Microbial Genomics

Article	Citations
Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139 Vibrio cholerae in foodborne outbreaks	111
Development and validation of a core-genome multilocus sequence typing scheme for Legionella longbeachae	109
Molecular characterization of Coxsackievirus A2 isolated from hand, foot and mouth disease in eastern China	92
Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T)	80
Identifying gene-level mechanisms of successful dispersal of Vibrio parahaemolyticus during El Niño events	64
Comparative genomics of a poinsettia-associated phytoplasma and functional validation of its SAP11-homologous effectors that induce plant branching	63
Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii	48
Genomic features of pneumococcal strains isolated from paediatric patients with invasive disease during pneumococcal conjugate vaccine introduction in Lima, Peru	46
Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus)	44
The primate gut microbiota contributes to interspecific differences in host metabolism	42
Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination	35
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom	35
First report of a nosocomial outbreak of ST101 Klebsiella pneumoniae carrying bla OXA-48 in Shandong, China	34
Genomic comparison of clinical strains of Mycobacterium shinjukuense in Japan reveals low diversity and stable genome structures	34
Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli	32
Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics	32
Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions	29
Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly	28
Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales	28
Genomic insights into the resistome, mobilome and functional adaptation of Achromobacter xylosoxidans across clinical and environmental contexts	28
Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions	27
A metagenomic approach to One Health surveillance of antimicrobial resistance in a UK veterinary centre	27
Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive	25
Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022	25
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens	25

Assessing the safety of microbiome perturbations	24
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling	24
Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen	23
Vibrio cholerae serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965	23
Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes	22
Harnessing gastrointestinal microbial co-association networks to predict feed efficiency and methane emissions across beef and dairy cattle	22
Canine Providencia alcalifaciens: virulence factors and phylogenetic analysis of an emerging enteropathogen	21
Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018	21
Comparative genomics of ‘Xanthomonas cannabis’ reveals an emerging, diverse pathogen	21
Global population structure of Shiga toxin-producing Escherichia coli O103:H2 and the variation in their major virulence factor-encoding genetic elements	21
Temporal dynamics of gene expression during the development of Campylobacter jejuni biofilms	20
Population structure and antimicrobial resistance of Corynebacterium diphtheriae in Victoria, Australia	19
dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data	19
Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment	18
Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs	18
Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction	18
Whole-genome analysis of rotavirus G1P[8] and other Wa-like strains in Mozambican children: evidence of genetic variations of pre-vaccine G1P[8] strains from Manhiça, Mozambique	18
The use of representative community samples to assess SARS-CoV-2 lineage competition: Alpha outcompetes Beta and wild-type in England from January to March 2021	17
Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi	17
Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host	17
IME_Rho_tet, a novel family of putative integrative mobilizable elements spreading tetracycline resistance genes tet(W) and tet(32) among human and animal gut bacteria	17
Complete genomes of Clostridium botulinum type B(F) isolates associated with a 1995 foodborne botulism outbreak from commercial pâté reveals a recombination event disrupting the ntnh gene	17
Insights into the genomic evolution and the alkali tolerance mechanisms of Agaricus sinodeliciosus by comparative genomic and transcriptomic analyses	17
Pathogenic potential and phylogenomic analysis of stx2-carrying O26:H11 Shiga toxin-producing Escherichia coli isolated from dairy products in France (2014–2024)	17
A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment	16
Genomic analysis of antibiotic resistance and virulence factors in the uropathogen Citrobacter koseri	16
Birmingham-group IncP-1α plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates	16
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics	16
Genome-wide characterization of sulphur metabolism gene families and recombination dynamics in mangrove-derived Bacillus aryabhattai NM1-A2 and Bacillus cereus NR1	16
High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy	16
Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways	16
Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes	15
Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK	15
Corrigendum: Genomic characterisation of a unique Panton-Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting Australian indige	15
A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis	15
Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya	15
A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin	15
Single-cell genome analysis of a feminizing Wolbachia in Eurema butterflies reveals a shared origin with male-killing Wolbachia	15
