Microbial Genomics

Article	Citations
Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/‘magdeburgensis’ complex	83
Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139 Vibrio cholerae in foodborne outbreaks	79
Development and validation of a core-genome multilocus sequence typing scheme for Legionella longbeachae	77
Molecular characterization of Coxsackievirus A2 isolated from hand, foot and mouth disease in eastern China	74
Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions	69
Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions	57
Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales	51
Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T)	46
Identifying gene-level mechanisms of successful dispersal of Vibrio parahaemolyticus during El Niño events	44
Comparative genomics of a poinsettia-associated phytoplasma and functional validation of its SAP11-homologous effectors that induce plant branching	43
Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii	41
Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly	41
Genomic features of pneumococcal strains isolated from paediatric patients with invasive disease during pneumococcal conjugate vaccine introduction in Lima, Peru	37
Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus)	32
Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022	31
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom	31
The primate gut microbiota contributes to interspecific differences in host metabolism	31
Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli	31
A metagenomic approach to One Health surveillance of antimicrobial resistance in a UK veterinary centre	30
Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination	28
Assessing the safety of microbiome perturbations	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	26
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens	26
Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics	26
Birmingham-group IncP-1α plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates	25

On the limits of 16S rRNA gene-based metagenome prediction and functional profiling	25
Vibrio cholerae serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965	24
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics	22
Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen	21
Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways	20
Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics	20
Harnessing gastrointestinal microbial co-association networks to predict feed efficiency and methane emissions across beef and dairy cattle	20
A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin	20
Global population structure of Shiga toxin-producing Escherichia coli O103:H2 and the variation in their major virulence factor-encoding genetic elements	19
High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy	19
Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018	19
Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes	19
Canine Providencia alcalifaciens: virulence factors and phylogenetic analysis of an emerging enteropathogen	19
Population structure and antimicrobial resistance of Corynebacterium diphtheriae in Victoria, Australia	18
A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment	17
Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK	17
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	17
Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya	17
Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host	17
No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis	17
Insights into the genomic evolution and the alkali tolerance mechanisms of Agaricus sinodeliciosus by comparative genomic and transcriptomic analyses	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	16
Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi	16
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	16
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	16
Pathogenic potential and phylogenomic analysis of stx2-carrying O26:H11 Shiga toxin-producing Escherichia coli isolated from dairy products in France (2014–2024)	16
Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment	15
Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs	15
dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data	15
Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction	15
Single-cell genome analysis of a feminizing Wolbachia in Eurema butterflies reveals a shared origin with male-killing Wolbachia	14
Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae	14
The possible impact of novel mutations in human papillomavirus 52 on the infection characteristics	14
Scalable genotyping of microbial colonies	14
Comparative genomics of ‘Xanthomonas cannabis’ reveals an emerging, diverse pathogen	14
Heritability and gene functions associated with sclerotia formation of Rhizoctonia solani AG-7 using whole genome sequencing and genome-wide association study	14
Corrigendum: Genomic characterisation of a unique Panton-Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting Australian indige	14
Aneuploidy, polyploidy and loss of heterozygosity distinguish serial bloodstream isolates of Candida albicans	14
Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases	14
A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis	14
Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes	14
An integrated multi-omic approach for discovery and dereplication of bioactive microbial natural products	14
Monkeypox virus: phylogenomics, host–pathogen interactome and mutational cascade	14
Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing	14
Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover	14
Temporal dynamics of gene expression during the development of Campylobacter jejuni biofilms	14
HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data	14
ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data	13
Type I-F CRISPR-associated transposons contribute to genomic plasticity in Shewanella and mediate efficient programmable DNA integration	13
Genomic investigations in animal enteric disease-associated Clostridium perfringens	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
Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations	13
Colonization and transmission of Staphylococcus aureus in schools: a citizen science project	13
Evolutionary dynamics in the genome of ocular Chlamydia trachomatis strains from Northern Tanzania following mass drug administration	13
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	13
Genomic sentinel surveillance: Salmonella Paratyphi B outbreak in travellers coinciding with a mass gathering in Iraq	12
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022	12
Rapid and recent evolution of fetA phase variability among hyperinvasive MenW:cc11 disease isolates	12
Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes for Escherichia coli sequence type 131 clade C surveillance across infection types	12
The characterization of Moraxella catarrhalis carried in the general population	12
Genomic and clinical characteristics of campylobacteriosis in Australia	12
20 years later: unravelling the genomic success of New Zealand’s home-grown AK3 community-associated methicillin-resistant Staphylococcus aureus	12
Dual RNA isolation from blood: an optimized protocol for host and bacterial RNA purification for dual RNA-sequencing analysis in whole blood sepsis samples	12
pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections	12
Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance	12
‘Vivaldi’: an amplicon-based whole-genome sequencing method for the four seasonal human coronaviruses, 229E, NL63, OC43 and HKU1, alongside SARS-CoV-2	12
Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia	12
Dominance of high-risk clones ST2 and ST571 and the diversity of resistance islands in clinical Acinetobacter baumannii isolates from Hanoi, Vietnam	11
Analysis of variola virus molecular evolution suggests an old origin of the virus consistent with historical records	11
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing	11
Genomic epidemiology and the evolution of erm(B)-mediated macrolide resistance in Campylobacter	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
An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows	11
Taking hospital pathogen surveillance to the next level	11
Discovery of a bacteriophage sequence in a mite genome assembly reveals bacterial contamination and opens new possibilities for exploring arthropod symbionts	11
Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis	11
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach	11
Identification of essential genes in Coxiella burnetii	11
Novel features of Mycoplasma genitalium genomes identified through Oxford Nanopore sequence analysis of isolates from Australia	11
Corrigendum: ‘Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae’	10
Plasmid conjugation drives within–patient plasmid diversity	10
Chlamydia trachomatis genomes from rectal samples: description of a new clade comprising ompA-genotype L4 from Argentina	10
Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance	10
In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors	10
Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma	10
Laboratory strains of Escherichia coli K-12: things are seldom what they seem	10
Are the genomes of motile Aeromonas species from the aquatic environment shaped by local geography and host species?	10
Acinetobacter variabilis represents a diverse species with novel regions associated with antibiotic resistance and surface polysaccharides	10
Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019—2022	10
Comprehensive analysis of molecular epidemiological characteristics of Morganella intermedius: a novel genospecies of Morganella morganii frequently isolated from environmental sources	10
Revisiting classical Escherichia coli cell division mutants by whole-genome sequencing	10
Comparative transcriptomics reveals context- and strain-specific regulatory programmes of Agrobacterium during plant colonization	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
Matching excellence: Oxford Nanopore Technologies’ rise to parity with Pacific Biosciences in genome reconstruction of non-model bacterium with high G+C content	10
Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species	10
Use of genome-scale metabolic reconstructions of avian pathogenic Escherichia coli (APEC) phylogroups for the identification of lineage-specific metabolic pathways	10
Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak-associated bacterial isolates in the clinical setting	10
Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution	10
Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies	10
The macronuclear genomic landscape within Tetrahymena thermophila	10
Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models	10
Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages	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
Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India	9
Population genomic variation in Staphylococcus aureus isolates from carriage and disease in Indigenous communities in the Southwest United States	9
Genomic diversity of non-typhoidal Salmonella found in patients suffering from gastroenteritis in Norfolk, UK	9
Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK	9
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies	9
Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations	9
Naturally occurring Neisseria gonorrhoeae can have large deletions in housekeeping gene abcZ, making them untypable with multilocus sequence typing	9
Genomics reveals multiple introductions of the seventh pandemic Vibrio cholerae O1 El Tor lineage into Iran since 1965	9
Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis	9
High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent	9
Increased clonality among Neisseria gonorrhoeae isolates during the COVID-19 pandemic in Amsterdam, the Netherlands	9
Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258	9
ChiVariARIBA: a modular, editable workflow and database for characterising chitin gene variation in Vibrio spp. and related bacteria	9
Genomic surveillance of multidrug-resistant Klebsiella in Wales reveals persistent spread of Klebsiella pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids	9
Genomic epidemiology of a Bacillus cereus bacteraemia outbreak linked to contaminated hospital laundry	9
Endemic erythromycin resistant Corynebacterium diphtheriae in Vietnam in the 1990s	9
Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam	8
Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives	8
Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages	8
A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression	8
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons	8
Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages	8
IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli	8
Profiling the plasmid conjugation potential of urinary Escherichia coli	8
Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit	8
Five centuries of genome evolution and multi-host adaptation of Campylobacter jejuni in Brazil	8

Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets	8
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families	8
Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area	8
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies	8
Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011–2018 determined through whole-genome sequencing	8
