First detection and characterization ofSalmonellaspp. in poultry and swine raised in backyard production systems in central Chile

Abstract

Little is known about Salmonella serovars circulating in backyard poultry and swine populations worldwide. Backyard production systems (BPS) that raise swine and/or poultry are distributed across Chile, but are more heavily concentrated in central Chile, where industrialized systems are in close contact with BPS. This study aims to detect and identify circulating Salmonella serovars in poultry and swine raised in BPS. Bacteriological Salmonella isolation was carried out for 1744 samples collected from 329 BPS in central Chile. Faecal samples were taken from swine, poultry, geese, ducks, turkeys and peacocks, as well as environmental faecal samples. Confirmation of Salmonella spp. was performed using invA-polymerase chain reaction (PCR). Identification of serovars was carried out using a molecular serotyping approach, where serogroups were confirmed by a multiplex PCR of Salmonella serogroup genes for five Salmonella O antigens (i.e., D, B, C1, C2-C3, and E1), along with two PCR amplifications, followed by sequencing of fliC and fljB genes. A total of 25 samples (1·4% of total samples) from 15 BPS (4·6 % of total sampled BPS) were found positive for Salmonella. Positive samples were found in poultry (chickens and ducks), swine and environmental sources. Molecular prediction of serovars on Salmonella isolated showed 52·0% of S. Typhimurium, 16·0% of S. Infantis, 16·0% S. Enteritidis, 8·0% S. Hadar, 4·0% S. Tennessee and 4·0% S. Kentucky. Poor biosecurity measures were found on sampled BPS, where a high percentage of mixed confinement systems (72·8%); and almost half of the sampled BPS with improper management of infected mortalities (e.g. selling the carcasses of infected animals for consumption). Number of birds other than chickens (P = 0·014; OR = 1·04; IC (95%) = 1·01-1·07), mixed productive objective (P = 0·030; OR = 5·35; IC (95%) = 1·24-27·59) and mixed animal replacement origin (P = 0017; OR = 5·19; IC (95%) = 1·35-20·47) were detected as risk factors for BPS positivity to Salmonella spp. This is the first evidence of serovars of Salmonella spp. circulating in BPS from central Chile. Detected serovars have been linked to human and animal clinical outbreaks worldwide and in Chile, highlighting the importance of BPS on the control and dissemination of Salmonella serovars potentially hazardous to public health.

Genomics of Salmonella contaminating backyard production systems reveals persistence and transmission of genetically related Salmonella on a farm basis

“…In the current study, we characterized the genomic diversity of 22 Salmonella isolates that were previously obtained from BPSs in Chile (Alegria‐Moran et al, ) and found that genetically related Salmonella are present in different animals of the same BPS over time. Salmonella g enomes obtained in this study ranged from 4.53 to 4.93 Mb and were assembled in a range between 43 and 101 contigs (Table ).…”

“…A recent publication reported deficiencies in biosecurity and in agricultural practices for the BPSs used in our study. Among the problems detected were deficient hand cleaning, insufficient disinfection after handling animals and improper disposal of dead animals (Alegria‐Moran et al, ). The persistence of certain Salmonella strains in these BPSs environments could be a direct consequence of these bad practices.…”

“…A total of 22 Salmonella isolates were previously obtained from 12 BPSs in central Chile from 2012 to 2014 (Alegria‐Moran et al, ). From each BPS, one to four isolates were obtained as described by Alegria‐Moran et al ().…”

“…A total of 22 Salmonella isolates were previously obtained from 12 BPSs in central Chile from 2012 to 2014 (Alegria‐Moran et al, ). From each BPS, one to four isolates were obtained as described by Alegria‐Moran et al (). Selected isolates, representing unique isolates from each sample, were obtained from chickens (16), pigs (4), duck (1) and the environment of a BPS (1) to be sequenced by WGS (Table ).…”

“…Tennessee and S . Kentucky (Alegria‐Moran, Rivera, Toledo, Moreno‐Switt, & Hamilton‐West, ) was determined. In this study, we report genomic diversity of 22 Salmonella isolates from different serovars, which were previously obtained from poultry and pigs raised in BPSs.…”