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Salmonellosis is one of the most frequently reported zoonotic foodborne diseases worldwide, and poultry is the most important reservoir of

The Type VI Secretion System (T6SS) is a multiprotein device that has emerged as an important fitness and virulence factor for many Gram-negative bacteria through the injection of effector proteins into prokaryotic or eukaryotic cells

Salmonella spp. is one of the most common foodborne pathogens worldwide, therefore, its control is highly relevant for the food industry. Phages of the Felixounavirus genus have the characteristic that one phage can infect a large number of different Salmonella serovars and, thus, are proposed as an alternative to antimicrobials in food production. Here, we describe two new members of the Felixounavirus genus named vB_Si_35FD and vB_Si_DR94, which can infect Salmonella Infantis. These new members were isolated and sequenced, and a subsequent comparative genomic analysis was conducted including 23 publicly available genomes of Felixounaviruses that infect Salmonella. The genomes of vB_Si_35FD and vB_Si_DR94 are 85,818 and 85,730 bp large and contain 129 and 125 coding sequences, respectively. The genomes did not show genes associated with virulence or antimicrobial resistance, which could be useful for candidates to use as biocontrol agents. Comparative genomics revealed that closely related Felixounavirus are found in distinct geographical locations and that this genus has a conserved genomic structure despite its worldwide distribution. Our study revealed a highly conserved structure of the phage genomes, and the two newly described phages could represent promising biocontrol candidates against Salmonella spp. from a genomic viewpoint.

Salmonella is a major bacterial foodborne pathogen that causes the majority of worldwide food-related outbreaks and hospitalizations. Salmonellosis outbreaks can be caused by multidrug-resistant (MDR) strains, emphasizing the importance of maintaining public health and safer food production. Nevertheless, the drivers of MDR Salmonella serovars have remained poorly understood. In this study, we compare the resistance profiles of Salmonella strains isolated from 4047 samples from domestic and wild animals in Chile. A total of 106 Salmonella strains (2.61%) are isolated, and their serogroups are characterized and tested for susceptibility to 16 different antimicrobials. The association between antimicrobial resistance (AMR) and a subset of independent variables is evaluated using multivariate logistic models. Our results show that 47 antimicrobial-resistant strains were found (44.3% of the total strains). Of the 47, 28 correspond to single-drug resistance (SDR = 26.4%) and 19 are MDR (17.9%). S. Enteritidis is highly persistent in animal production systems, however, we report that serogroup D strains are 18 times less likely to be resistant to at least one antimicrobial agent than the most common serogroup (serogroup B). The antimicrobials presenting the greatest contributions to AMR are ampicillin, streptomycin and tetracycline. Additionally, equines and industrial swine are more likely to acquire Salmonella strains with AMR. This study reports antimicrobial-susceptible and resistant Salmonella in Chile by expanding the extant literature on the potential variables affecting antimicrobial-resistant Salmonella.

Objective The objective of this scoping review is to identify and map existing evidence of antimicrobial resistance (AMR) in water in Latin America and the Caribbean (LAC), while also identifying the gaps in AMR information in the region in eight themes of interest. Introduction Antimicrobial resistance is a public health concern that has gained increasing global awareness. Concerns have been raised toward the importance of the environment's role in the dissemination of clinically relevant AMR. Although studies on AMR have been conducted, the reality of the role of the environment in the LAC region has not been studied. Inclusion criteria Articles that examine AMR in water in the LAC region will be considered for inclusion. Antimicrobial resistance will be defined as a natural process that arises when the microorganisms that cause infection (e.g. bacteria) survive exposure to a drug that would normally kill them or stop their growth. The search will focus on eight themes of interest, as defined in the protocol, relating to the presence of resistant microorganisms in water sources and reported negative health effects. Qualitative and quantitative studies will be considered for inclusion. Reviews and gray literature will be excluded. Methods The proposed scoping review will be conducted in accordance with the JBI methodology for scoping reviews. A search for published literature will be performed in PubMed, Web of Science and Scopus. Independent screening of articles will be performed by examining the abstracts and then the full texts, utilizing pre-defined inclusion and exclusion criteria. Data for specific variables will be extracted, and descriptive examination will be performed.

Antimicrobial resistance is an increasing problem worldwide, and Salmonella spp. resistance to quinolone was classified by WHO in the high priority list. Recent studies in Europe and in the US reported the presence of small plasmids carrying quinolone resistance in Enterobacteriaceae isolated from poultry and poultry products. The aims of this study were to identify and characterize plasmid mediated quinolone resistance in Salmonella spp., and to investigate transduction as a possible mechanism associated to its dissemination. First, we assessed resistance to nalidixic acid and / or ciprofloxacin in 64 Salmonella spp. and detected resistance in 8 of them. Genomic analyses determined that 6 isolates of different serotypes and sources carried an identical 2.7 kb plasmid containing the gene qnrB19 which confers quinolone resistance. The plasmid detected also has high identity with plasmids reported in the US, Europe, and South America. The presence of similar plasmids was later surveyed by PCR in a local Salmonella collection (n=113) obtained from diverse sources: food (eggs), wild and domestic animals (pigs, horse, chicken), and human clinical cases. qnrB19-carrying plasmids were found in 8/113 Salmonella tested strains. A bioinformatics analysis including Chilean and previously described plasmids revealed over 95.0% of nucleotide identity among all the sequences obtained in this study. Furthermore, we found that a qnrB19-carrying plasmid can be transferred between Salmonella of different serotypes through a P22-mediated transduction. Altogether our results demonstrate that plasmid mediated quinolone resistance (PMQR) is widespread in Salmonella enterica of different serotypes isolated from human clinical samples, wild and domestic animals and food in Chile and suggest that transduction could be a plausible mechanism for its dissemination. The occurrence of these antimicrobial resistance elements in Salmonella in a widespread area is of public health and food safety concern, and it indicates the need for increased surveillance for the presence of these plasmids in Salmonella strains and to assess their actual impact in the raise and spread of quinolone resistance.

