Genomic Epidemiology of Salmonella enterica Circulating in Surface Waters Used in Agriculture and Aquaculture in Central Mexico

Abstract

Salmonella enterica (SE) can survive in surface waters (SuWa) and the role of non-host environments in its transmission has acquired increasing relevance. In this study, we conducted comparative genomic analyses of 172 SE isolates collected from SuWa across three months in six states of central Mexico during 2019. SE transmission dynamics were assessed using 87 experimental and 112 public isolates from Mexico collected during 2002-2019. We also studied genetic relatedness between SuWa isolates and human clinical strains collected in North America during 2005-2020. Among experimental isolates, we identified 41 SE serovars and 56 multi-locus sequence types (ST). Predominant serovars were Senftenberg (n=13), Meleagridis, Agona, and Newport (n=12 each), Give (n=10), Anatum (n=8), Adelaide (n=7), and Infantis, Mbandaka, Ohio and Typhimurium (n=6 each). We observed a high genetic diversity in the sample under study, as well as clonal dissemination of strains across distant regions. Some of these strains are epidemiologically important (ST14, ST45, ST118, ST132, ST198, and ST213), and were genotypically close to those involved in clinical cases in North America. Transmission network analysis suggests that SuWa are a relevant source of SE (0.7 source/hub ratio) and contributes to its dissemination as isolates from varied sources and clinical cases have SuWa isolates as common ancestors. Overall, the study shows SuWa act as reservoir of various SE serovars of public health significance. Further research is needed to better understand the mechanisms involved in SuWa contamination by SE, as well as develop interventions to contain its dissemination to food production settings. Study importance Surface waters are heavily used in food production worldwide. Several human pathogens can survive in these waters for long periods and disseminate to food production environments, contaminating our food supply. One of these pathogens is Salmonella enterica , a leading cause of foodborne infections, hospitalizations and deaths in many countries. This research demonstrates the role of surface waters as a vehicle for the transmission of Salmonella along food production chains. It also shows some strains circulating in surface waters are very similar to those implicated in human infections and harbor genes that confer resistance to multiple antibiotics, posing a risk to public health. The study contributes to expand our current knowledge on the ecology and epidemiology of Salmonella in surface waters.

Serovars, Virulence and Antimicrobial Resistance Genes of Non-Typhoidal Salmonella Strains from Dairy Systems in Mexico

“…This sequence type has been identified in healthy cattle isolated from fecal samples and lymph nodes [48]. Salmonella Give ST 654 has been isolated from surface water used for aquaculture and crop production in Mexico, along with serovars Meleagridis, Newport, and Anatum [18].…”

“…In Mexico, there is little information about the prevalence of Salmonella enterica in apparently healthy cattle and farm environments, the diversity of serovars associated with livestock, and the presence of antimicrobial resistance and virulence genes [17,18]. Therefore, the objectives of this study were to determine the prevalence of Salmonella enterica in dairy systems, examine the serovars and sequence types, and evaluate the presence of virulence and antimicrobial resistance genes circulating in 13 states of Mexico.…”

Prevalence and Genomic Diversity of Salmonella enterica Recovered from River Water in a Major Agricultural Region in Northwestern Mexico

“…According to the SNP phylogenetic analysis conducted in the present study, S. enterica isolates belonging to same serovar clustered together by MLST and had similar phylogenies according to the analysis of core genome SNPs and highly variable SNPs. Recently, a report on S. enterica isolates recovered from surface waters in central Mexico identified significantly higher intraserovar diversity based on the CSIPhylogeny analysis of highly variable SNPs [23]. Moreover, SNP phylogeny identified that some isolates belonging to the same serovar were grouped in different SNP clusters [23].…”

“…Recently, a report on S. enterica isolates recovered from surface waters in central Mexico identified significantly higher intraserovar diversity based on the CSIPhylogeny analysis of highly variable SNPs [23]. Moreover, SNP phylogeny identified that some isolates belonging to the same serovar were grouped in different SNP clusters [23]. By contrast, the S. enterica isolates from river water in the Culiacan Valley in northwestern Mexico were closely related with lower intraserovar diversity and were found to have less than 400 SNP if they belonged to the same serovar.…”

“…The low environmental prevalence of clinically relevant serovars provides a challenge for accurately determining the origin of the source of contamination and the identification of conducive conditions promoting the prevalence of these serovars in aquatic environments [9,18,22]. To aid in identifying sources of contamination, the use of high-resolution sequencing methods, such as whole genome sequencing, in conjunction with bioinformatic approaches can assist with the identification of genetic markers distinguishing environmental and clinical isolates, allowing a better understanding of the genotypic profiles of Salmonella strains recovered from aquatic environments in Mexico [23].…”