Microbial Genomics

Article	Citations
Genomic and pathogenicity analyses to identify the causative agent from multiple serogroups of non-O1, non-O139 Vibrio cholerae in foodborne outbreaks	90
Development and validation of a core-genome multilocus sequence typing scheme for Legionella longbeachae	89
Molecular characterization of Coxsackievirus A2 isolated from hand, foot and mouth disease in eastern China	83
Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions	76
Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales	58
Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T)	54
Identifying gene-level mechanisms of successful dispersal of Vibrio parahaemolyticus during El Niño events	44
Comparative genomics of a poinsettia-associated phytoplasma and functional validation of its SAP11-homologous effectors that induce plant branching	43
Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii	41
Genomic features of pneumococcal strains isolated from paediatric patients with invasive disease during pneumococcal conjugate vaccine introduction in Lima, Peru	41
Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus)	40
The primate gut microbiota contributes to interspecific differences in host metabolism	32
Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022	32
Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive	32
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom	31
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling	31
Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions	31
A metagenomic approach to One Health surveillance of antimicrobial resistance in a UK veterinary centre	30
Assessing the safety of microbiome perturbations	27
Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination	27
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens	26
Genomic comparison of clinical strains of Mycobacterium shinjukuense in Japan reveals low diversity and stable genome structures	26
First report of a nosocomial outbreak of ST101 Klebsiella pneumoniae carrying bla OXA-48 in Shandong, China	25
Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli	25
Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics	23

Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly	23
Vibrio cholerae serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965	22
Birmingham-group IncP-1α plasmids revisited: RP4, RP1 and RK2 are identical and their remnants can be detected in environmental isolates	22
Genomic resistance in historical clinical isolates increased in frequency and mobility after the age of antibiotics	21
Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen	21
Harnessing gastrointestinal microbial co-association networks to predict feed efficiency and methane emissions across beef and dairy cattle	20
Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes	20
Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways	20
A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin	20
High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy	19
Canine Providencia alcalifaciens: virulence factors and phylogenetic analysis of an emerging enteropathogen	18
Temporal dynamics of gene expression during the development of Campylobacter jejuni biofilms	17
Population structure and antimicrobial resistance of Corynebacterium diphtheriae in Victoria, Australia	17
Global population structure of Shiga toxin-producing Escherichia coli O103:H2 and the variation in their major virulence factor-encoding genetic elements	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
Comparative genomics of ‘Xanthomonas cannabis’ reveals an emerging, diverse pathogen	17
Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs	17
Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018	17
A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment	16
Genome-wide characterization of sulphur metabolism gene families and recombination dynamics in mangrove-derived Bacillus aryabhattai NM1-A2 and Bacillus cereus NR1	16
Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host	16
Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction	16
No innocent bystanders: pertussis vaccination and evolutionary parallelisms between Bordetella parapertussis and Bordetella pertussis	16
Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya	16
Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment	16
IME_Rho_tet, a novel family of putative integrative mobilizable elements spreading tetracycline resistance genes tet(W) and tet(32) among human and animal gut bacteria	15
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	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
Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK	15
Enteric fever cluster identification in South Africa using genomic surveillance of Salmonella enterica serovar Typhi	15
Insights into the genomic evolution and the alkali tolerance mechanisms of Agaricus sinodeliciosus by comparative genomic and transcriptomic analyses	15
Pathogenic potential and phylogenomic analysis of stx2-carrying O26:H11 Shiga toxin-producing Escherichia coli isolated from dairy products in France (2014–2024)	15
An integrated multi-omic approach for discovery and dereplication of bioactive microbial natural products	14
The possible impact of novel mutations in human papillomavirus 52 on the infection characteristics	14
A host shift as the origin of tomato bacterial canker caused by Clavibacter michiganensis	14
Corrigendum: Genomic characterisation of a unique Panton-Valentine leucocidin-positive community-associated methicillin-resistant Staphylococcus aureus lineage increasingly impacting Australian indige	14
Type I-F CRISPR-associated transposons contribute to genomic plasticity in Shewanella and mediate efficient programmable DNA integration	14
Monkeypox virus: phylogenomics, host–pathogen interactome and mutational cascade	14
Integration of bioinformatic tools for the detection of SARS-CoV-2 co-infection cases	14
Systematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes	14
