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

Harry Thorpe (1) , Ross Booton (2) , Teemu Kallonen (3) , Marjorie Gibbon (4) , Natacha Couto (4) , Virginie Passet (5) , Sebastián López-Fernández (5) , Carla Rodrigues (5) , Louise Matthews (6) , Sonia Mitchell (6) , Richard Reeve (6) , Sophia David (7) , Cristina Merla (8) , Marta Corbella (8) , Carolina Ferrari (8) , Francesco Comandatore (9) , Piero Marone (8) , Sylvain Brisse (5) , Davide Sassera (10) , Jukka Corander (1, 7, 11) , Edward Feil (4)

1 UiO - University of Oslo
2 University of Bristol [Bristol]
3 TYKS - Turku University Hospital
4 University of Bath [Bath]
5 Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens
6 University of Glasgow
7 The Wellcome Trust Sanger Institute [Cambridge]
8 IRCCS - Istituto di Ricovero e Cura a Carattere Scientifico
9 UNIMI - Università degli Studi di Milano = University of Milan
10 UNIPV - Università degli Studi di Pavia = University of Pavia
11 Helsingin yliopisto = Helsingfors universitet = University of Helsinki

The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-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 17-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 found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.

Domains: Infectious diseases

Harry Thorpe, Ross Booton, Teemu Kallonen, Marjorie Gibbon, Natacha Couto, et al.. A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nature Microbiology, 2022, 7 (12), pp.2054-2067. ⟨10.1038/s41564-022-01263-0⟩. ⟨pasteur-03930553⟩