Bacterial Genomics

Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong - Nature Communications E. coli is common in humans, animals and the environment but the extent of circulation between ecological niches is unclear. Here, the authors sample ~1,000 E. coli strains from different urban aquati...

Ecological connectivity of genomic markers of antimicrobial resistance in Escherichia coli in Hong Kong www.nature.com/articles/s41...

Genome-based reclassification of Micromonospora veneta Kaewkla et al. 2022 as a later heterotypic synonym of Micromonospora coerulea Jensen 1932 (Approved lists 1980) - Scientific Reports Scientific Reports - Genome-based reclassification of Micromonospora veneta Kaewkla et al. 2022 as a later heterotypic synonym of Micromonospora coerulea Jensen 1932 (Approved lists 1980)

Genome-based reclassification of Micromonospora veneta Kaewkla et al. 2022 as a later heterotypic synonym of Micromonospora coerulea Jensen 1932 (Approved lists 1980) www.nature.com/articles/s41...

Pan-genus analysis and typing of antimicrobial resistance plasmids in Acinetobacter www.nature.com/articles/s44...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria - Nature Communications The authors investigate the distribution of the aminoglycoside resistance gene npmA in Gram-positive bacteria via a mobile genetic element, highlighting its global presence and cross-species transfer ...

Global dissemination of npmA mediated pan-aminoglycoside resistance via a mobile genetic element in Gram-positive bacteria www.nature.com/articles/s41...

Genomes of 211 Actinomycete Strains from Diverse Environments - Scientific Data Scientific Data - Genomes of 211 Actinomycete Strains from Diverse Environments

Genomes of 211 Actinomycete Strains from Diverse Environments www.nature.com/articles/s41...

Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh - Scientific Reports Scientific Reports - Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh

Molecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh www.nature.com/articles/s41...

Streptomyces maremycinicus sp. nov. and its secondary metabolite-biosynthetic gene clusters - The Journal of Antibiotics The Journal of Antibiotics - Streptomyces maremycinicus sp. nov. and its secondary metabolite-biosynthetic gene clusters

Streptomyces maremycinicus sp. nov. and its secondary metabolite-biosynthetic gene clusters www.nature.com/articles/s41...

Global pneumococcal sequence cluster lineage for invasive pneumococcal isolates in Denmark from summer 2019 to 2023 - Scientific Reports Scientific Reports - Global pneumococcal sequence cluster lineage for invasive pneumococcal isolates in Denmark from summer 2019 to 2023

Global pneumococcal sequence cluster lineage for invasive pneumococcal isolates in Denmark from summer 2019 to 2023 www.nature.com/articles/s41...

Halomonas sp. MC140, a polyhydroxyalkanoate (PHA) producer isolated from the Arctic environment - Scientific Reports Scientific Reports - Halomonas sp. MC140, a polyhydroxyalkanoate (PHA) producer isolated from the Arctic environment

Halomonas sp. MC140, a polyhydroxyalkanoate (PHA) producer isolated from the Arctic environment www.nature.com/articles/s41...

Universal rules govern plasmid copy number - Nature Communications Plasmids exhibit a broad range of sizes and copies per cell, and these two parameters appear to be negatively correlated. Here, Ramiro-Martínez et al. analyse the copy number of thousands of diverse b...

Universal rules govern plasmid copy number www.nature.com/articles/s41...

Scaling laws of bacterial and archaeal plasmids - Nature Communications The capacity of a plasmid to express genes is constrained by parameters such as its length and copy number. Here, Maddamsetti et al. present a computational method that enables rapid and accurate dete...

Scaling laws of bacterial and archaeal plasmids www.nature.com/articles/s41...

Complete genome analysis of the cellulose producing strain Komagataeibacter sucrofermentans SMEG01 - Scientific Reports Scientific Reports - Complete genome analysis of the cellulose producing strain Komagataeibacter sucrofermentans SMEG01

Complete genome analysis of the cellulose producing strain Komagataeibacter sucrofermentans SMEG01 www.nature.com/articles/s41...

The identification Mycobacterium tuberculosis genes that modulate long term survival in the presence of rifampicin and streptomycin - Scientific Reports Scientific Reports - The identification Mycobacterium tuberculosis genes that modulate long term survival in the presence of rifampicin and streptomycin

The identification Mycobacterium tuberculosis genes that modulate long term survival in the presence of rifampicin and streptomycin www.nature.com/articles/s41...

Multidrug-resistant Klebsiella pneumoniae ST70 harboring blaNDM in a migratory Penguin - Scientific Reports Scientific Reports - Multidrug-resistant Klebsiella pneumoniae ST70 harboring blaNDM in a migratory Penguin

Multidrug-resistant Klebsiella pneumoniae ST70 harboring blaNDM in a migratory Penguin www.nature.com/articles/s41...

Tracking international and regional dissemination of the KPC/NDM co-producing Klebsiella pneumoniae - Nature Communications This study is an analysis of carbapenem-resistant Klebsiella pneumoniae from 2005 to 2024, which showed significant differences across countries, and Clone Group 1 emerged as the principal disseminati...

Tracking international and regional dissemination of the KPC/NDM co-producing Klebsiella pneumoniae www.nature.com/articles/s41...