Heritability and gene functions associated with sclerotia formation of Rhizoctonia solani AG-7 using whole genome sequencing and genome-wide association study	14
Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover	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	13
Aneuploidy, polyploidy and loss of heterozygosity distinguish serial bloodstream isolates of Candida albicans	13
Sulphur metabolism as a key factor in the evolution of environmental adaptation of Acidihalobacter	13
Conserved patterns of sequence diversification provide insight into the evolution of two-component systems in Enterobacteriaceae	13
ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data	13
Scalable genotyping of microbial colonies	13

Colonization and transmission of Staphylococcus aureus in schools: a citizen science project	13
Genomic investigations in animal enteric disease-associated Clostridium perfringens	13
Split k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospi	13
Reconstructing NOD-like receptor alleles with high internal conservation in Podospora anserina using long-read sequencing	13
Genomic surveillance identifies SARS-CoV-2 transmission patterns in local university populations, Wisconsin, USA, 2020–2022	12
Genomic and clinical characteristics of campylobacteriosis in Australia	12
20 years later: unravelling the genomic success of New Zealand’s home-grown AK3 community-associated methicillin-resistant Staphylococcus aureus	12
Genomic signatures of dominant clones and evolutionary divergence of Acinetobacter baumannii in Thailand	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
Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes for Escherichia coli sequence type 131 clade C surveillance across infection types	12
Genomic characterization of respiratory syncytial virus genotypes circulating in the paediatric population of Sydney, NSW, Australia	12
Evidence of potential Campylobacter jejuni zooanthroponosis in captive macaque populations	12
Comparative genome analysis of human pathogen Parvimonas micra revealed strain JM503A as potential novel species in the genus Parvimonas and high intra-species functional diversity	12
Bioinformatic investigation of discordant sequence data for SARS-CoV-2: insights for robust genomic analysis during pandemic surveillance	12
Vitamin B12-associated interactions between Mesorhizobium sp. TaiHu and Synechococcus sp. PCC 7002 revealed by multi-omics analysis	12
HAIviz: an interactive dashboard for visualising and integrating healthcare-associated genomic epidemiological data	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	11
An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in Mycobacterium tuberculosis using a reproducible algorithmic approach	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
Taking hospital pathogen surveillance to the next level	11
Rapid and recent evolution of fetA phase variability among hyperinvasive MenW:cc11 disease isolates	11
Giants’ cooperation: a draft genome of the giant ciliate Muniziella cunhai suggests its ecological role in the capybara’s digestive metabolism	11
Identification of essential genes in Coxiella burnetii	11
Analysis of variola virus molecular evolution suggests an old origin of the virus consistent with historical records	11
Dominance of high-risk clones ST2 and ST571 and the diversity of resistance islands in clinical Acinetobacter baumannii isolates from Hanoi, Vietnam	11
Evaluation of the accuracy of bacterial genome reconstruction with Oxford Nanopore R10.4.1 long-read-only sequencing	11
Genetic insights into Shewanella spp., progenitor of the bla OXA-48-like genes: a large-scale study	11
Genomic epidemiology and the evolution of erm(B)-mediated macrolide resistance in Campylobacter	10
Revisiting classical Escherichia coli cell division mutants by whole-genome sequencing	10
Comparative transcriptomics reveals context- and strain-specific regulatory programmes of Agrobacterium during plant colonization	10
Corrigendum: ‘Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae’	10
Phylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species	10
Comprehensive analysis of molecular epidemiological characteristics of Morganella intermedius: a novel genospecies of Morganella morganii frequently isolated from environmental sources	10
Erratum: Global population structure of Shiga toxin-producing Escherichia coli O103:H2 and the variation in their major virulence factor-encoding genetic elements	10
Discovery of a bacteriophage sequence in a mite genome assembly reveals bacterial contamination and opens new possibilities for exploring arthropod symbionts	10
Pan-genomic characterization and structural variant analysis reveal insights into spore development and species diversity in Ganoderma	10
Population structure of Mycobacterium avium subsp. hominissuis provides new insights into genomic evolution	10
Decoding the interconnected splicing patterns of hepatitis B virus and host using large language and deep learning models	10
The macronuclear genomic landscape within Tetrahymena thermophila	10
pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections	10
Novel features of Mycoplasma genitalium genomes identified through Oxford Nanopore sequence analysis of isolates from Australia	10
Acinetobacter variabilis represents a diverse species with novel regions associated with antibiotic resistance and surface polysaccharides	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
Plasmid conjugation drives within–patient plasmid diversity	10
Expanded roles of lactate-sensing LldR in transcription regulation of the Escherichia coli K-12 genome: lactate utilisation and acid resistance	10
The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies	9
Increased clonality among Neisseria gonorrhoeae isolates during the COVID-19 pandemic in Amsterdam, the Netherlands	9
Chlamydia trachomatis genomes from rectal samples: description of a new clade comprising ompA-genotype L4 from Argentina	9
