in southern Brazil	7
Genome analyses of 174 strains of Mycobacterium tuberculosis provide insight into the evolution of drug resistance and reveal potential drug targets	7
Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance	7
High molecular weight DNA extraction methods lead to high quality filamentous ascomycete fungal genome assemblies using Oxford Nanopore sequencing	7
Genomic epidemiology of Staphylococcus aureus isolated from bloodstream infections in South America during 2019 supports regional surveillance	7
In vitro exploration of the Xanthomonas hortorum pv. vitians genome using transposon insertion sequencing and comparative genomics to discriminate between core and contextual essential genes	7
Population structure and transmission of Mycobacterium bovis in Ethiopia	7
RND pumps across the genus Acinetobacter: AdeIJK is the universal efflux pump	7
A global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology	7
Targeted control of pneumolysin production by a mobile genetic element in Streptococcus pneumoniae	7
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing	6
The bacterial biome of ticks and their wildlife hosts at the urban–wildland interface	6
Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses	6
NonClasGP-Pred: robust and efficient prediction of non-classically secreted proteins by integrating subset-specific optimal models of imbalanced data	6
A lung-specific mutational signature enables inference of viral and bacterial respiratory niche	6
Genome reorganization during emergence of host-associated Mycobacterium abscessus	6
Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity	6
Genomic differentiation within East Asian Helicobacter pylori	6
DNA isolation methods for Nanopore sequencing of the Streptococcus mitis genome	6
Population genomics of the food-borne pathogen Vibrio fluvialis reveals lineage associated pathogenicity-related genetic elements	6
Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption	6
SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021	6
Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes	6
Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions	6
Genomic diversity, life strategies and ecology of marine HTVC010P-type pelagiphages	6
Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of Escherichia coli	6
Insight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activ	6
Identification of the conjugative and mobilizable plasmid fragments in the plasmidome using sequence signatures	6
Genetic diversity and transmission patterns of Burkholderia pseudomallei on Hainan island, China, revealed by a population genomics analysis	6
A Campylobacter integrative and conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?	6
PanGraph: scalable bacterial pan-genome graph construction	6
Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity	6
Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations	6
TransAAP: an automated annotation pipeline for membrane transporter prediction in bacterial genomes	6
Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022	6
Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations	6
Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi	6
The glycan alphabet is not universal: a hypothesis	6
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens	6
Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways	6
Biosynthetic novelty index reveals the metabolic potential of rare actinobacteria isolated from highly oligotrophic sediments	6
Unveiling the genomic potential of Pseudomonas type strains for discovering new natural products	6
Comparative genome analyses of Mycobacteroides immunogenum reveals two potential novel subspecies	6
Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes	6
Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen	6
Functional genomics reveals the toxin–antitoxin repertoire and AbiE activity in Serratia	6
A random forest model based on core genome allelic profiles of MRSA for penicillin plus potassium clavulanate susceptibility prediction	6
PneumoKITy: A fast, flexible, specific, and sensitive tool for Streptococcus pneumoniae serotype screening and mixed serotype detection from genome sequence data	6
Genome structural variation in Escherichia coli O157:H7	6
Laboratory strains of Escherichia coli K-12: things are seldom what they seem	6
Differential nasopharyngeal microbiota composition in children according to respiratory health status	6
Genomic epidemiology of tuberculosis in eastern Malaysia: insights for strengthening public health responses	6
A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England	6
Phylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate vast taxonomic diversity, open genomes and an abundance of carbohydrate-active enzyme family isoforms	6
Exploring the evolution and epidemiology of European CC1-MRSA-IV: tracking a multidrug-resistant community-associated meticillin-resistant Staphylococcus aureus clone	6