Microbial Genomics

Article	Citations
Corrigendum: Genomic evolution and local epidemiology of Klebsiella pneumoniae from a major hospital in Beijing, China, over a 15 year period: dissemination of known and novel high-risk clones	513
Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/‘magdeburgensis’ complex	290
Bilateral symmetry of linear streptomycete chromosomes	115
Dairy streptococcal cell wall and exopolysaccharide genome diversity	60
Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139 Vibrio cholerae in foodborne outbreaks	59
Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption	48
Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions	46
Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus)	46
Identifying gene-level mechanisms of successful dispersal of Vibrio parahaemolyticus during El Niño events	41
A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids	35
Genomic comparisons of Escherichia coli ST131 from Australia	34
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae	34
Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022	33
Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii	33
Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive	31
The primate gut microbiota contributes to interspecific differences in host metabolism	30
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling	30
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom	29
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens	29
Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T)	28
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
Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics	26
Assessing the safety of microbiome perturbations	25
Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin	24

Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination	23
Different evolutionary trends form the twilight zone of the bacterial pan-genome	23
Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom	23
Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions	23
Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps	23
Third generation cephalosporin resistance in clinical non-typhoidal Salmonella enterica in Germany and emergence of bla CTX-M-harbouring pESI plasmids	23
Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli	23
A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment	22
Temporal dynamics of gene expression during the development of Campylobacter jejuni biofilms	22
Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs	22
Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi	21
Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen	21
Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018	21
Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK	21
Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment	19
Birmingham-group IncP-1α plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates	19
High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy	19
Vibrio cholerae serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965	19
Insights into the genomic evolution and the alkali tolerance mechanisms of Agaricus sinodeliciosus by comparative genomic and transcriptomic analyses	18
A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin	18
Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host	18
Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi	18
Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya	17
Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution	17
Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes	17
Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction	17
Fatal affairs – conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales	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
dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data	17
GBS-SBG - GBS Serotyping by Genome Sequencing	17
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
Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics	16
Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes	15
Colonization and transmission of Staphylococcus aureus in schools: a citizen science project	15
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations	15
Piperacillin/tazobactam-resistant, cephalosporin-susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types	15
Corrigendum: Genomic characterisation of a unique Panton-Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting Australian indige	15
Population structure of ocular Streptococcus pneumoniae is highly diverse and formed by lineages that escape current vaccines	15
The possible impact of novel mutations in human papillomavirus 52 on the infection characteristics	15
Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways	15
Scalable genotyping of microbial colonies	15
Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes	15
Evolutionary dynamics in the genome of ocular Chlamydia trachomatis strains from Northern Tanzania following mass drug administration	14
Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae	14
Heritability and gene functions associated with sclerotia formation of Rhizoctonia solani AG-7 using whole genome sequencing and genome-wide association study	14
A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis	14
ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data	14
SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments	14
Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover	14
Monkeypox virus: phylogenomics, host–pathogen interactome and mutational cascade	14

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	14
Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing	14
Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems	14
HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data	14
Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex	14
A new perspective on ancient Mitis group streptococcal genetics	14
Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations	13
pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections	13
Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage	13
An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows	13
Genetic insights into Shewanella spp., progenitor of the bla OXA-48-like genes: a large-scale study	13
Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance	13
Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping	13
Revisiting the heterogeneous global genomic population structure of Leishmania infantum	13
Taking hospital pathogen surveillance to the next level	13
Genomic and clinical characteristics of campylobacteriosis in Australia	13
