Epidemiological Characterization of Isolates of Salmonella enterica and Shiga Toxin-Producing Escherichia coli from Backyard Production System Animals in the Valparaíso and Metropolitana Regions

SIMPLE SUMMARY: This study aimed to investigate the prevalence and risk factors for Salmonella enterica and Shiga toxin-producing Escherichia coli (STEC) in backyard production systems (BPS) from central Chile. BPS were determined as the epidemiologic unit, collecting, for every sampled PS, cloacal or rectal swabs, which were then analyzed by bacterial culture and confirmed by conventional PCR. A positivity rate of 4.17% was estimated among BPS for S. enterica in the Metropolitana region, while no positive samples were found in the Valparaíso region. For STEC, a positivity rate among BPS of 11.76% in the Metropolitana region and 18.52% in the Valparaíso region was estimated. The study also identifies different antimicrobial phenotypical resistance profiles in both S. enterica and STEC, including multiresistant strains, considered critically important under the One Health approach. The presence of ruminants inside BPS was identified as a factor that raises the risk of positivity for STEC and S. enterica/STEC. The study highlights the need for improved biosecurity measures and education regarding zoonotic agents in BPS. The findings of this study are of high importance, providing evidence to policymakers and stakeholders to develop strategies to reduce the risk of transmission of zoonotic agents from BPS to humans and other animals. BPS managed exclusively by women were shown to be at a greater risk for S. entarica/STEC positivity compared to men of the family, emphasizing the need to implement and deliver training to women to reduce the current consequences of the gender gap and its potential impact on this animal and human neglected population in Chile. ABSTRACT: Backyard production systems (BPS) are distributed worldwide, rearing animals recognized as reservoirs of Salmonella enterica and Shiga toxin-producing Escherichia coli (STEC), both zoonotic pathogens. The aim of this study was to characterize isolates of both pathogens obtained from animals raised in BPS from two central Chile regions. The presence of pathogens was determined by bacterial culture and confirmatory PCR for each sampled BPS, calculating positivity rates. Multivariate logistic regression was used to determine risk factors. Additionally, phenotypic antimicrobial resistance was determined. A positivity rate of 2.88% for S. enterica and 14.39% for STEC was determined for the complete study region (Valparaíso and Metropolitana regions). Risk factor analysis suggests that the presence of ruminants (OR = 1.03; 95% CI = 1.002–1.075) increases the risk of STEC-positive BPS, and the presence of ruminants (OR = 1.05; 95% CI = 1.002–1.075) and the animal handlers being exclusively women (OR = 3.54; 95% CI = 1.029–12.193) increase the risk for S. enterica/STEC positivity. Eighty percent of S. enterica isolates were multidrug resistant, and all STEC were resistant to Cephalexin. This study evidences the circulation of multidrug-resistant zoonotic bacterial strains in animals kept in BPS and the presence of factors that modify the risk of BPS positivity for both pathogens.