Within-host genetic diversity of extended-spectrum beta-lactamase-producing Enterobacterales in long-term colonized patients

Lisandra Aguilar-Bultet, Ana B. García-Martín, Isabelle Vock, Laura Maurer Pekerman, Rahel Stadler, Ruth Schindler, Manuel Battegay, Tanja Stadler, Elena Gómez-Sanz and Sarah Tschudin-Sutter ()
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Lisandra Aguilar-Bultet: University Hospital Basel, University of Basel
Ana B. García-Martín: University Hospital Basel, University of Basel
Isabelle Vock: University Hospital Basel, University of Basel
Laura Maurer Pekerman: University Hospital Basel, University of Basel
Rahel Stadler: University Hospital Basel, University of Basel
Ruth Schindler: University Hospital Basel, University of Basel
Manuel Battegay: University Hospital Basel, University of Basel
Tanja Stadler: Swiss Institute of Bioinformatics
Elena Gómez-Sanz: University Hospital Basel, University of Basel
Sarah Tschudin-Sutter: University Hospital Basel, University of Basel

Nature Communications, 2023, vol. 14, issue 1, 1-14

Abstract: Abstract Despite recognition of the immediate impact of infections caused by extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) on human health, essential aspects of their molecular epidemiology remain under-investigated. This includes knowledge on the potential of a particular strain to persist in a host, mutational events during colonization, and the genetic diversity in individual patients over time. To investigate long-term genetic diversity of colonizing and infecting ESBL-Klebsiella pneumoniae species complex and ESBL-Escherichia coli in individual patients over time, we performed a ten-year longitudinal retrospective study and extracted clinical and microbiological data from electronic health records. In this investigation, 76 ESBL-K. pneumoniae species complex and 284 ESBL-E. coli isolates were recovered from 19 and 61 patients. Strain persistence was detected in all patients colonized with ESBL-K. pneumoniae species complex, and 83.6% of patients colonized with ESBL-E. coli. We frequently observed isolates of the same strain recovered from different body sites associated with either colonization or infection. Antimicrobial resistance genes, plasmid replicons, and whole ESBL-plasmids were shared between isolates regardless of chromosomal relatedness. Our study suggests that patients colonized with ESBL-producers may act as durable reservoirs for ongoing transmission of ESBLs, and that they are at prolonged risk of recurrent infection with colonizing strains.

Date: 2023
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DOI: 10.1038/s41467-023-44285-w

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