Microbial Genomics

Article	Citations
Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/‘magdeburgensis’ complex	355
Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli	134
Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139 Vibrio cholerae in foodborne outbreaks	67
Dairy streptococcal cell wall and exopolysaccharide genome diversity	64
Development and validation of a core-genome multilocus sequence typing scheme for Legionella longbeachae	60
Molecular characterization of Coxsackievirus A2 isolated from hand, foot and mouth disease in eastern China	55
Assessing the safety of microbiome perturbations	51
Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii	49
Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination	47
The primate gut microbiota contributes to interspecific differences in host metabolism	43
Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions	42
Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales	42
Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T)	37
Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly	37
Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus)	33
Identifying gene-level mechanisms of successful dispersal of Vibrio parahaemolyticus during El Niño events	31
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom	31
Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022	31
A metagenomic approach to One Health surveillance of antimicrobial resistance in a UK veterinary centre	30
Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions	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	27
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens	27
Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics	26
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling	25
Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption	25

Birmingham-group IncP-1α plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates	24
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	24
Vibrio cholerae serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965	23
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	23
Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host	23
Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018	22
Temporal dynamics of gene expression during the development of Campylobacter jejuni biofilms	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
Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs	20
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
Population structure and antimicrobial resistance of Corynebacterium diphtheriae in Victoria, Australia	19
No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis	18
Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya	18
Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes	18
Insights into the genomic evolution and the alkali tolerance mechanisms of Agaricus sinodeliciosus by comparative genomic and transcriptomic analyses	18
Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction	18
Fatal affairs – conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales	18
High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy	17
Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics	17
Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK	17
dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data	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
Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution	16
Comparative genomics of ‘Xanthomonas cannabis’ reveals an emerging, diverse pathogen	16
Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen	16
Piperacillin/tazobactam-resistant, cephalosporin-susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types	15
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics	15
Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi	15
A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin	15
Colonization and transmission of Staphylococcus aureus in schools: a citizen science project	15
A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment	15
A new perspective on ancient Mitis group streptococcal genetics	14
ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data	14
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
Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover	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
HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data	14
Single-cell genome analysis of a feminizing Wolbachia in Eurema butterflies reveals a shared origin with male-killing Wolbachia	14
Evolutionary dynamics in the genome of ocular Chlamydia trachomatis strains from Northern Tanzania following mass drug administration	14
Corrigendum: Genomic characterisation of a unique Panton-Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting Australian indige	14
Genomic investigations in animal enteric disease-associated Clostridium perfringens	14
Type I-F CRISPR-associated transposons contribute to genomic plasticity in Shewanella and mediate efficient programmable DNA integration	14
Heritability and gene functions associated with sclerotia formation of Rhizoctonia solani AG-7 using whole genome sequencing and genome-wide association study	14
Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing	14
Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes	14
A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis	13
Global population structure of the Serratia marcescens complex and identification of hospital-adapted lineages in the complex	13
Giants’ cooperation: a draft genome of the giant ciliate Muniziella cunhai suggests its ecological role in the capybara’s digestive metabolism	13

Scalable genotyping of microbial colonies	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
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
Population structure of ocular Streptococcus pneumoniae is highly diverse and formed by lineages that escape current vaccines	13
Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations	13
Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations	13
Identifying large-scale recombination and capsular switching events in Streptococcus agalactiae strains causing disease in adults in the UK between 2014 and 2015	12
Analysis of variola virus molecular evolution suggests an old origin of the virus consistent with historical records	12
Genomic characterization of multidrug-resistant Salmonella serovar Kentucky ST198 isolated in poultry flocks in Spain (2011–2017)	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
Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance	12
