Temporal genome dynamics of ST39 Klebsiella pneumoniae in a neonatal unit in Blantyre, Malawi
Zuza, A. M.; Pearse, O.; Domman, D. B.; Dyson, Z. A.; Kawaza, K.; Musicha, P.; Feasey, N. A.; Heinz, E.
Show abstract
BackgroundKlebsiella pneumoniae (Kpn) is an important cause of healthcare-associated infections (HAI). In low and middle-income countries, HAI due to Kpn disproportionally affects neonates. In this study, we investigated the genomic changes that occurred during long-term circulation of a Kpn ST39 clone, causing a disproportionate number of infections on the neonatal ward at a tertiary healthcare facility in Malawi in 2017. MethodsWe analyzed whole genome sequences of Klebsiella pneumoniae ST39 collected from Queen Elizabeth Central Hospital over a 20-year period, including generation of several high-quality hybrid genomes. We compared virulence markers, antibiotic resistance determinants, and mobile genetic elements, focusing on variable regions between strains from the outbreak clone in 2017 to genomes from other co-occurring ST39 lineages. ResultsWe identified eight variable genomic regions that demonstrate the plasticity of Kpn within-ST, including the role of bacteriophages in shaping the genome of ST39. ConclusionsThe analyzed Klebsiella pneumoniae ST39 lineages have a highly variable genome capable of incorporating large genomic regions during prolonged hospital circulation, which may offer a selective advantage in hospital environments and provide resistance to antimicrobial agents. Data summaryAll sequencing data is available in BioProject PRJEB102175; detailed accession numbers are provided in Table S1. The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Matching journals
The top 1 journal accounts for 50% of the predicted probability mass.
Similar papers in this journal
- Resolving plasmid-encoded carbapenem resistance dynamics and reservoirs in a hospital setting through nanopore sequencing 97%
- Genomic surveillance of Escherichia coli ST131 identifies local expansion and serial replacement of subclones 97%
- Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia 96%
Similar papers in this journal
- The emergence of successful Streptococcus pyogenes lineages through convergent pathways of capsule loss and recombination directing high toxin expression 96%
- Persistence of rare Salmonella Typhi genotypes susceptible to first-line antibiotics in the remote islands of Samoa 96%
- Phage-plasmids spread antibiotic resistance genes through infection and lysogenic conversion 96%
Similar papers in this journal
- Putative conjugative plasmids with tcdB and cdtAB genes in clinical Clostridium difficile strains 2 from MLST clades C-I, 2 and 4 94%
- Large-scale genomic analysis of SARS-CoV-2 Omicron BA.5 emergence in the United States 92%
- Salmonella Infantis, the emerging human multidrug resistant pathogen - a One Health perspective 92%
Similar papers in this journal
- Species-wide phylogenomics of the Staphylococcus aureus agr operon reveals convergent evolution of frameshift mutations 96%
- Genetic Determinants Underlying the Progressive Phenotype of Beta-lactam/Beta-lactamase Inhibitor Resistance in Escherichia coli 95%
- Escherichia marmotae - a human pathogen easily misidentified as Escherichia coli 95%
Similar papers in this journal
- A global resource for genomic predictions of antimicrobial resistance and surveillance of Salmonella Typhi at Pathogenwatch 97%
- Genomic dissection of the bacterial population underlying Klebsiella pneumoniae infections in hospital patients: insights into an opportunistic pathogen 95%
- The global phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.