Microbial Genomics

Article	Citations
Genomic insights into the circulation of pandemic fluoroquinolone-resistant extra-intestinal pathogenic Escherichia coli ST1193 in Vietnam	311
Independent origins and evolution of the secondary replicons of the class Gammaproteobacteria	199
Third generation cephalosporin resistance in clinical non-typhoidal Salmonella enterica in Germany and emergence of bla CTX-M-harbouring pESI plasmids	72
Analysis of putative quadruplex-forming sequences in fungal genomes: novel antifungal targets?	72
The rate and role of pseudogenes of the Mycobacterium tuberculosis complex	42
How public health authorities can use pathogen genomics in health protection practice: a consensus-building Delphi study conducted in the United Kingdom	39
Optimization of high-throughput 16S rRNA gene amplicon sequencing: an assessment of PCR pooling, mastermix use and contamination	34
A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids	33
DNA isolation methods for Nanopore sequencing of the Streptococcus mitis genome	32
Metagenomic comparisons reveal a highly diverse and unique viral community in a seasonally fluctuating hypersaline microbial mat	32
Acquisition of Type I methyltransferase via horizontal gene transfer increases the drug resistance of Aeromonas veronii	28
Diversity of the type VI secretion systems in the Neisseria spp	24
Genome plasticity driven by aneuploidy and loss of heterozygosity in Trypanosoma cruzi	24
Plasmids encode niche-specific traits in Lactobacillaceae	24
Comparative genomics of a novel Erwinia species associated with the Highland midge (Culicoides impunctatus)	24
Phylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction	23
Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics	22
The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis	21
Whole-Genome sequencing in routine Mycobacterium bovis epidemiology – scoping the potential	20
IS1-related large-scale deletion of chromosomal regions harbouring the oxygen-insensitive nitroreductase gene nfsB causes nitrofurantoin heteroresistance in Escherichia coli	20
The Gonococcal Genetic Island defines distinct sub-populations of Neisseria gonorrhoeae	19
Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions	19
Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland	19
CRISPR dynamics during the interaction between bacteria and phage in the first year of life	19
Comparative genomic analysis of obligately piezophilic Moritella yayanosii DB21MT-5 reveals bacterial adaptation to the Challenger Deep, Mariana Trench	19

Prevalence, antibiotic resistance, and genomic characterisation of Campylobacter spp. in retail chicken in Hanoi, Vietnam	19
Evaluation of variant calling algorithms for wastewater-based epidemiology using mixed populations of SARS-CoV-2 variants in synthetic and wastewater samples	18
Genomic characterization of Achromobacter species isolates from chronic and occasional lung infection in cystic fibrosis patients	18
Introduction and adaptation of an emerging pathogen to olive trees in Italy	18
Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing	18
Erratum: In silico identification of bacterial seaweed-degrading bioplastic producers	17
Comparative genomics reveals distinct diversification patterns among LysR-type transcriptional regulators in the ESKAPE pathogen Pseudomonas aeruginosa	17
Evaluating the impact of genomic epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) on hospital infection prevention and control decisions	16
ShigaPass: an in silico tool predicting Shigella serotypes from whole-genome sequencing assemblies	16
Novel canine high-quality metagenome-assembled genomes, prophages and host-associated plasmids provided by long-read metagenomics together with Hi-C proximity ligation	16
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogen Ralstonia pseudosolanacearum	16
Genome editing reveals that pSCL4 is required for chromosome linearity in Streptomyces clavuligerus	15
Corrigendum: Coupling next-generation sequencing to dominant positive screens for finding antibiotic cellular targets and resistance mechanisms in Escherichia coli	15
Whole genome sequencing reveals large deletions and other loss of function mutations in Mycobacterium tuberculosis drug resistance genes	15
Genome analysis of a new sulphur disproportionating species Thermosulfurimonas strain F29 and comparative genomics of sulfur-disproportionating bacteria from marine hydrothermal vents	15
Contrasting long-term dynamics of antimicrobial resistance and virulence plasmids in Salmonella Typhimurium from animals	15
The evolutionary history of Shigella flexneri serotype 6 in Asia	14
Dissemination of metaldehyde catabolic pathways is driven by mobile genetic elements in Proteobacteria	14
Whole genome sequence analysis of ESBL-producing Escherichia coli recovered from New Zealand freshwater sites	14
A global survey of Salmonella plasmids and their associations with antimicrobial resistance	14
wMel Wolbachia genome remains stable after 7 years in Australian Aedes aegypti field populations	14
Profiling the plasmid conjugation potential of urinary Escherichia coli	14
Palidis: fast discovery of novel insertion sequences	14
Key features of pneumococcal isolates recovered in Central and Northwestern Russia in 2011–2018 determined through whole-genome sequencing	14
Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets	14
Analysis of genome instability and implications for the consequent phenotype in Plasmodium falciparum containing mutated MSH2-1 (P513T)	14
Identification of further variation at the lipooligosaccharide outer core locus in Acinetobacter baumannii genomes and extension of the OCL reference sequence database for Kaptive	13
Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages	13
Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing	13
Genome-wide analysis of fitness-factors in uropathogenic Escherichia coli during growth in laboratory media and during urinary tract infections	13
Development of a novel streamlined workflow (AACRE) and database (inCREDBle) for genomic analysis of carbapenem-resistant Enterobacterales	13
Complete, closed and curated genome sequences of Photobacterium damselae subsp. piscicida isolates from Australia indicate mobilome-driven localized evolution and novel pathogenicity determinants	13
Alterations in chromosomal genes nfsA, nfsB, and ribE are associated with nitrofurantoin resistance in Escherichia coli from the United Kingdom	13
A conserved uORF in the ilvBNC mRNA of Corynebacterium species regulates ilv operon expression	13
The Canadian VirusSeq Data Portal and Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology	13
Unique roles of vaginal Megasphaera phylotypes in reproductive health	12
Emergence of linezolid-resistant Enterococcus faecium in a tertiary hospital in Copenhagen	12
Genomic characterization of cocirculating Corynebacterium diphtheriae and non-diphtheritic Corynebacterium species among forcibly displaced Myanmar nationals, 2017–2019	12
Applied Bioinformatics and Public Health Microbiology: challenges, discoveries and innovations during a pandemic	12
Discovery and biosynthetic assessment of 'Streptomyces ortus' sp. nov. isolated from a deep-sea sponge	12
Genetic diversity and variation in antimicrobial-resistance determinants of non-serotype 2 Streptococcus suis isolates from healthy pigs	12
Comparative genomic analysis of Staphylococcus aureus isolates associated with either bovine intramammary infections or human infections demonstrates the importance of restriction-modification systems	12
At the threshold of symbiosis: the genome of obligately endosymbiotic ‘Candidatus Nebulobacter yamunensis’ is almost indistinguishable from that of a cultivable strain	12
Differential nasopharyngeal microbiota composition in children according to respiratory health status	12
Genomic and antigenic diversity of colonizing Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi	12
Genome-wide association studies reveal distinct genetic correlates and increased heritability of antimicrobial resistance in Vibrio cholerae under anaerobic conditions	12
Bilateral symmetry of linear streptomycete chromosomes	11
SARS-CoV-2 Omicron variants BA.4 and BA.5 dominated the fifth COVID-19 epidemiological wave in Mexico	11
Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/‘magdeburgensis’ complex	11
Results of the 2020 Genomic Proficiency Test for the network of European Union Reference Laboratory for Antimicrobial Resistance assessing whole-genome-sequencing capacities	11

Infectious bronchitis virus vaccination, but not the presence of XCR1, is correlated with large differences in chicken caecal microbiota	11
Distribution and genomic characterization of tigecycline-resistant tet(X4)-positive Escherichia coli of swine farm origin	11
Genomic and phenotypic characterization of Salmonella enterica serovar Kentucky	11
Phylogenomics of two ST1 antibiotic-susceptible non-clinical Acinetobacter baumannii strains reveals multiple lineages and complex evolutionary history in global clone 1	11
Different evolutionary trends form the twilight zone of the bacterial pan-genome	11
Achromobacter spp. genetic adaptation in cystic fibrosis	11
Subtelomeres are fast-evolving regions of the Streptomyces linear chromosome	11
Nanopore-only assemblies for genomic surveillance of the global priority drug-resistant pathogen, Klebsiella pneumoniae	11
A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia	11
Context-aware genomic surveillance reveals hidden transmission of a carbapenemase-producing Klebsiella pneumoniae	11
Novel emm4 lineage associated with an upsurge in invasive group A streptococcal disease in the Netherlands, 2022	11
gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae	11
Dairy streptococcal cell wall and exopolysaccharide genome diversity	11
Assembly collapsing versus heterozygosity oversizing: detection of homokaryotic and heterokaryotic Laccaria trichodermophora strains by hybrid genome assembly	11
Characterisation of neonatal Staphylococcus capitis NRCS-A isolates compared with non NRCS-A Staphylococcus capitis from neonates and adults	10
Association between metabolic status and gut microbiome in obese populations	10
Long-read sequencing reveals genomic diversity and associated plasmid movement of carbapenemase-producing bacteria in a UK hospital over 6 years	10
A chromosome-scale genome assembly of the tomato pathogen Cladosporium fulvum reveals a compartmentalized genome architecture and the presence of a dispensable chromosome	10
Occurrence of genes encoding spore germination in Clostridium species that cause meat spoilage	10