A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections - Nature Communications Bacteria can undergo adaptive evolution during severe infections, leading to treatment failure. The authors use within-host evolution genomic analysis to investigate persistent Staphylococcus aureus i...

A multi-hospital, clinician-initiated bacterial genomics programme to investigate treatment failure in severe Staphylococcus aureus infections www.nature.com/articles/s41...

TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity - npj Vaccines npj Vaccines - TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity

TnSeq identifies genetic requirements of Mycobacterium tuberculosis for survival under vaccine-induced immunity www.nature.com/articles/s41...

Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA - Nature Communications A large outbreak of shigellosis occurred in Albuquerque, New Mexico in 2021–2023 and affected non-human primates at a local zoo as well as humans. Here, the authors describe the outbreak investigation...

Multidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA www.nature.com/articles/s41...

Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut - Scientific Reports Scientific Reports - Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut

Massive acquisition of conjugative and mobilizable integrated elements fuels Faecalibacterium plasticity and hints at their adaptation to the gut www.nature.com/articles/s41...

Cas3 of type I-Fa CRISPR-Cas system upregulates bacterial biofilm formation and virulence in Acinetobacter baumannii - Communications Biology Deletion of cas3(type I-Fa) significantly reduced the biofilm formation, virulence and pathogenicity to mice. Mechanism analysis proved that this maybe because cas3 can lead to the down-regulation of ...

Cas3 of type I-Fa CRISPR-Cas system upregulates bacterial biofilm formation and virulence in Acinetobacter baumannii www.nature.com/articles/s42...

HiBC: a publicly available collection of bacterial strains isolated from the human gut - Nature Communications Here, the authors present and characterise a collection of human gut bacteria including novel taxa associated with health conditions and a large diversity of plasmids. All isolates, their genomes and ...

HiBC: a publicly available collection of bacterial strains isolated from the human gut www.nature.com/articles/s41...

Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens - Nature Communications In the era of global foodborne pathogens’ genomic surveillance, this study shows that large-scale inter-laboratory comparisons are needed and feasible, opening good perspectives for efficient and coop...

Multi-country and intersectoral assessment of cluster congruence between pipelines for genomics surveillance of foodborne pathogens www.nature.com/articles/s41...

Genomic epidemiology and characterization of difficult-to-treat resistant Pseudomonas aeruginosa isolates co-harboring blaOXA-50 and crpP causing bronchiectasis - Scientific Reports Scientific Reports - Genomic epidemiology and characterization of difficult-to-treat resistant Pseudomonas aeruginosa isolates co-harboring blaOXA-50 and crpP causing bronchiectasis

Genomic epidemiology and characterization of difficult-to-treat resistant Pseudomonas aeruginosa isolates co-harboring blaOXA-50 and crpP causing bronchiectasis www.nature.com/articles/s41...

Comprehensive serotyping of Mannheimia haemolytica by a PCR system using the diversity of capsule biosynthesis genes - Scientific Reports Scientific Reports - Comprehensive serotyping of Mannheimia haemolytica by a PCR system using the diversity of capsule biosynthesis genes

Comprehensive serotyping of Mannheimia haemolytica by a PCR system using the diversity of capsule biosynthesis genes www.nature.com/articles/s41...

Plasmid-driven strategies for clone success in Escherichia coli - Nature Communications Plasmids can encode multiple traits that contribute to the emergence and dissemination of their bacterial hosts. Here the authors use Nanopore long-read technology to sequence the complete genomes of ...

Plasmid-driven strategies for clone success in Escherichia coli www.nature.com/articles/s41...

Quantitative prediction of disinfectant tolerance in Listeria monocytogenes using whole genome sequencing and machine learning - Scientific Reports Scientific Reports - Quantitative prediction of disinfectant tolerance in Listeria monocytogenes using whole genome sequencing and machine learning

Quantitative prediction of disinfectant tolerance in Listeria monocytogenes using whole genome sequencing and machine learning www.nature.com/articles/s41...

Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii - Nature Communications In this study, authors conduct a genomic analysis of 15,000 Acinetobacter baumannii isolates, revealing a dominant multidrug-resistant super-lineage (accounting for approximately 70% global isolates),...

Emergence and global spread of a dominant multidrug-resistant clade within Acinetobacter baumannii www.nature.com/articles/s41...

Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data - Nature Communications Authors present results from a national surveillance in Japan that found MRSA strains causing bloodstream infections are predominantly from three clonal lineages. They also identified the emergence of...

Staphylococcus aureus ST764-SCCmecII high-risk clone in bloodstream infections revealed through national genomic surveillance integrating clinical data www.nature.com/articles/s41...

Genomically defined hypervirulent Klebsiella pneumoniae contributed to early-onset increased mortality - Nature Communications Using an accurate genomic biomarker signature as a means to identify hypervirulent Klebsiella pneumoniae (hvKp-p), authors perform a longitudinal cohort study to provide insight into the clinical and ...

Genomically defined hypervirulent Klebsiella pneumoniae contributed to early-onset increased mortality www.nature.com/articles/s41...

Streamlining whole genome sequencing for clinical diagnostics with ONT technology - Scientific Reports Scientific Reports - Streamlining whole genome sequencing for clinical diagnostics with ONT technology

Streamlining whole genome sequencing for clinical diagnostics with ONT technology www.nature.com/articles/s41...