A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings

Edward Feil, Ross Booton, Teemu Kallonen, Marjorie Gibbon, Natacha Monge Gomes Do Couto, Virginie Passet, Sebastian Fernandez, Carla Rodrigues, Louise Matthews, Sonia Mitchell, Richard Reeve, Sophia David, Cristina Merla, Marta Corbella, Carolina Ferrari, Francesco Comandatore, Piero Manone, Sylvain Brisse, Davide Sassera, Jukka Corander

Research output: Contribution to journalArticlepeer-review

Abstract

The Klebsiella group is genetically and ecologically diverse, being found in humans, livestock, plants, soil, water, and wild animals. Many species are opportunistic pathogens, and can harbour diverse classes of antimicrobial resistance (AMR) genes. Health-care associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public-health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 15-month period from a wide range of clinical, community, animal, and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired Carbapenem non-susceptible Klebsiella, and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We find no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside of the clinical environment. Although we note occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of novel groups.
Original languageEnglish
JournalNature Microbiology
Publication statusAcceptance date - 10 Oct 2022

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