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.

Listeria monocytogenes is the causative agent of listeriosis, which is an uncommon but severe infection associated with high mortality rates in humans especially in high-risk groups. This bacterium survives a variety of stress conditions (e.g., high osmolality, low pH), which allows it to colonize different niches especially niches found in food processing environments. Additionally, a considerable heterogeneity in pathogenic potential has been observed in different strains. In this study, 38 isolates of L. monocytogenes collected in Chile from clinical samples (n = 22) and non-clinical samples (n = 16) were analyzed using whole genome sequencing (WGS) to determine their genomic diversity. A core genome Single Nucleotide Polymorphism (SNP) tree using 55 additional L. monocytogenes accessions classified the Chilean isolates in lineages I (n = 25) and II (n = 13). In silico, Multi-locus sequence typing (MLST) differentiated the isolates into 13 sequence types (ST) in which the most common were ST1 (15 isolates) and ST9 (6 isolates) and represented 55% of the isolates. Genomic elements associated with virulence (i.e., LIPI-1, LIPI-3, inlA, inlB, inlC, inlG, inlH, inlD, inlE, inlK, inlF, and inlJ) and stress survival (i.e., stress survival islet 1 and stress survival islet 2) were unevenly distributed among clinical and non-clinical isolates. In addition, one novel inlA premature stop codon (PMSC) was detected. Comparative analysis of L. monocytogenes circulating in Chile revealed the presence of globally distributed sequence types along with differences among the isolates analyzed at a genomic level specifically associated with virulence and stress survival.

The genus Salmonella has more than 2,600 serovars, and this trait is important when considering interventions for Salmonella control. Bacteriophages that are used for biocontrol must have an exclusively lytic cycle and the ability to lyse several Salmonella serovars under a wide range of environmental conditions. Salmonella phages were isolated and characterized from 34 backyard production systems (BPSs) with a history of Salmonella infections. BPSs were visited once, and cloacal or fecal samples were processed for phage isolation. Four hosts, Salmonella serovars Enteritidis, Heidelberg, Infantis, and Typhimurium, were used for phage isolation. The host range of the phages was later characterized with a panel of 23 Salmonella serovars (serovar diversity set) and 31 isolates obtained from the same farms (native set). Genetic relatedness for 10 phages with a wide host range was characterized by restriction fragment length polymorphism, and phages clustered based on the host range. We purified 63 phages, and 36 phage isolates were obtained on Salmonella Enteritidis, 16 on Salmonella Heidelberg, and 11 on Salmonella Infantis. Phages were classified in three clusters: (i) phages with a wide host range (cluster I), (ii) phages that lysed the most susceptible Salmonella serovars (serogroup D) and other isolates (cluster II), and (iii) phages that lysed only isolates of serogroup D (cluster III). The most susceptible Salmonella serovars were Enteritidis, Javiana, and Dublin. Seven of 34 farms yielded phages with a wide host range, and these phages had low levels of genetic relatedness. Our study showed an adaptation of the phages in the sampled BPSs to serogroup D Salmonella isolates and indicated that isolation of Salmonella phages with wide host range differs by farm. A better understanding of the factors driving the Salmonella phage host range could be useful when designing risk-based sampling strategies to obtain phages with a wide lytic host range for biocontrol purposes.

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Salmonella enterica can cause disease and mortality in calves. This pathogen is also a zoonosis that can be transmitted by animal contact or by food. The prevalence of Salmonella in dairy farms has been reported to range from 0 to 64%, and, due to the diversity of Salmonella serovars that can be circulating, Salmonella is an important concern for dairy production. Bacteriophages that infect Salmonella have been documented to be abundant and widely distributed in the dairy environment. The current study investigated the diversity of Salmonella serovars and Salmonella phages in 8 dairy farms with a history of diarrhea in southern Chile. A total of 160 samples from sick calves, healthy calves, and the environment were analyzed for Salmonella and phage. Isolated phages were characterized and classified by their host range using a panel of 26 Salmonella isolates representing 23 serovars. Host ranges were classified according to lysis profiles (LP) and their spatial distribution was mapped. Salmonella-infecting phages were identified, but none of the 160 samples were positive for Salmonella. A total of 45 phage isolates were obtained from sick calves (11), healthy calves (16), or the environment (18). According to their host range, 19 LP were identified, with LP1 being the most common on all 8 farms; LP1 represents phages that only lyse serogroup D Salmonella. The identification of Salmonella phages but not Salmonella in the same samples could suggest that these phages are controlling Salmonella in these farms.

Animals raised in backyard productive systems (BPS) have been frequently associated with Salmonella outbreaks. Several serovars have caused these events, showing that different BPSs can be contaminated by distinct Salmonella serovars. The aim of this study was to characterize the genomic diversity of Salmonella isolates obtained from BPSs in Central Chile to understand their genomic relatedness. A whole‐genome SNP‐based phylogenetic analysis of 22 Salmonella isolates from 12 locations revealed that S. Typhimurium isolates clustered based on the BPS that they were originally isolated from, and the same was established for S. Enteritidis isolates. Furthermore, our genomic analysis shows that animals from different species (i.e., a chicken, a duck and a pig) carried genetically related S. Typhimurium strains within the same BPS. Moreover, some of these genetically related isolates were obtained in different years (2013 and 2014), indicating that farm‐specific Salmonella can persist in BPSs for multiple years and that interspecies transmission is plausible in this environment. Understanding the dynamics of interspecies transmission of Salmonella serovars within a contaminated BPS is fundamental to the design of mitigation strategies to reduce outbreaks of human Salmonella associated with backyard production systems.

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