Comparative genomic insights into culturable symbiotic cyanobacteria from the water fern Azolla	10
The importance of utilizing travel history metadata for informative phylogeographical inferences: a case study of early SARS-CoV-2 introductions into Australia	10
Whole-genome assembly of a novel invertebrate herpesvirus from the gastropod Babylonia areolata	10
The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom	10
Genomic analysis of an outbreak of Shiga toxin-producing Escherichia coli O183:H18 in the United Kingdom, 2023	10
Mutations in the gdpP gene are a clinically relevant mechanism for β-lactam resistance in meticillin-resistant Staphylococcus aureus lacking mec determinants	10
Multidrug-resistant toxigenic Corynebacterium diphtheriae sublineage 453 with two novel resistance genomic islands	10
Leveraging comparative genomics to uncover alien genes in bacterial genomes	10
Single nucleotide variants in Pseudomonas aeruginosa populations from sputum correlate with baseline lung function and predict disease progression in individuals with cystic fibrosis	10
Strain features of pneumococcal isolates in the pre- and post-PCV10 era in Pakistan	10
Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history	10
Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils	10
Detection of plasmid contigs in draft genome assemblies using customized Kraken databases	10
Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families	10
Shooting hoops: globetrotting plasmids spreading more than just antimicrobial resistance genes across One Health	9
Complete genome for Actinobacillus pleuropneumoniae serovar 8 reference strain 405: comparative analysis with draft genomes for different laboratory stock cultures indicates little genetic variation	9
An update to the database for Acinetobacter baumannii capsular polysaccharide locus typing extends the extensive and diverse repertoire of genes found at and outside the K locus	9
Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics	9
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	9
Identification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans	9
Whole-genome sequencing and phylogenetic analysis of coxsackievirus-A16 strains causing hand, foot and mouth disease (HFMD) in India	9
High-resolution microbiome analysis enabled by linking of 16S rRNA gene sequences with adjacent genomic contexts	9
Introduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST	9
Comparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of Streptococcus pneumoniae	9
On the limits of 16S rRNA gene-based metagenome prediction and functional profiling	9
The highly diverse plasmid population found in Escherichia coli colonizing travellers to Laos and its role in antimicrobial resistance gene carriage	9
Genomic epidemiology of Streptococcus pneumoniae serotype 16F lineages	9
Chromosome architecture as a determinant for biosynthetic diversity in Micromonospora	9
Hackflex: low-cost, high-throughput, Illumina Nextera Flex library construction	9
The evolutionary tale of eight novel plasmids in a colistin-resistant environmental Acinetobacter baumannii isolate	9
Genomic comparisons of Escherichia coli ST131 from Australia	9
Evaluation of commercial RNA extraction kits for long-read metatranscriptomics in soil	9
Rapid and accurate SNP genotyping of clonal bacterial pathogens with BioHansel	9
From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools	9
A high prevalence of bla OXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England	9
Identifying gene-level mechanisms of successful dispersal of Vibrio parahaemolyticus during El Niño events	9
Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster	9
Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes	8
A lung-specific mutational signature enables inference of viral and bacterial respiratory niche	8
One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia	8
Multiple independent losses of sporulation and peptidoglycan in the Mycoplasmatales and related orders of the class Bacilli	8
Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks	8
Genomic epidemiology of Staphylococcus aureus isolated from bloodstream infections in South America during 2019 supports regional surveillance	8
Rapid nanopore-based DNA sequencing protocol of antibiotic-resistant bacteria for use in surveillance and outbreak investigation	8
Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons	8
Fatal affairs – conjugational transfer of a dinoflagellate-killing plasmid between marine Rhodobacterales	8
Origin and evolution of nonulosonic acid synthases and their relationship with bacterial pathogenicity revealed by a large-scale phylogenetic analysis	8
The primate gut microbiota contributes to interspecific differences in host metabolism	8
A systematic review of economic evaluations of whole-genome sequencing for the surveillance of bacterial pathogens	8
Transcriptomic analysis of Pseudomonas ogarae F113 reveals the antagonistic roles of AmrZ and FleQ during rhizosphere adaption	8
RFPlasmid: predicting plasmid sequences from short-read assembly data using machine learning	8
Fine-grain population structure and transmission patterns of Mycobacterium tuberculosis in southern Mozambique, a high TB/HIV burden area	8
Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction	8