Genomic insights into the diversity, virulence and resistance of Klebsiella pneumoniae extensively drug resistant clinical isolates	13
Identifying large-scale recombination and capsular switching events in Streptococcus agalactiae strains causing disease in adults in the UK between 2014 and 2015	13
The characterization of Moraxella catarrhalis carried in the general population	12
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach	12
The macronuclear genomic landscape within Tetrahymena thermophila	12
Revealing microbial species diversity using sequence capture by hybridization	12
Chlamydia trachomatis genomes from rectal samples: description of a new clade comprising ompA-genotype L4 from Argentina	12
Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)	12
Analysis of variola virus molecular evolution suggests an old origin of the virus consistent with historical records	12
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022	12
Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia	12
Comparative genome analyses of five Vibrio penaeicida strains provide insights into their virulence-related factors	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
Giants’ cooperation: a draft genome of the giant ciliate Muniziella cunhai suggests its ecological role in the capybara’s digestive metabolism	12
Genomic sentinel surveillance: Salmonella Paratyphi B outbreak in travellers coinciding with a mass gathering in Iraq	12
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection	12
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing	12
Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia	12
Identification of essential genes in Coxiella burnetii	12
Increased clonality among Neisseria gonorrhoeae isolates during the COVID-19 pandemic in Amsterdam, the Netherlands	11
Corrigendum: ‘Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae’	11
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies	11
The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps?	11
The roles of antimicrobial resistance, phage diversity, isolation source and selection in shaping the genomic architecture of Bacillus anthracis	11
Population genomics of the food-borne pathogen Vibrio fluvialis reveals lineage associated pathogenicity-related genetic elements	11
Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432	11
Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages	11
Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species	11
In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors	11
Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance	11
Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019—2022	11
Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations	11
SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021	11
Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa	11
Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma	11
Plasmid conjugation drives within–patient plasmid diversity	11
Using whole-genome sequencing to assess the diversity of Paenibacillus larvae within an outbreak and a beekeeping operation	11
Genomic characterization of enterohaemolysin-encoding haemolytic Escherichia coli of animal and human origin	10
Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis	10
Naturally occurring Neisseria gonorrhoeae can have large deletions in housekeeping gene abcZ, making them untypable with multilocus sequence typing	10
The antimicrobial resistance landscape of Neisseria gonorrhoeae in New Zealand from November 2018 to March 2019 and the role of sexual orientation in transmission	10
A Streptococcus pneumoniae lineage usually associated with pneumococcal conjugate vaccine (PCV) serotypes is the most common cause of serotype 35B invasive disease in South Africa, following routine u	10
Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales	10
Exploring the microbial communities in coastal cenote and their hidden biotechnological potential	10
Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit	10
Genomic surveillance of multidrug-resistant Klebsiella in Wales reveals persistent spread of Klebsiella pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids	10
Five centuries of genome evolution and multi-host adaptation of Campylobacter jejuni in Brazil	10
Laboratory strains of Escherichia coli K-12: things are seldom what they seem	10
Endemic erythromycin resistant Corynebacterium diphtheriae in Vietnam in the 1990s	10
Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India	10
IS26-mediated plasmid reshuffling results in convergence of toxin–antitoxin systems but loss of resistance genes in XDR Klebsiella pneumoniae from a chronic infection	10
Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK	10
Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258	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
Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399	9
Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives	9
Leveraging comparative genomics to uncover alien genes in bacterial genomes	9
High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts	9
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families	9
Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area	9
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies	9
Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach	9
High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent	9
Profiling the plasmid conjugation potential of urinary Escherichia coli	9

Corrigendum: Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli	9
Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae bloodstream infections from Aberdeen, Scotland, and their comparison to isolates from England	9
Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota	9
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019	9
Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets	9
Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam	9
ChiVariARIBA: a modular, editable workflow and database for characterising chitin gene variation in Vibrio spp. and related bacteria	9
Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage	9
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons	9
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum	9
A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression	9
Centre-specific bacterial pathogen typing affects infection-control decision making	8
Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993–2019	8
Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa	8
Vibrio cholerae O37: one of the exceptions that prove the rule	8
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses	8
Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers	8
Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years	8
Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011–2018 determined through whole-genome sequencing	8
A panoramic view of the genomic landscape of the genus Streptomyces	8
wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations	8
Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)	8
Genome and antibiotic resistance characteristics of Shigella clinical isolates in Fujian Province, Southeast China, 2005–2019	8
Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh	8
Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria	8
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.	8
Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence	8
Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages	8
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	8
IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli	8
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing	8
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	8
Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium	8
Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes	8
Parallel genetic adaptation of Bacillus subtilis to different plant species	8
Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato	8
Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA	8
Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi	8
Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST	8
Putative genome contamination has minimal impact on the GTDB taxonomy	8
Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France	8
Biomolecule sulphation and novel methylations related to Guillain-Barré syndrome-associated Campylobacter jejuni serotype HS:19	7
Taxonomic distribution of SbmA/BacA and BacA-like antimicrobial peptide transporters suggests independent recruitment and convergent evolution in host–microbe interactions	7
Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways	7
Evolution and spread of Xanthomonas citri subsp. citri in the São Paulo, Brazil, citrus belt inferred from 758 novel genomes	7
BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata	7
Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities	7
GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes	7
The Dynamic Codon Biaser: calculating prokaryotic codon usage biases	7
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia	7
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria	7
A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco	7
Insights into microbial dysbiosis and Cutibacterium acnes CAMP factor interactions in acne vulgaris	7
Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria	7
Detection of novel Plasmodium falciparum haplotypes under treatment pressure in paediatric severe malaria	7
Linear plasmids in Klebsiella and other Enterobacteriaceae	7
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli	7
Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria	7
Genomic analysis of Legionella pneumophila in the drinking water system of a large building over 25 years	7
Flanker: a tool for comparative genomics of gene flanking regions	7
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	7
Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity	7
High-quality genome assembly and comparative analysis reveal extensive genomic variation in Talaromyces marneffei	7
Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010−2021	7
Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k-mers	7
Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications	7
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli	7
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	7
Genetic variation in symbiotic islands of natural variant strains of soybean Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens differing in competitiveness and in the efficiency of nitrogen f	7
Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of Escherichia coli	7
Compatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis of Listeria monocytogenes	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
Bacterial genomic epidemiology with mixed samples	7
Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis	6
Whole-genome sequencing of Western Canadian Borrelia spp. collected from diverse tick and animal hosts reveals short-lived local genotypes interspersed with longer-lived continental genotypes	6
Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough	6
Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications	6
Modelling evolutionary pathways for commensalism and hypervirulence in Neisseria meningitidis	6
Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France	6
Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study	6
Whole set of constitutive promoters for RpoN sigma factor and the regulatory role of its enhancer protein NtrC in Escherichia coli K-12	6
Genomic insights into the beneficial potential of Bifidobacterium and Enterococcus strains isolated from Cameroonian infants	6
AMRColab – a user-friendly antimicrobial resistance detection and visualization tool	6
Vibrio aestuarianus clade A and clade B isolates are associated with Pacific oyster (Magallana gigas) disease outbreaks across Ireland	6
Travel-associated lineages and unique endemic antimicrobial-susceptible lineages of Neisseria gonorrhoeae predominate in Western Australia	6
Evolution and emergence of multidrug-resistant Mycobacterium tuberculosis in Chisinau, Moldova	6
Genomic characterization of a unique Panton–Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting on Australian indigenous commu	6
The pet café is a neglected site for transmission of antimicrobial-resistant Escherichia coli in urban life	6
A global genomic perspective on the multidrug-resistant Streptococcus pneumoniae 15A-CC63 sub-lineage following pneumococcal conjugate vaccine introduction	6
A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler’s hybrid assemblies	6
Global population structure, genomic diversity and carbohydrate fermentation characteristics of clonal complex 119 (CC119), an understudied Shiga toxin-producing E. coli (STEC) lineage including O165:	6
Dissecting the genotypic features of a fluoroquinolone-resistant Pseudomonas aeruginosa ST316 sublineage causing ear infections in Shanghai, China	6
Machine learning prediction of novel pectinolytic enzymes in Aspergillus niger through integrating heterogeneous (post-) genomics data	6
Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis	6
Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK	6