Dominance of high-risk clones ST2 and ST571 and the diversity of resistance islands in clinical Acinetobacter baumannii isolates from Hanoi, Vietnam	12
Genomic sentinel surveillance: Salmonella Paratyphi B outbreak in travellers coinciding with a mass gathering in Iraq	12
An imputed ancestral reference genome for the Mycobacterium tuberculosis complex better captures structural genomic diversity for reference-based alignment workflows	12
Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia	12
Unusual SARS-CoV-2 intrahost diversity reveals lineage superinfection	12
The characterization of Moraxella catarrhalis carried in the general population	12
Taking hospital pathogen surveillance to the next level	12
Genetic insights into Shewanella spp., progenitor of the bla OXA-48-like genes: a large-scale study	12
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022	12
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach	12
pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections	11
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing	11
Chlamydia trachomatis genomes from rectal samples: description of a new clade comprising ompA-genotype L4 from Argentina	11
20 years later: unravelling the genomic success of New Zealand’s home-grown AK3 community-associated methicillin-resistant Staphylococcus aureus	11
Genomic and clinical characteristics of campylobacteriosis in Australia	11
Genomic epidemiology and the evolution of erm(B)-mediated macrolide resistance in Campylobacter	11
Identification of essential genes in Coxiella burnetii	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
Corrigendum: ‘Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae’	11
Discovery of a bacteriophage sequence in a mite genome assembly reveals bacterial contamination and opens new possibilities for exploring arthropod symbionts	11
Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma	10
Increased clonality among Neisseria gonorrhoeae isolates during the COVID-19 pandemic in Amsterdam, the Netherlands	10
Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019—2022	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
Comprehensive analysis of molecular epidemiological characteristics of Morganella intermedius: a novel genospecies of Morganella morganii frequently isolated from environmental sources	10
Genomic diversity and antimicrobial resistance among non-typhoidal Salmonella associated with human disease in The Gambia	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
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
Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance	10
Comparative transcriptomics reveals context- and strain-specific regulatory programmes of Agrobacterium during plant colonization	10
Laboratory strains of Escherichia coli K-12: things are seldom what they seem	10
Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species	10
Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages	10
In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors	10
Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa	10
Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution	10
Revisiting classical Escherichia coli cell division mutants by whole-genome sequencing	10
Plasmid conjugation drives within–patient plasmid diversity	10
High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent	9
Hospital outbreak of carbapenem-resistant Enterobacterales associated with a bla OXA-48 plasmid carried mostly by Escherichia coli ST399	9
Endemic erythromycin resistant Corynebacterium diphtheriae in Vietnam in the 1990s	9
Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis	9
Use of genome-scale metabolic reconstructions of avian pathogenic Escherichia coli (APEC) phylogroups for the identification of lineage-specific metabolic pathways	9
Comparative genome analyses of five Vibrio penaeicida strains provide insights into their virulence-related factors	9
Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit	9
ChiVariARIBA: a modular, editable workflow and database for characterising chitin gene variation in Vibrio spp. and related bacteria	9
Exploring the microbial communities in coastal cenote and their hidden biotechnological potential	9
Genomic diversity of non-typhoidal Salmonella found in patients suffering from gastroenteritis in Norfolk, UK	9
Five centuries of genome evolution and multi-host adaptation of Campylobacter jejuni in Brazil	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
Genomics reveals multiple introductions of the seventh pandemic Vibrio cholerae O1 El Tor lineage into Iran since 1965	9
Population genomics of the food-borne pathogen Vibrio fluvialis reveals lineage associated pathogenicity-related genetic elements	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
Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales	9
Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives	9
Serotype replacement and mobile genetic elements in Streptococcus pneumoniae: a systematic review	9
Genomic epidemiology of a Bacillus cereus bacteraemia outbreak linked to contaminated hospital laundry	9
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies	9
Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258	9
Naturally occurring Neisseria gonorrhoeae can have large deletions in housekeeping gene abcZ, making them untypable with multilocus sequence typing	9
Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets	8
Corrigendum: Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli	8
Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India	8
Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam	8
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons	8
Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota	8
Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011–2018 determined through whole-genome sequencing	8

Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage	8
Leveraging comparative genomics to uncover alien genes in bacterial genomes	8
Genomic characterization of enterohaemolysin-encoding haemolytic Escherichia coli of animal and human origin	8
A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression	8
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies	8
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families	8
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum	8
Profiling the plasmid conjugation potential of urinary Escherichia coli	8
Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK	8
Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae bloodstream infections from Aberdeen, Scotland, and their comparison to isolates from England	8
Lung microbiome dynamics in health and lung cancer	8
Cappable-Seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia	8
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019	8
Enteric microbiome and obesity: a multidimensional narrative review	8
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria	7
Natural variation of the streptococcal group A carbohydrate biosynthesis genes impacts host–pathogen interaction	7
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	7
Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023	7
Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area	7
Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi	7
Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA	7
Oxford nanopore sequencing as a useful tool for investigating the population dynamics of invasive begomoviruses in Sicily	7
Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993–2019	7
Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes	7
Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence	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
A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco	7
IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli	7
Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST	7
Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years	7
Vibrio cholerae O37: one of the exceptions that prove the rule	7
Putative genome contamination has minimal impact on the GTDB taxonomy	7
Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France	7
Parallel genetic adaptation of Bacillus subtilis to different plant species	7
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.	7
Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria	7
Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh	7
Insights into microbial dysbiosis and Cutibacterium acnes CAMP factor interactions in acne vulgaris	7
Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa	7
Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers	7
Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages	7
Genome and antibiotic resistance characteristics of Shigella clinical isolates in Fujian Province, Southeast China, 2005–2019	7
A panoramic view of the genomic landscape of the genus Streptomyces	7
Biodiscovery of Actinomycetota through metabolo-genomics reveals functional diversity across contrasting Mexican ecosystems	7
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing	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
Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria	6
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli	6
Phenotypic and genomic analysis of the emerging poultry pathogen Enterococcus cecorum in UK isolates	6
GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes	6
High genomic diversity of Vibrio parahaemolyticus from underexplored tropical northern Australia: a baseline for future surveillance	6
SyFi: generating and using sequence fingerprints to distinguish SynCom isolates	6
An integrated One Health initiative for pathogen genomic surveillance in the UK	6
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses	6
Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)	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
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
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
High-quality genome assembly and comparative analysis reveal extensive genomic variation in Talaromyces marneffei	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
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
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli	6
Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato	6
BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata	6
Genomic variation during culture adaptation of genetically complex Plasmodium falciparum clinical isolates	6
Clonal expansion and rapid characterization of Klebsiella pneumoniae ST1788, an otherwise uncommon strain spreading in Wales, UK	6
Evolution and spread of Xanthomonas citri subsp. citri in the São Paulo, Brazil, citrus belt inferred from 758 novel genomes	6
Compatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis of Listeria monocytogenes	6
High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche	6
Linear plasmids in Klebsiella and other Enterobacteriaceae	6
Genomic analysis of Legionella pneumophila in the drinking water system of a large building over 25 years	6
Erratum: Cappable-seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia	6
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia	6
Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity	6
Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity	6
Genome analysis of Neisseria gonorrhoeae in Norway, 2016–2023, reveals shifting epidemiology in the wake of the COVID-19 pandemic	6
Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010−2021	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
Virulence genes, resistome and mobilome of Streptococcus suis strains isolated in France	5
A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler’s hybrid assemblies	5
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:	5
Comparative genomics of Bordetella pertussis isolates from New Zealand, a country with an uncommonly high incidence of whooping cough	5
A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex	5
Diversity, functional classification and genotyping of SHV β-lactamases in Klebsiella pneumoniae	5
Vibrio aestuarianus clade A and clade B isolates are associated with Pacific oyster (Magallana gigas) disease outbreaks across Ireland	5
Genome-wide fitness analysis identifies genes required for in vitro growth and macrophage infection by African and global epidemic pathovariants of Salmonella enterica Enteritidis	5
Dissecting the genotypic features of a fluoroquinolone-resistant Pseudomonas aeruginosa ST316 sublineage causing ear infections in Shanghai, China	5
Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis	5
Dissemination of carbapenemase-producing Enterobacterales in Ireland from 2012 to 2017: a retrospective genomic surveillance study	5
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	5
AMRColab – a user-friendly antimicrobial resistance detection and visualization tool	5
Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2	5
Widespread sharing of pneumococcal strains in a rural African setting: proximate villages are more likely to share similar strains that are carried at multiple timepoints	5