Genomic Diversity of Campylobacter lari Group Isolates from Europe and Australia in a One Health Context

Type Article
Date 2022-12
Language English
Author(s) Gourmelon MicheleORCID1, Boukerb Amine M.ORCID1, 2, Nabi Nesrine1, Banerji Sangeeta3, Joensen Katrine G.4, Serghine Joelle1, Cormier AlexandreORCID5, Megraud FrancisORCID6, Lehours PhilippeORCID6, 7, Alter Thomas8, Ingle Danielle J.9, 10, Kirk Martyn D.ORCID9, Nielsen Eva M.4
Affiliation(s) 1 : Ifremer, RBE-SGMM-LSEM, Plouzané, France
2 : University of Rouen Normandy, Laboratory of Microbiology Bacterial Communication and Anti-infectious Strategies (CBSA), Evreux, France
3 : Robert Koch Institute, Wernigerode, Germany
4 : Statens Serum Institut, Copenhagen, Denmark
5 : IFREMER, IRSI-SeBiMER, Plouzané, France
6 : BRIC Bordeaux Institute of Oncology, BRIC U1312, INSERM, University of Bordeaux, Bordeaux Hospital, Bordeaux, France
7 : French National Reference Centre for Campylobacters and Helicobacters, Bordeaux Hospital, Bordeaux, France
8 : Freie Universität Berlin, Berlin, Germany
9 : National Centre for Epidemiology and Population Health, Australian National University, Canberra, Australia
10 : Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
Source Applied And Environmental Microbiology (0099-2240) (American Society for Microbiology), 2022-12 , Vol. 88 , N. 23 , P. 21p.
DOI 10.1128/aem.01368-22
WOS© Times Cited 5
Keyword(s) Campylobacter lad group, whole-genome sequencing, virulence genes, genomic diversity, One Health
Abstract

Members of the Campylobacter lari group are causative agents of human gastroenteritis and are frequently found in shellfish, marine waters, shorebirds, and marine mammals. Within a One Health context, we used comparative genomics to characterize isolates from a diverse range of sources and geographical locations within Europe and Australia and assess possible transmission of food, animal, and environmental isolates to the human host. A total of 158 C. lari isolates from Australia, Denmark, France, and Germany, which included 82 isolates from human stool and blood, 12 from food, 14 from domestic animal, 19 from waterbirds, and 31 from the environment were analyzed. Genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance (AMR) traits was carried-out. Most of the isolates belonged to C. lari subsp. lari (Cll; 98, 62.0%), while C. lari subsp. concheus and C. lari urease-positive thermotolerant Campylobacter (UPTC) were represented by 12 (7.6%) and 15 (9.5%) isolates, respectively. Furthermore, 33 (20.9%) isolates were not assigned a subspecies and were thus attributed to distant Campylobacter spp. clades. Whole-genome sequence-derived multilocus sequence typing (MLST) and core-genome MLST (cgMLST) analyses revealed a high genetic diversity with 97 sequence types (STs), including 60 novel STs and 14 cgMLST clusters (≤10 allele differences), respectively. The most prevalent STs were ST-21, ST-70, ST-24, and ST-58 (accounting for 13.3%, 4.4%, 3.8%, and 3.2% of isolates, respectively). A high prevalence of the 125 examined virulence-related loci (from 76.8 to 98.4% per isolate) was observed, especially in Cll isolates, suggesting a probable human pathogenicity of these strains.

IMPORTANCE Currently, relatedness between bacterial isolates impacting human health is easily monitored by molecular typing methods. These approaches rely on discrete loci or whole-genome sequence (WGS) analyses. Campylobacter lari is an emergent human pathogen isolated from diverse ecological niches, including fecal material from humans and animals, aquatic environments, and seafood. The presence of C. lari in such diverse sources underlines the importance of adopting an integrated One Health approach in studying C. lari population structure for conducting epidemiological risk assessment. This retrospective study presents a comparative genomics analysis of C. lari isolates retrieved from two different continents (Europe and Australia) and from different sources (human, domestic animals, waterbirds, food, and environment). It was designed to improve knowledge regarding C. lari ecology and pathogenicity, important for developing effective surveillance and disease prevention strategies.

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Gourmelon Michele, Boukerb Amine M., Nabi Nesrine, Banerji Sangeeta, Joensen Katrine G., Serghine Joelle, Cormier Alexandre, Megraud Francis, Lehours Philippe, Alter Thomas, Ingle Danielle J., Kirk Martyn D., Nielsen Eva M. (2022). Genomic Diversity of Campylobacter lari Group Isolates from Europe and Australia in a One Health Context. Applied And Environmental Microbiology, 88(23), 21p. Publisher's official version : https://doi.org/10.1128/aem.01368-22 , Open Access version : https://archimer.ifremer.fr/doc/00804/91613/