| ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping |
41 |
| chewBBACA: A complete suite for gene-by-gene schema creation and strain identification |
26 |
| Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes |
26 |
| Genetic diversity, mobilisation and spread of the yersiniabactin-encoding mobile element ICEKp in Klebsiella pneumoniae populations |
25 |
| Emergence, molecular mechanisms and global spread of carbapenem-resistant Acinetobacter baumannii |
24 |
| Trends in fluoroquinolone resistance in Campylobacter |
19 |
| Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence |
18 |
| mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species |
17 |
| Whole genome sequence analysis of Australian avian pathogenic Escherichia coli that carry the class 1 integrase gene |
15 |
| Genome analysis of clinical multilocus sequence Type 11 Klebsiella pneumoniae from China |
14 |
| Fluoroquinolone resistance in Salmonella: insights by whole-genome sequencing |
14 |
| MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies |
14 |
| Correlation between bacterial G plus C content, genome size and the G plus C content of associated plasmids and bacteriophages |
14 |
| Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198 |
13 |
| Expanding an expanded genome: long-read sequencing of Trypanosoma cruzi |
13 |
| Multifactorial chromosomal variants regulate polymyxin resistance in extensively drug-resistant Klebsiella pneumoniae |
11 |
| Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection |
11 |
| A complete high-quality MinION nanopore assembly of an extensively drug-resistant Mycobacterium tuberculosis Beijing lineage strain identifies novel variation in repetitive PE/PPE gene regions |
11 |
| Comparative 'omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli |
10 |
| The return of Pfeiffer's bacillus: Rising incidence of ampicillin resistance in Haemophilus influenzae |
10 |
| Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages |
10 |
| The diversity of ice algal communities on the Greenland Ice Sheet as revealed by oligotyping |
9 |
| LiSEQ - whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe |
9 |
| Transcriptional changes when Myxococcus xanthus preys on Escherichia coli suggest myxobacterial predators are constitutively toxic but regulate their feeding |
8 |
| Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains |
8 |
| Evolution of a clade of Acinetobacter baumannii global clone lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1 |
8 |
| Clinical and laboratory-induced colistin-resistance mechanisms in Acinetobacter baumannii |
8 |
| Genetic analysis of invasive Escherichia coli in Scotland reveals determinants of healthcare-associated versus community-acquired infections |
8 |
| Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients |
7 |
| An analysis of the IS6/IS26 family of insertion sequences: is it a single family? |
7 |
| Not all Pseudomonas aeruginosa are equal: strains from industrial sources possess uniquely large multireplicon genomes |
7 |
| Genome analysis of methicillin resistance in Macrococcus caseolyticus from dairy cattle in England and Wales |
7 |
| Characterization of capsule genes in non-pathogenic Neisseria species |
7 |
| Extended-spectrum beta-lactamase-producing and carbapenemase-producing Enterobacteriaceae |
7 |
| MentaLiST - A fast MLST caller for large MLST schemes |
6 |
| Evaluation of SNP calling methods for closely related bacterial isolates and a novel high-accuracy pipeline: BactSNP |
6 |
| HomoplasyFinder: a simple tool to identify homoplasies on a phylogeny |
6 |
| Genomic analysis of bacteria in the Acute Oak Decline pathobiome |
6 |
| GenomeTrakr proficiency testing for foodborne pathogen surveillance: an exercise from 2015 |
6 |
| Australian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny |
6 |
| SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data |
6 |
| SuperDCA for genome-wide epistasis analysis |
6 |
| Domestication of Campylobacter jejuni NCTC 11168 |
6 |
| Pangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation |
5 |
| Genomic epidemiology of penicillin-non-susceptible Streptococcus pneumoniae |
5 |
| Enterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization |
5 |
| Genomics of vancomycin-resistant Enterococcus faecium |
5 |
| Clonal ST131-H22 Escherichia coli strains from a healthy pig and a human urinary tract infection carry highly similar resistance and virulence plasmids |
5 |
| Within-host Mycobacterium tuberculosis diversity and its utility for inferences of transmission |
5 |
| Identification of novel adenovirus genotype 90 in children from Bangladesh |
5 |