Corrigendum: Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli	8
Serotype replacement and mobile genetic elements in Streptococcus pneumoniae: a systematic review	8
Exploring the microbial communities in coastal cenote and their hidden biotechnological potential	8
Genomic characterization of enterohaemolysin-encoding haemolytic Escherichia coli of animal and human origin	8
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum	8
Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers	8
Enteric microbiome and obesity: a multidimensional narrative review	8
Cappable-Seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia	8
Oxford nanopore sequencing as a useful tool for investigating the population dynamics of invasive begomoviruses in Sicily	7
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	7
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses	7
Lung microbiome dynamics in health and lung cancer	7
The risk of pig and chicken farming for carriage and transmission of Escherichia coli containing extended-spectrum beta-lactamase (ESBL) and mobile colistin resistance (mcr) genes in Thailand	7
A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco	7
Vibrio cholerae O37: one of the exceptions that prove the rule	7
Natural variation of the streptococcal group A carbohydrate biosynthesis genes impacts host–pathogen interaction	7
Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity	7
The natural history of the emergence of sexually transmissible shigellosis	7
Leveraging comparative genomics to uncover alien genes in bacterial genomes	7
Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)	7
Insights into microbial dysbiosis and Cutibacterium acnes CAMP factor interactions in acne vulgaris	7
Parallel genetic adaptation of Bacillus subtilis to different plant species	7
Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993–2019	7
Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota	7
Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate	7
Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years	7
Biodiscovery of Actinomycetota through metabolo-genomics reveals functional diversity across contrasting Mexican ecosystems	7
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019	7
Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France	7
Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST	7
Genome and antibiotic resistance characteristics of Shigella clinical isolates in Fujian Province, Southeast China, 2005–2019	7
Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023	7
Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae bloodstream infections from Aberdeen, Scotland, and their comparison to isolates from England	7
High-quality genome assembly and comparative analysis reveal extensive genomic variation in Talaromyces marneffei	6
High genomic diversity of Vibrio parahaemolyticus from underexplored tropical northern Australia: a baseline for future surveillance	6
Metagenomic identification of disease-causing Salmonella enterica serovars and antimicrobial resistance genes from paediatric faecal samples	6
Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK	6
Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity	6
Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria	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
bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization	6
High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche	6
BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata	6
Compatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis of Listeria monocytogenes	6
SyFi: generating and using sequence fingerprints to distinguish SynCom isolates	6
Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato	6
Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria	6
An integrated One Health initiative for pathogen genomic surveillance in the UK	6
Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae	6
Genomic analysis of the zooplankton-associated pathogenic bacterium Spirobacillus cienkowskii reveals its functional and metabolic capacities	6
Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities	6
Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k-mers	6
The pet café is a neglected site for transmission of antimicrobial-resistant Escherichia coli in urban life	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
Genome analysis of Neisseria gonorrhoeae in Norway, 2016–2023, reveals shifting epidemiology in the wake of the COVID-19 pandemic	6
Phenotypic and genomic analysis of the emerging poultry pathogen Enterococcus cecorum in UK isolates	6
Genomic analysis of Legionella pneumophila in the drinking water system of a large building over 25 years	6
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia	6
Erratum: Cappable-seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia	6
Erratum: Host–virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier	6
A panoramic view of the genomic landscape of the genus Streptomyces	6
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria	6
Comparative genomic analysis of Clostridioides difficile isolates from symptomatic and asymptomatic paediatric patients	6
Emergence of multidrug-resistant blaCTX-M-65/gyrA_D87Y clones among the circulating Salmonella Infantis population in Mexico	6
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli	6
Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa	6
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	6
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli	6
Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly	6
Direct whole-genome sequencing enables strain typing of unculturable Neisseria meningitidis from oropharyngeal carriage specimens	6
Putative genome contamination has minimal impact on the GTDB taxonomy	6
GWarrange: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events	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
Whole-genome sequencing and bioinformatic tools powered by machine learning to identify antibiotic-resistant genes and virulence factors in Escherichia coli from sepsis	6
Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010−2021	6
GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes	6
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing	6
The Resistance-Nodulation-Division efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection	6
Genomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa	6
Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh	6
Phylodynamic analysis of Salmonella Enteritidis ST183 in Aotearoa New Zealand finds no evidence for introduction via European hedgehogs (Erinaceus europaeus)	6
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	6
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.	6