Escherichia coli multilocus sequence type 38 from humans and broiler production represent distinct monophyletic groups

Solveig Sølverød Mo; Eve Zeyl Fiskebeck; Jannice Schau Slettemeås; Karin Lagesen; Oskar Nilsson; Umaer Naseer; Silje Bakken Jørgensen; Thorunn Rafnar Thorsteinsdottir; Marianne Sunde

doi:10.3389/fmicb.2023.1173287

Escherichia coli multilocus sequence type 38 from humans and broiler production represent distinct monophyletic groups

Front Microbiol. 2023 May 2:14:1173287. doi: 10.3389/fmicb.2023.1173287. eCollection 2023.

Authors

Solveig Sølverød Mo¹, Eve Zeyl Fiskebeck², Jannice Schau Slettemeås¹, Karin Lagesen², Oskar Nilsson³, Umaer Naseer⁴, Silje Bakken Jørgensen^{5

6}, Thorunn Rafnar Thorsteinsdottir⁷, Marianne Sunde¹

Affiliations

¹ Section for Food Safety and Animal Health Research, Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, Ås, Norway.
² Section for Epidemiology, Department of Animal Health, Welfare and Food Safety, Norwegian Veterinary Institute, Ås, Norway.
³ Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute (SVA), Uppsala, Sweden.
⁴ Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway.
⁵ Department of Clinical Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway.
⁶ Department for Laboratory Medicine, Vestre Viken Hospital Trust, Drammen, Norway.
⁷ Institute for Experimental Pathology, University of Iceland, Keldur, Iceland.

Abstract

Escherichia coli belonging to multilocus sequence type 38 (ST38) is a well-known cause of extra-intestinal infections in humans, and are frequently associated with resistance to extended-spectrum cephalosporins (ESCs). Resistance to carbapenems, mediated by bla_OXA-genes has also been reported in this ST. Recently, the European Centre for Disease Prevention and Control (ECDC) released a rapid risk assessment on the increased detection of OXA-244 producing E. coli ST38 in humans, requesting further knowledge to determine the source. ST38 is also one of the most common STs among ESC-resistant E. coli from broiler production. Our aim was to investigate the genetic characteristics and relationship between E. coli ST38 from broiler production and humans, and to investigate if there has been a potential spillover between these sources. A total of 288 E. coli ST38 genomes isolated from humans in Europe (collected 2009-2019) and from Nordic broiler production (collected 2011-2014) were analyzed. The results showed distinct monophyletic clades associated to humans and broiler production. Furthermore, there were differences in the ESC resistance genes present in E. coli ST38 from the two sources. The bla_OXA-244 gene was not present in E. coli from broiler production. Our results show that ST38 from humans and broiler production belong to well-separated clades, and suggest that the increased detection of OXA-244-producing E. coli ST38 in humans is not associated with spillover from broiler production.

Keywords: ESC; Escherichia coli; OXA-244; ST38; broilers; comparative genomics.