No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis	15
The possible impact of novel mutations in human papillomavirus 52 on the infection characteristics	14
Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae	14
ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data	14
Monkeypox virus: phylogenomics, host–pathogen interactome and mutational cascade	14
Scalable genotyping of microbial colonies	14
Type I-F CRISPR-associated transposons contribute to genomic plasticity in Shewanella and mediate efficient programmable DNA integration	14
Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover	14
Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing	14
Colonization and transmission of Staphylococcus aureus in schools: a citizen science project	14
HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data	13
Genomic outbreak investigation of biosafety-level-3 pathogens using nanopore sequencing	13

Comparative genomics and methylome profiling of Pseudolactococcus laudensis reveal signatures of niche adaptation and strain-level variation in mobile genetic elements and phage defence	13
Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases	13
Genomic investigations in animal enteric disease-associated Clostridium perfringens	13
Evolutionary dynamics in the genome of ocular Chlamydia trachomatis strains from Northern Tanzania following mass drug administration	13
Heritability and gene functions associated with sclerotia formation of Rhizoctonia solani AG-7 using whole genome sequencing and genome-wide association study	13
Aneuploidy, polyploidy and loss of heterozygosity distinguish serial bloodstream isolates of Candida albicans	13
Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospi	13
Sulphur metabolism as a key factor in the evolution of environmental adaptation of Acidihalobacter	13
Genomic surveillance of post-immunization pneumococcal carriage in Ghana	13
Genomic signatures of dominant clones and evolutionary divergence of Acinetobacter baumannii in Thailand	13
Refining Salinivibrio pangenome dynamics and biotechnological potential through comparative analysis	13
An integrated multi-omic approach for discovery and dereplication of bioactive microbial natural products	13
Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis	12
Comparative genome analysis of human pathogen Parvimonas micra revealed strain JM503A as potential novel species in the genus Parvimonas and high intra-species functional diversity	12
Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes for Escherichia coli sequence type 131 clade C surveillance across infection types	12
Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations	12
Genomic sentinel surveillance: Salmonella Paratyphi B outbreak in travellers coinciding with a mass gathering in Iraq	12
Analysis of variola virus molecular evolution suggests an old origin of the virus consistent with historical records	12
Genomic and clinical characteristics of campylobacteriosis in Australia	12
Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia	12
Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance	12
Rapid and recent evolution of fetA phase variability among hyperinvasive MenW:cc11 disease isolates	11
Dominance of high-risk clones ST2 and ST571 and the diversity of resistance islands in clinical Acinetobacter baumannii isolates from Hanoi, Vietnam	11
‘Vivaldi’: an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2	11
pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections	11
Genetic insights into Shewanella spp., progenitor of the bla OXA-48-like genes: a large-scale study	11
Giants’ cooperation: a draft genome of the giant ciliate Muniziella cunhai suggests its ecological role in the capybara’s digestive metabolism	11
Beyond livestock: the genomic evolution and expansion of MRSA CC398 as a healthcare- and community-associated pathogen (2017–2024)	11
Taking hospital pathogen surveillance to the next level	11
Dual RNA isolation from blood: an optimized protocol for host and bacterial RNA purification for dual RNA-sequencing analysis in whole blood sepsis samples	11
Identification of essential genes in Coxiella burnetii	11
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022	11
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach	11
20 years later: unravelling the genomic success of New Zealand’s home-grown AK3 community-associated methicillin-resistant Staphylococcus aureus	10
Genomic epidemiology and the evolution of erm(B)-mediated macrolide resistance in Campylobacter	10
Increased clonality among Neisseria gonorrhoeae isolates during the COVID-19 pandemic in Amsterdam, the Netherlands	10
Comprehensive analysis of molecular epidemiological characteristics of Morganella intermedius: a novel genospecies of Morganella morganii frequently isolated from environmental sources	10
Comparative transcriptomics reveals context- and strain-specific regulatory programmes of Agrobacterium during plant colonization	10
Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models	10
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing	10
Acinetobacter variabilis represents a diverse species with novel regions associated with antibiotic resistance and surface polysaccharides	10
An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows	10
Novel features of Mycoplasma genitalium genomes identified through Oxford Nanopore sequence analysis of isolates from Australia	10
Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution	10
Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance	10
Are the genomes of motile Aeromonas species from the aquatic environment shaped by local geography and host species?	10
