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	418
Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics	253
Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T)	102
Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales	55
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae	51
Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions	45
Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly	44
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom	42
Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom	36
Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/‘magdeburgensis’ complex	31
Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin	30
Bilateral symmetry of linear streptomycete chromosomes	29
Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption	29
Dairy streptococcal cell wall and exopolysaccharide genome diversity	28
Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139 Vibrio cholerae in foodborne outbreaks	27
The primate gut microbiota contributes to interspecific differences in host metabolism	27
Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli	27
Identifying gene-level mechanisms of successful dispersal of Vibrio parahaemolyticus during El Niño events	27
Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus)	26
Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii	24
Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive	24
Achromobacter spp. genetic adaptation in cystic fibrosis	22
Different evolutionary trends form the twilight zone of the bacterial pan-genome	22
Genomic comparisons of Escherichia coli ST131 from Australia	22
Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps	21

A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids	21
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling	21
Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022	21
Third generation cephalosporin resistance in clinical non-typhoidal Salmonella enterica in Germany and emergence of bla CTX-M-harbouring pESI plasmids	21
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens	20
Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution	20
Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination	20
A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment	20
Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions	20
Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya	19
Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen	19
Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways	19
Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018	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	17
A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin	17
Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi	17
dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data	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	17
Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK	17
Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes	16
Vibrio cholerae serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965	15
Fatal affairs – conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales	15
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	15
Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics	15
Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host	15
Birmingham-group IncP-1α plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates	15
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
GBS-SBG - GBS Serotyping by Genome Sequencing	15
Insights into the genomic evolution and the alkali tolerance mechanisms of Agaricus sinodeliciosus by comparative genomic and transcriptomic analyses	15
Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi	15
High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy	15
Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes	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	14
Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex	14
The possible impact of novel mutations in human papillomavirus 52 on the infection characteristics	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	14
Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover	14
Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv	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	13
Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes	13
A new perspective on ancient Mitis group streptococcal genetics	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
Monkeypox virus: phylogenomics, host–pathogen interactome and mutational cascade	13
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations	13
A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis	13
Population structure of ocular Streptococcus pneumoniae is highly diverse and formed by lineages that escape current vaccines	13

SNPPar: identifying convergent evolution and other homoplasies from microbial whole-genome alignments	13
Scalable genotyping of microbial colonies	13
Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad	13
Lipopolysaccharide core type diversity in the Escherichia coli species in association with phylogeny, virulence gene repertoire and distribution of type VI secretion systems	13
Heritability and gene functions associated with sclerotia formation of Rhizoctonia solani AG-7 using whole genome sequencing and genome-wide association study	13
Taking hospital pathogen surveillance to the next level	12
An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows	12
Revisiting the heterogeneous global genomic population structure of Leishmania infantum	12
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022	12
The characterization of Moraxella catarrhalis carried in the general population	12
Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance	12
Giants’ cooperation: a draft genome of the giant ciliate Muniziella cunhai suggests its ecological role in the capybara’s digestive metabolism	12
Genomic and clinical characteristics of campylobacteriosis in Australia	12
Genomic sentinel surveillance: Salmonella Paratyphi B outbreak in travellers coinciding with a mass gathering in Iraq	12
Cryptosporidium felis differs from other Cryptosporidium spp. in codon usage	12
Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia	12
Analysis of variola virus molecular evolution suggests an old origin of the virus consistent with historical records	12
Genomic insights into the diversity, virulence and resistance of Klebsiella pneumoniae extensively drug resistant clinical isolates	12
pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections	12
Identification of essential genes in Coxiella burnetii	11
Identifying large-scale recombination and capsular switching events in Streptococcus agalactiae strains causing disease in adults in the UK between 2014 and 2015	11
Increased clonality among Neisseria gonorrhoeae isolates during the COVID-19 pandemic in Amsterdam, the Netherlands	11
Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance	11
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	11
Cluster-specific gene markers enhance Shigella and enteroinvasive Escherichia coli in silico serotyping	11
Phylogenetic analysis of the salinipostin γ-butyrolactone gene cluster uncovers new potential for bacterial signalling-molecule diversity	11
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing	11
Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019—2022	11
Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432	11
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection	11
bla OXA-48-like genome architecture among carbapenemase-producing Escherichia coli and Klebsiella pneumoniae in the Netherlands	11
Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)	11
Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations	11
The macronuclear genomic landscape within Tetrahymena thermophila	11
In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors	11
Laboratory strains of Escherichia coli K-12: things are seldom what they seem	10
Corrigendum: ‘Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae’	10
Comparative genome analyses of five Vibrio penaeicida strains provide insights into their virulence-related factors	10
SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021	10
Plasmid conjugation drives within–patient plasmid diversity	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
Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives	10
Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales	10
Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma	10
Chlamydia trachomatis genomes from rectal samples: description of a new clade comprising ompA-genotype L4 from Argentina	10
Revealing microbial species diversity using sequence capture by hybridization	10
The roles of antimicrobial resistance, phage diversity, isolation source and selection in shaping the genomic architecture of Bacillus anthracis	10
Using whole-genome sequencing to assess the diversity of Paenibacillus larvae within an outbreak and a beekeeping operation	10
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies	10
High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent	10
Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis	10
Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations	10
Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia	10
Population genomics of the food-borne pathogen Vibrio fluvialis reveals lineage associated pathogenicity-related genetic elements	10
The fall and rise of group B Streptococcus in dairy cattle: reintroduction due to human-to-cattle host jumps?	10
Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa	10
Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages	10
Endemic erythromycin resistant Corynebacterium diphtheriae in Vietnam in the 1990s	10
Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species	10
Streptococcus pneumoniae genomic datasets from an Indian population describing pre-vaccine evolutionary epidemiology using a whole genome sequencing approach	9
Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota	9
Profiling the plasmid conjugation potential of urinary Escherichia coli	9
Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit	9
Genomic characterization of enterohaemolysin-encoding haemolytic Escherichia coli of animal and human origin	9
Five centuries of genome evolution and multi-host adaptation of Campylobacter jejuni in Brazil	9
Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India	9
A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression	9
Leveraging comparative genomics to uncover alien genes in bacterial genomes	9
Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage	9
Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam	9
The antimicrobial resistance landscape of Neisseria gonorrhoeae in New Zealand from November 2018 to March 2019 and the role of sexual orientation in transmission	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
Exploring the microbial communities in coastal cenote and their hidden biotechnological potential	9
Potential syntrophic relationship between coral-associated Prosthecochloris and its companion sulfate-reducing bacterium unveiled by genomic analysis	9
IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli	9
Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers	9
Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK	9
Naturally occurring Neisseria gonorrhoeae can have large deletions in housekeeping gene abcZ, making them untypable with multilocus sequence typing	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
Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258	9

Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399	9
Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets	8
Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi	8
Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages	8
wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations	8
Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France	8
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families	8
Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato	8
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.	8
Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011–2018 determined through whole-genome sequencing	8
Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area	8
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	8
Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh	8
Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years	8
Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)	8
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum	8
Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity	8
Corrigendum: Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli	8
High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts	8
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies	8
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019	8
Vibrio cholerae O37: one of the exceptions that prove the rule	8
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons	8
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria	8
Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST	8
A panoramic view of the genomic landscape of the genus Streptomyces	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
The Dynamic Codon Biaser: calculating prokaryotic codon usage biases	7
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli	7
Putative genome contamination has minimal impact on the GTDB taxonomy	7
Genome and antibiotic resistance characteristics of Shigella clinical isolates in Fujian Province, Southeast China, 2005–2019	7
Centre-specific bacterial pathogen typing affects infection-control decision making	7
Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa	7
Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium	7
A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco	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
Flanker: a tool for comparative genomics of gene flanking regions	7
Parallel genetic adaptation of Bacillus subtilis to different plant species	7
Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA	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
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses	7
Bacterial genomic epidemiology with mixed samples	7
Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes	7
Genome placement of alpha-haemolysin cluster is associated with alpha-haemolysin sequence variation, adhesin and iron acquisition factor profile of Escherichia coli	7
Biomolecule sulphation and novel methylations related to Guillain-Barré syndrome-associated Campylobacter jejuni serotype HS:19	7
Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence	7
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing	7
Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993–2019	7
GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes	6
Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways	6
Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria	6
Evaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations	6
Population structure, serotype distribution and antibiotic resistance of Streptococcus pneumoniae causing invasive disease in Victoria, Australia	6
Diverse mobile genetic elements shaped the evolution of Streptomyces virulence	6
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia	6
Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k-mers	6
Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates	6
Genomic study of European Clostridioides difficile ribotype 002/sequence type 8	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
Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010−2021	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
Multi-laboratory evaluation of the Illumina iSeq platform for whole genome sequencing of Salmonella, Escherichia coli and Listeria	6
Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health	6
Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis	6
Taxonomic distribution of SbmA/BacA and BacA-like antimicrobial peptide transporters suggests independent recruitment and convergent evolution in host–microbe interactions	6
Evaluation of tangential flow filtration coupled to long-read sequencing for ostreid herpesvirus type 1 genome assembly	6
Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications	6
Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK	6
GWarrange: a pre- and post- genome-wide association studies pipeline for detecting phenotype-associated genome rearrangement events	6
The dynamics of the microbiome in Ixodidae are shaped by tick ontogeny and pathogens in Sarawak, Malaysian Borneo	6
High-quality genome assembly and comparative analysis reveal extensive genomic variation in Talaromyces marneffei	6
Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities	6
Experimental evolution in morbidostat reveals converging genomic trajectories on the path to triclosan resistance	6
BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata	6
Investigation into the effect of mannan-rich fraction supplementation on the metagenome of broiler chickens	6
Comparison of direct cDNA and PCR-cDNA Nanopore sequencing of RNA from Escherichia coli isolates	6
Accuracy of an amplicon-sequencing nanopore approach to identify variants in tuberculosis drug-resistance-associated genes	6
Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study	6
Evolution and spread of Xanthomonas citri subsp. citri in the São Paulo, Brazil, citrus belt inferred from 758 novel genomes	6
Linear plasmids in Klebsiella and other Enterobacteriaceae	6
A critical role for iron and zinc homeostatic systems in the evolutionary adaptation of Escherichia coli to metal restriction	6
Model-driven characterization of functional diversity of Pseudomonas aeruginosa clinical isolates with broadly representative phenotypes	6
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli	6
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	6