From classification to confirmation: verifying taxonomic classifications by mapping metagenomic reads to reference genomes	9
Naturally occurring Neisseria gonorrhoeae can have large deletions in housekeeping gene abcZ, making them untypable with multilocus sequence typing	9
Genomic diversity and epidemiological significance of non-typhoidal Salmonella found in retail food collected in Norfolk, UK	9
Exploring the microbial communities in coastal cenote and their hidden biotechnological potential	9
Global phylogenomic analysis of Staphylococcus pseudintermedius reveals genomic and prophage diversity in multidrug-resistant lineages	9
Evaluation of Oxford Nanopore Technologies workflows for genomic epidemiology of outbreak-associated bacterial isolates in the clinical setting	9
Use of genome-scale metabolic reconstructions of avian pathogenic Escherichia coli (APEC) phylogroups for the identification of lineage-specific metabolic pathways	9
Laboratory strains of Escherichia coli K-12: things are seldom what they seem	9
ChiVariARIBA: a modular, editable workflow and database for characterising chitin gene variation in Vibrio spp. and related bacteria	9
Population genomic variation in Staphylococcus aureus isolates from carriage and disease in Indigenous communities in the Southwest United States	9
Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis	9
Phylogenomic analysis of the genus Delftia reveals distinct major lineages with ecological specializations	9
Are the genomes of motile Aeromonas species from the aquatic environment shaped by local geography and host species?	9
Implementation of national whole-genome sequencing of Mycobacterium tuberculosis, National Public Health Laboratory, Singapore, 2019—2022	9
In silico investigation of the genus Campylobacter type VI secretion system reveals genetic diversity in organization and putative effectors	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
Genomics reveals multiple introductions of the seventh pandemic Vibrio cholerae O1 El Tor lineage into Iran since 1965	9
Exploring the IS-capades of Klebsiella pneumoniae: insertion sequences drive metabolic loss in obscure sub-lineages	9
Subinhibitory antibiotic concentrations promote the excision of a genomic island carried by the globally spread carbapenem-resistant Klebsiella pneumoniae sequence type 258	9
Corrigendum: Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli	8
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons	8
Genomic epidemiology of a Bacillus cereus bacteraemia outbreak linked to contaminated hospital laundry	8
Endemic erythromycin resistant Corynebacterium diphtheriae in Vietnam in the 1990s	8
Genomic characterization of enterohaemolysin-encoding haemolytic Escherichia coli of animal and human origin	8
Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam	8
Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets	8
Five centuries of genome evolution and multi-host adaptation of Campylobacter jejuni in Brazil	8
Genomic surveillance of multidrug-resistant Klebsiella in Wales reveals persistent spread of Klebsiella pneumoniae ST307 and adaptive evolution of pOXA-48-like plasmids	8
Serotype replacement and mobile genetic elements in Streptococcus pneumoniae: a systematic review	8
Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India	8

Genome sequencing and multifaceted taxonomic analysis of novel strains of violacein-producing bacteria and non-violacein-producing close relatives	8
A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression	8
High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent	8
Whole-genome sequencing enhances existing pathogen and antimicrobial-resistance surveillance schemes within a neonatal unit	8
Genomic diversity of non-typhoidal Salmonella found in patients suffering from gastroenteritis in Norfolk, UK	8
IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli	7
Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota	7
Lung microbiome dynamics in health and lung cancer	7
Dynamics of a large multidrug-resistant plasmid encoding New Delhi metallo-β-lactamase-1 and oxacillinase-58 carbapenemases in Acinetobacter baumannii clinical isolates from a tertiary hospital in Mal	7
Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh	7
Bioinformatic discovery of type 11 secretion system (T11SS) cargo across the Proteobacteria	7
Genomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993–2019	7
Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato	7
Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST	7
Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area	7
Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers	7
Towards accurate genomic detection of fungal antimicrobial resistance: progress in fungal resistance databases and bioinformatic tools	7
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies	7
Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages	7
Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)	7
Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France	7
Oxford nanopore sequencing as a useful tool for investigating the population dynamics of invasive begomoviruses in Sicily	7
Genomic surveillance of Salmonella enterica serotype Minnesota strains from poultry products imported into South Africa	7
Vibrio cholerae O37: one of the exceptions that prove the rule	7
Natural variation of the streptococcal group A carbohydrate biosynthesis genes impacts host–pathogen interaction	7
Leveraging comparative genomics to uncover alien genes in bacterial genomes	7
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019	7
Plasmid genomic epidemiology of bla NDM carbapenemase-producing Enterobacterales in Canada from 2010 to 2023	7
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	7
Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011–2018 determined through whole-genome sequencing	7
Cappable-Seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia	7