Discovery of a bacteriophage sequence in a mite genome assembly reveals bacterial contamination and opens new possibilities for exploring arthropod symbionts	10
Erratum: Global population structure of Shiga toxin-producing Escherichia coli O103:H2 and the variation in their major virulence factor-encoding genetic elements	10
Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages	10
The macronuclear genomic landscape within Tetrahymena thermophila	10
Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies	10
Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species	9
Matching excellence: Oxford Nanopore Technologies’ rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content	9
From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes	9
In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors	9
Naturally occurring Neisseria gonorrhoeae can have large deletions in housekeeping gene abcZ, making them untypable with multilocus sequence typing	9
Corrigendum: ‘Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae’	9
New isolates from the 1970s to early 2000s provide insights into the evolution of Acinetobacter baumannii international clone 2 and its resistome	9
Use of genome-scale metabolic reconstructions of avian pathogenic Escherichia coli (APEC) phylogroups for the identification of lineage-specific metabolic pathways	9
Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma	9
Revisiting classical Escherichia coli cell division mutants by whole-genome sequencing	9
Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019—2022	9
IS26-mediated plasmid reshuffling results in convergence of toxin–antitoxin systems but loss of resistance genes in XDR Klebsiella pneumoniae from a chronic infection	9
Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations	9
Plasmid conjugation drives within–patient plasmid diversity	9
Chlamydia trachomatis genomes from rectal samples: description of a new clade comprising ompA-genotype L4 from Argentina	9
Genomic analysis of environmentally sourced Stenotrophomonas species from Fiji and Australia	9
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies	9
Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak-associated bacterial isolates in the clinical setting	9
Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258	9
Laboratory strains of Escherichia coli K-12: things are seldom what they seem	9
Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK	8
Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets	8
High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent	8
Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India	8
ChiVariARIBA: a modular, editable workflow and database for characterising chitin gene variation in Vibrio spp. and related bacteria	8
Population genomic variation in Staphylococcus aureus isolates from carriage and disease in Indigenous communities in the Southwest United States	8
Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis	8
Genomic surveillance of multidrug-resistant Klebsiella in Wales reveals persistent spread of Klebsiella pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids	8
Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives	8

Corrigendum: Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli	8
Salmonella bloodstream infection and concurrent intestinal colonization in children with severe acute malnutrition in Niger	8
Genomic diversity of non-typhoidal Salmonella found in patients suffering from gastroenteritis in Norfolk, UK	8
Genomic characterization of enterohaemolysin-encoding haemolytic Escherichia coli of animal and human origin	8
Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages	8
Genomic epidemiology of a Bacillus cereus bacteraemia outbreak linked to contaminated hospital laundry	8
Serotype replacement and mobile genetic elements in Streptococcus pneumoniae: a systematic review	8
A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression	8
Five centuries of genome evolution and multi-host adaptation of Campylobacter jejuni in Brazil	8
Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam	8
Genomics reveals multiple introductions of the seventh pandemic Vibrio cholerae O1 El Tor lineage into Iran since 1965	8
Exploring the microbial communities in coastal cenote and their hidden biotechnological potential	8
Endemic erythromycin resistant Corynebacterium diphtheriae in Vietnam in the 1990s	8
Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years	7
Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993–2019	7
Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST	7
Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages	7
Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers	7
Cappable-Seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia	7
Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011–2018 determined through whole-genome sequencing	7
The natural history of the emergence of sexually transmissible shigellosis	7
Vibrio cholerae O37: one of the exceptions that prove the rule	7
Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria	7
Emergence of multidrug-resistant blaCTX-M-65/gyrA_D87Y clones among the circulating Salmonella Infantis population in Mexico	7
Evolving strategies for virus discovery	7
Parallel genetic adaptation of Bacillus subtilis to different plant species	7
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies	7
Genomic surveillance reveals long-term endemicity and outbreak potential of Klebsiella pneumoniae sequence type 48 in a German hospital and its global context	7
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families	7
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons	7
Enteric microbiome and obesity: a multidimensional narrative review	7
Towards accurate genomic detection of fungal antimicrobial resistance: progress in fungal resistance databases and bioinformatic tools	7
Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023	7
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019	7
Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa	7
Natural variation of the streptococcal group A carbohydrate biosynthesis genes impacts host–pathogen interaction	7
Biodiscovery of Actinomycetota through metabolo-genomics reveals functional diversity across contrasting Mexican ecosystems	7
Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato	7
Mobile genetic element-driven genomic changes in a community-associated methicillin-resistant Staphylococcus aureus clone during its transmission in a regional community outbreak in Japan	7
Insights into microbial dysbiosis and Cutibacterium acnes CAMP factor interactions in acne vulgaris	7
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing	7
Dynamics of a large multidrug-resistant plasmid encoding New Delhi metallo-β-lactamase-1 and oxacillinase-58 carbapenemases in Acinetobacter baumannii clinical isolates from a tertiary hospital in Mal	7
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	7
Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae bloodstream infections from Aberdeen, Scotland, and their comparison to isolates from England	7
Epidemiological characterization and phylogenetic analysis of human metapneumovirus isolated from children in Ningbo, China, 2020–2024	7
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses	7
IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli	7
Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)	7
Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota	7
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum	7
Genomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa	7
Leveraging comparative genomics to uncover alien genes in bacterial genomes	7
Public and patient involvement: exploring public partnership in pathogen whole-genome sequencing research and its data visualisation	7
Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh	7
Oxford nanopore sequencing as a useful tool for investigating the population dynamics of invasive begomoviruses in Sicily	7
A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco	7
Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae	7
Lung microbiome dynamics in health and lung cancer	7
Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France	7
The pQBR mercury resistance plasmids: a model set of sympatric environmental mobile genetic elements	6
Erratum: Host–virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier	6
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli	6
Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK	6
The dynamics of the microbiome in Ixodidae are shaped by tick ontogeny and pathogens in Sarawak, Malaysian Borneo	6
Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria	6
BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata	6
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli	6
Erratum: Cappable-seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia	6
Genome analysis of Neisseria gonorrhoeae in Norway, 2016–2023, reveals shifting epidemiology in the wake of the COVID-19 pandemic	6
Whole-genome sequencing of Staphylococcus capitis isolates from neonates with healthcare-associated bacteraemia in neonatal intensive care units in Taiwan: comparison between the NRCS-A strain and a n	6
Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate	6
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.	6
Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis	6
SyFi: generating and using sequence fingerprints to distinguish SynCom isolates	6
A discovery down under: decoding the draft genome sequence of Pantoea stewartii from Australia’s Critically Endangered western ground parrot/kyloring (Pezoporus flaviventris)	6
Diverse genomic landscape of swine influenza A virus in England (2014–2021)	6
Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-su	6
An integrated One Health initiative for pathogen genomic surveillance in the UK	6
Using a combination of short- and long-read sequencing to investigate the diversity in plasmid- and chromosomally encoded extended-spectrum beta-lactamases (ESBLs) in clinical Shigella and Salmonella	6
High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche	6
Phylodynamic analysis of Salmonella Enteritidis ST183 in Aotearoa New Zealand finds no evidence for introduction via European hedgehogs (Erinaceus europaeus)	6
Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity	6
Genome and antibiotic resistance characteristics of Shigella clinical isolates in Fujian Province, Southeast China, 2005–2019	6
A panoramic view of the genomic landscape of the genus Streptomyces	6
The Resistance-Nodulation-Division efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection	6
Direct whole-genome sequencing enables strain typing of unculturable Neisseria meningitidis from oropharyngeal carriage specimens	6
GWarrange: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events	6
Detection of novel Plasmodium falciparum haplotypes under treatment pressure in paediatric severe malaria	6
Comparative genomic analysis of Clostridioides difficile isolates from symptomatic and asymptomatic paediatric patients	6
Phenotypic and genomic analysis of the emerging poultry pathogen Enterococcus cecorum in UK isolates	6
Genomic analysis of the zooplankton-associated pathogenic bacterium Spirobacillus cienkowskii reveals its functional and metabolic capacities	6
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia	6
Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010−2021	6
Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities	6
Putative genome contamination has minimal impact on the GTDB taxonomy	6