RETRACTED: Comparative genomic analysis of Escherichia coli isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes	8
Genomic and phenotypic analyses of diverse non-clinical Acinetobacter baumannii strains reveals strain-specific virulence and resistance capacity	8
Genetic association of toxin production in the dinoflagellate Alexandrium minutum	8
Prophages encoding human immune evasion cluster genes are enriched in Staphylococcus aureus isolated from chronic rhinosinusitis patients with nasal polyps	8
Genomic dissection of the Vibrio cholerae O-serogroup global reference strains: reassessing our view of diversity and plasticity between two chromosomes	8
Microbial genetic potential differs among cryospheric habitats of the Damma glacier	8
Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts	8
Uncovering the transcriptome-wide RNA modifications in Acinetobacter baumannii	8

Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages	7
Vibrio cholerae serogroup O5 was responsible for the outbreak of gastroenteritis in Czechoslovakia in 1965	7
An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi	7
Impacts of Mycoplasma agalactiae restriction-modification systems on pan-epigenome dynamics and genome plasticity	7
Direct identification and molecular characterization of zoonotic hazards in raw milk by metagenomics using Brucella as a model pathogen	7
Acidovorax pan-genome reveals specific functional traits for plant beneficial and pathogenic plant-associations	7
Benchmarking the topological accuracy of bacterial phylogenomic workflows using in silico evolution	7
Phylogenetic and antimicrobial drug resistance analysis of Vibrio cholerae O1 isolates from Ghana	7
Lack of methoxy-mycolates characterizes the geographically restricted lineage 7 of Mycobacterium tuberculosis complex	7
The taxonomy of the Trichophyton rubrum complex: a phylogenomic approach	7
Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh	7
Piperacillin/tazobactam-resistant, cephalosporin-susceptible Escherichia coli bloodstream infections are driven by multiple acquisition of resistance across diverse sequence types	7
Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital	7
Large-scale comparative genomics to refine the organization of the global Salmonella enterica population structure	7
Globetrotting strangles: the unbridled national and international transmission of Streptococcus equi between horses	7
Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis	7
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	7
Genomic epidemiology of human candidaemia isolates in a tertiary hospital	7
Evidence for common ancestry and microevolution of passerine-adapted Salmonella enterica serovar Typhimurium in the UK and USA	7
Evolutionary changes between pre- and post-vaccine South African group A G2P[4] rotavirus strains, 2003–2017	7
Prediction of prokaryotic transposases from protein features with machine learning approaches	7
A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment	7
Vibrio cholerae O37: one of the exceptions that prove the rule	7
Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus)	7
Discerning the role of a functional arsenic-resistance cassette in the evolution and adaptation of a rice pathogen	7
Spatiotemporal evolution of SARS-CoV-2 in the Bangkok metropolitan region, Thailand, 2020–2022: implications for future outbreak preparedness	7
Novel internalin P homologs in Listeria	7
Desulfuromonas sp. 'CSMB_57’, isolation and genomic insights from the most abundant bacterial taxon in eastern Australian coals	7
Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK	7
Local accessory gene sharing among Egyptian Campylobacter potentially promotes the spread of antimicrobial resistance	7
Towards comprehensive understanding of bacterial genetic diversity: large-scale amplifications in Bordetella pertussis and Mycobacterium tuberculosis	6
Patterns recovered in phylogenomic analysis of Candida auris and close relatives implicate broad environmental flexibility in Candida/Clavispora clade yeasts	6
Draft genomes of novel avian Chlamydia abortus strains from Australian Torresian crows (Corvus orru) shed light on possible reservoir hosts and evolutionary pathways	6
Molecular epidemiology and phylogenomic analysis of Mycobacterium abscessus clinical isolates in an Asian population	6
Characterization of the RofA regulon in the pandemic M1global and emergent M1UK lineages of Streptococcus pyogenes	6
A bittersweet fate: detection of serotype switching in Pseudomonas aeruginosa	6
Population genomics of Bacillus anthracis from an anthrax hyperendemic area reveals transmission processes across spatial scales and unexpected within-host diversity	6
Deep population structure linked to host vernalization requirement in the barley net blotch fungal pathogen	6
Using 16s rRNA sequencing to characterize the microbiome of tropical cutaneous ulcer disease: insights into the microbial landscape and implications for diagnosis and treatment	6
Parallel genetic adaptation of Bacillus subtilis to different plant species	6
PanGraph: scalable bacterial pan-genome graph construction	6
Pathogen genomics in public health laboratories: successes, challenges, and lessons learned from California’s SARS-CoV-2 Whole-Genome Sequencing Initiative, California COVIDNet	6