Molecular epidemiology of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae bloodstream infections from Aberdeen, Scotland, and their comparison to isolates from England	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
Putative genome contamination has minimal impact on the GTDB taxonomy	7
The natural history of the emergence of sexually transmissible shigellosis	7
Tn4661-mediated transfer of bla CTX-M-15 from Klebsiella michiganensis to an outbreak clone of Pseudomonas aeruginosa	7
Genome and antibiotic resistance characteristics of Shigella clinical isolates in Fujian Province, Southeast China, 2005–2019	7
Biodiscovery of Actinomycetota through metabolo-genomics reveals functional diversity across contrasting Mexican ecosystems	7
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum	7
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families	7
Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years	7
Enteric microbiome and obesity: a multidimensional narrative review	7
The dynamics of the microbiome in Ixodidae are shaped by tick ontogeny and pathogens in Sarawak, Malaysian Borneo	6
Detection of novel Plasmodium falciparum haplotypes under treatment pressure in paediatric severe malaria	6
Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities	6
Genomic analysis of the zooplankton-associated pathogenic bacterium Spirobacillus cienkowskii reveals its functional and metabolic capacities	6
Diverse mobile genetic elements shaped the evolution of Streptomyces virulence	6
Genomic analysis of Legionella pneumophila in the drinking water system of a large building over 25 years	6
Phenotypic and genomic analysis of the emerging poultry pathogen Enterococcus cecorum in UK isolates	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
Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteraemia	6
Independent, ongoing clade-specific expansions of IS5 elements in Pseudomonas syringae	6
Erratum: Host–virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier	6
Insights into microbial dysbiosis and Cutibacterium acnes CAMP factor interactions in acne vulgaris	6
A comparative genomics approach reveals a local genetic signature of Leishmania tropica in Morocco	6
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria	6
BakRep – a searchable large-scale web repository for bacterial genomes, characterizations and metadata	6
Diverse genomic landscape of swine influenza A virus in England (2014–2021)	6
Shared properties of gene transfer agent and core genes revealed by comparative genomics of Alphaproteobacteria	6
A panoramic view of the genomic landscape of the genus Streptomyces	6
Hybrid sequencing reveals incompleteness of the H37Rv reference genome and highlights lineage-specific genomic divergence in Mycobacterium tuberculosis	6
Erratum: Cappable-seq reveals the transcriptional landscape of stress responses in the bacterial endosymbiont Wolbachia	6
SyFi: generating and using sequence fingerprints to distinguish SynCom isolates	6
Plasmid genomic epidemiology of carbapenem-hydrolysing class D β-lactamase (CDHL)-producing Enterobacterales in Canada, 2010−2021	6
bifidoAnnotator: fine-grained annotation of bifidobacterial glycoside hydrolases for human milk glycan utilization	6
Monensin phase-out in Norwegian turkey production decreases Bifidobacterium spp. abundance while enhancing microbial diversity	6
The Resistance-Nodulation-Division efflux pump EefABC is highly conserved within lineages of E. coli commonly associated with infection	6
Prevalence and diversity of TAL effector-like proteins in fungal endosymbiotic Mycetohabitans spp.	6
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	6
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing	6
Discordance between different bioinformatic methods for identifying resistance genes from short-read genomic data, with a focus on Escherichia coli	6
GR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes	6
Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications	6
Comparison of the genetic basis of biofilm formation between Salmonella Typhimurium and Escherichia coli	6
High-quality genome assembly and comparative analysis reveal extensive genomic variation in Talaromyces marneffei	6
Genome analysis of Neisseria gonorrhoeae in Norway, 2016–2023, reveals shifting epidemiology in the wake of the COVID-19 pandemic	6
High-resolution Staphylococcus profiling reveals intra-species diversity in a single skin niche	6
An integrated One Health initiative for pathogen genomic surveillance in the UK	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
Compatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis of Listeria monocytogenes	6
High genomic diversity of Vibrio parahaemolyticus from underexplored tropical northern Australia: a baseline for future surveillance	6
Comparative genomic analysis of Clostridioides difficile isolates from symptomatic and asymptomatic paediatric patients	6
Parallel genetic adaptation of Bacillus subtilis to different plant species	6
Nanopore long-read-only genome assembly of clinical Enterobacterales isolates is complete and accurate	6
Emergence of multidrug-resistant blaCTX-M-65/gyrA_D87Y clones among the circulating Salmonella Infantis population in Mexico	6
Phylodynamic analysis of Salmonella Enteritidis ST183 in Aotearoa New Zealand finds no evidence for introduction via European hedgehogs (Erinaceus europaeus)	6
A practical guide and Galaxy workflow to avoid inter-plasmidic repeat collapse and false gene loss in Unicycler’s hybrid assemblies	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
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
Host interactions of novel Crassvirales species belonging to multiple families infecting bacterial host, Bacteroides cellulosilyticus WH2	5
Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis	5
AMRColab – a user-friendly antimicrobial resistance detection and visualization tool	5
A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex	5