Whole-genome sequencing for One Health surveillance of antimicrobial resistance in conflict zones: a case study of Salmonella spp. and Campylobacter spp. in the West Bank, Palestine

Abstract

Antimicrobial resistance (AMR) is a critical global concern driven by the overuse, misuse, and/or usage of inadequate antibiotics on humans, animals' agriculture, and as a result of contaminated environments. This study is the first One Health survey in the Middle East that incorporated whole-genome sequencing (WGS) to examine the spread of AMR in Campylobacter spp. and Salmonella spp. This cross-sectional study was conducted to examine the role of AMR at the human-animal-environmental interface and was performed in Ramallah/Al-Bireh and Jerusalem governorates of the central West Bank, Palestine. In 2021 and 2022, a total of 592 samples were collected and analyzed. From a total of 65 Campylobacter jejuni and 19 Salmonella spp. isolates, DNA was extracted for WGS using Oxford Nanopore Technologies MinION platform. We found that the dominant serotypes of C. jejuni and Salmonella enterica were present in chicken manure, chicken meat sold in markets, and feces of asymptomatic farm workers, with high genetic similarities between the isolates regardless of origin. Additionally, our results showed rapid strain turnover in C. jejuni from the same sites between 2021 and 2022. Most of the positive Salmonella spp. samples were multidrug-resistant (MDR) S. enterica serovar Muenchen carrying the plasmid of emerging S. infantis (pESI) megaplasmid, conferring resistance to multiple antibiotics. Our findings highlight the spread of MDR foodborne pathogens from animals to humans through the food chain, emphasizing the importance of a One Health approach that considers the interconnections between human, animal, and environmental health. IMPORTANCE Prior to this study, there existed hardly an integrated human-animal-environmental study of Salmonellosis and Campylobacteriosis and related AMR in Middle Eastern countries. The few existing studies lack robust epidemiological study designs, adequate for a One Health approach, and did not use WGS to determine the circulating serotypes and their AMR profiles. Civil unrest and war in Middle Eastern countries drive AMR because of the breakdown of public health and food security services. This study samples simultaneously humans, animals, and the environment to comprehensively investigate foodborne pathogens in the broiler chicken production chain in Palestine using WGS. We show that identical serotypes of C. jejuni and S. enterica can be found in samples from chicken farms, chicken meat sold in markets, and asymptomatic broiler chicken production workers. The most striking feature is the rapid dynamic of change in the genetic profile of the detected species in the same sampling locations. The majority of positive Salmonella spp. samples are MDR S. enterica serovar Muenchen isolates carrying the pESI megaplasmid. The results demonstrate a close relationship between the S. enterica serovar Muenchen isolates found in our sample collection and those responsible for 40% of all clinical Salmonella spp. isolates in Israel as previously reported, with a sequence identity of over 99.9%. These findings suggest the transboundary spread of MDR S. enterica serovar Muenchen strains from animals to humans through the food chain. The study underscores the importance of combining integrated One Health studies with WGS for detecting environmental-animal-human transmission of foodborne pathogens that could not be detected otherwise. This study showcases the benefits of integrated environmental-animal-human sampling and WGS for monitoring AMR. Environmental samples, which may be more accessible in conflict-torn places where monitoring systems are limited and regulations are weak, can provide an effective AMR surveillance solution. WGS of bacterial isolates provides causal inference of the distribution and spread of bacterial serotypes and AMR in complex social-ecological systems. Consequently, our results point toward the expected benefits of operationalizing a One Health approach through closer cooperation of public and animal health and food safety authorities.

Keywords: AMR; Campylobacter; One Health; Palestine; Salmonella; WGS.

Fig 1

Epidemiology of C. jejuni and S. enterica in broiler chicken production chain in Palestine. (A) Positivity rate of C. jejuni and S. enterica among samples tested from different sources. (B) Univariable analysis of risk factors for C. jejuni infection among workers’ sociodemographic characteristics and health status. filled circles are the reference group.

Fig 2

Phylogenetic analysis of C. jejuni isolates. (A) Average nucleotide identities between all 47 isolates collected in 2021 and all 16 isolates collected in 2022. (B) C. jejuni phylogenetic tree with 10 representative genomes from Palestine and 51 closely related genomes from different countries collected between 1997 and 2019. MLST-based sequence types are shown for the sequence types represented by Palestinian isolates. The presence of AMR markers is shown in light gray if located in the genome or an unidentified contig or dark gray if located on a plasmid. sample sources are depicted by colored, filled circles. Genomes generated in this study are in bold text. All human isolates collected in 2021 are from broiler chicken production chain workers, while all four human isolates collected in 2022 are from hospitalized gastroenteritis patients.

Fig 3

Phylogenetic analysis of S. enterica isolates. (A) Phylogenetic tree for S. enterica with 17 genomes from Palestine and 31 closely related genomes belonging to the three serotypes found in this study from different countries collected between 1987 and 2020. The presence of AMR markers is shown in light gray if located in the genome or an unidentified plasmid or dark gray if located on a plasmid. Sample sources are depicted by colored, filled circles. Genomes generated in this study are in bold text. Genomes used for Fig. 3B and C are marked with an asterisk. Comparison of Palestinian S. enterica serotype Muenchen chromosome (B) and pESI plasmid (C) from chicken manure and human feces as well as meat with a clinical isolate from Israel collected in 2018. The presence and location of antibiotic-resistance genes are shown in red. The human isolate collected in 2021 is from a broiler chicken production chain worker, while all three human isolates collected in 2022 are from hospitalized gastroenteritis patients.