Corrigendum: ‘Implementation of routine genomic surveillance provided insights into a locally acquired outbreak caused by a rare clade of Salmonella enterica serovar Enteritidis in Queensland, Austral	6
Pyridoxal 5’-phosphate synthesis and salvage in Bacteria and Archaea: predicting pathway variant distributions and holes	6
Emergence and genomic characteristics of multi-drug-resistant Salmonella in pet turtles and children with diarrhoea	6
Post-weaning shifts in microbiome composition and metabolism revealed by over 25 000 pig gut metagenome-assembled genomes	6
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	6
Delineating bacterial genera based on gene content analysis: a case study of the Mycoplasmatales–Entomoplasmatales clade within the class Mollicutes	6
Mobility of β-lactam resistance under ampicillin treatment in gut microbiota suffering from pre-disturbance	6
A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains	6
Evidence of horizontal gene transfer within porB in 19 018 whole-genome Neisseria spp. isolates: a global phylogenetic analysis	6
Corrigendum: ‘A comparative genome analysis of the Bacillota (Firmicutes) class Dehalobacteriia’	6
Small and intermediate size structural RNAs in the unicellular parasite Cryptosporidium parvum as revealed by sRNA-seq and comparative genomics	6
Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses	6
The promiscuous and highly mobile resistome of Acinetobacter baumannii	6
Advantages of analysing both pairwise SNV-distance and differing SNVs between Mycobacterium tuberculosis isolates for recurrent tuberculosis cause determination	6
Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France	6
Fast and cost-effective SARS-CoV-2 variant detection using Oxford Nanopore full-length spike gene sequencing	6
Corrigendum: Whole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes	6
Delivery mode is a larger determinant of infant gut microbiome composition at 6 weeks than exposure to peripartum antibiotics	6
Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks	6
Non-toxigenic cases of Vibrio cholerae in Spain from 2012 to 2022	6
Characterization of Pantoea ananatis from rice planthoppers reveals a clade of rice-associated P. ananatis undergoing genome reduction	6
RND pumps across the genus Acinetobacter: AdeIJK is the universal efflux pump	6
Ceftazidime–avibactam resistance in Klebsiella pneumoniae sequence type 37: a decade of persistence and concealed evolution	6
Comparative genomic epidemiology of serotype 3 IPD and carriage isolates from Southampton, UK between 2005 and 2017	6
Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host	6
Reciprocally rewiring and repositioning the Integration Host Factor (IHF) subunit genes in Salmonella enterica serovar Typhimurium: impacts on physiology and virulence	6
Compensatory mutations are associated with increased in vitro growth in resistant clinical samples of Mycobacterium tuberculosis	6
PfaSTer: a machine learning-powered serotype caller for Streptococcus pneumoniae genomes	6
Rapid identification and subsequent contextualization of an outbreak of methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit using nanopore sequencing	6
ActinoBase: tools and protocols for researchers working on Streptomyces and other filamentous actinobacteria	6
Streptococcus pneumoniae serotype 3 population structure in the era of conjugate vaccines, 2001–2018	5
Comparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures	5
The gut microbiome and resistome of conventionally vs. pasture-raised pigs	5
Comparative genomics of Staphylococcus epidermidis from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence	5
Monomorphic Trypanozoon: towards reconciling phylogeny and pathologies	5
Genome and Methylome analysis of a phylogenetic novel Campylobacter coli cluster with C. jejuni introgression	5
Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types	5
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	5
Multiple introductions of NRCS-A Staphylococcus capitis to the neonatal intensive care unit drive neonatal bloodstream infections: a case-control and environmental genomic survey	5
Characterization of a P1-bacteriophage-like plasmid (phage-plasmid) harbouring bla CTX-M-15 in Salmonella enterica serovar Typhi	5
Phylogenetic context of Shiga toxin-producing Escherichia coli serotype O26:H11 in England	5
Putative genome contamination has minimal impact on the GTDB taxonomy	5
Chemical biology-whole genome engineering datasets predict new antibacterial combinations	5
Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity	5
dRNASb: a systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data	5
Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya	5
Exploring SNP filtering strategies: the influence of strict vs soft core	5
A novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin	5
Geographical distribution, disease association and diversity of Klebsiella pneumoniae K/L and O antigens in India: roadmap for vaccine development	5
Remote homology clustering identifies lowly conserved families of effector proteins in plant-pathogenic fungi	5
Insertion sequences related to ISAjo2 target pdif and dif sites and belong to a new IS family, the IS1202 family	5
Capturing clinically relevant Campylobacter attributes through direct whole genome sequencing of stool	5
Contrasting genes conferring short- and long-term biofilm adaptation in Listeria	5