The aim of this review was to understand the research that has been conducted in South American countries to detect or quantify major water and foodborne pathogens, with the aim of identifying advancements and gaps in food safety in the region. This systematic review focused on the following major bacterial pathogens: Salmonella spp., Shiga-toxin producing Escherichia coli, Listeria monocytogenes, and Campylobacter spp., along with the protozoal pathogens Cryptosporidium and Giardia. For this review, we searched for research articles conducted in Argentina, Bolivia, Brazil, Chile, Colombia, Ecuador, Paraguay, Peru, Uruguay, and Venezuela. This study identified the following as major advancements: (i) research articles on pathogens in the food chain in South America have increased in this decade and (ii) studies have diversified detection methods in different food groups. In addition, the following points were identified as major gaps: (i) most of the food safety research has been conducted in Brazil and Argentina and (ii) scarce studies have quantified foodborne pathogens, which is crucial for risk assessment. Strengthening the scientific evidence of human exposure to major pathogens in food and water is necessary in this region, and it should be prioritized in public research funding.

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.

Artisanal cheese from southern Chile is made primarily by rural families who raise dairy cows and produce cheese as a way to add value to their milk. The most common cheese produced is chanco, a semi-hard cheese that is typically sold in unauthorized markets. The methods of chanco production do not always follow good manufacturing practices; however, the presence of Listeria monocytogenes contamination in this cheese has not been previously documented. To better understand production practices and L. monocytogenes contamination, 39 cheese producers were surveyed with regard to infrastructure, cleaning and sanitation, pest control, personal hygiene, training, raw materials, and manufacturing. During four sampling trips in 2016 (March, May, August, and November), 546 samples were collected (468 cheese samples and 78 milk samples). For producers that tested positive for L. monocytogenes, environmental monitoring was also conducted, for which 130 additional samples were collected. Presumptive L. monocytogenes isolates (N = 94) were further characterized and subtyped using standard techniques and qPCR-based species/subtype verification; a subset of 52 isolates were also subtyped by Pulsed Field Gel Electrophoresis (PFGE). L. monocytogenes was found in 19 cheeses (4.1%) from five producers (12.8%). The most frequent serotypes were 1/2b (48.9%), group 4B (4b, 4d, 4e) (45.7%), and serotype 1/2a (5.4%). Although no milk samples tested positive for L. monocytogenes, all cheese samples from two producers tested positive during two of the samplings. Distinct PFGE types were recovered from each facility, demonstrating persistence of certain subtypes of the pathogen that ultimately caused end-product contamination. Environmental monitoring of the five positive producers revealed a prevalence of L. monocytogenes ranging from 0 to 30%, with food contact surfaces having the highest incidence of this organism. The findings of this study contribute to the understanding of L. monocytogenes incidence in artisanal cheese in the region of southern Chile.

Salmonella enterica is one of the main causes of gastrointestinal disease worldwide. Wild birds are capable of harboring a variety of Salmonella serovars, which could have an important role in the epidemiology of salmonellosis in humans and production animals. We tested 519 fecal samples from raptors and aquatic birds from different regions of central (three rehabilitation centers for wildlife and the coastal area) and southern areas of Chile for Salmonella. All samples were obtained in 2015 and 2017, covering all four seasons. Salmonella was isolated from 12 of the 519 samples (2%) analyzed, from two carnivorous birds, four birds with generalist habits, and six waterfowl. Among the isolates obtained, one showed resistance to gentamicin, and one showed a multidrug-resistance phenotype, with resistance to ampicillin, ceftriaxone, ciprofloxacin, chloramphenicol, streptomycin, gentamicin, kanamycin, trimethoprim-sulfamethoxazole, and tetracycline. These results demonstrated the importance of characterizing Salmonella in wild birds because previous studies have shown genetic and phenotypic evidence suggesting interspecies transmission of Salmonella enterica that is resistant to antimicrobials between humans and wild and domestic birds.

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.

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.

SUMMARYLittle is known aboutSalmonellaserovars 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 circulatingSalmonellaserovars in poultry and swine raised in BPS. BacteriologicalSalmonellaisolation 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 ofSalmonellaspp. was performed usinginvA-polymerase chain reaction (PCR). Identification of serovars was carried out using a molecular serotyping approach, where serogroups were confirmed by a multiplex PCR ofSalmonellaserogroup genes for fiveSalmonellaO antigens (i.e., D, B, C1, C2-C3, and E1), along with two PCR amplifications, followed by sequencing offliCandfljBgenes. A total of 25 samples (1·4% of total samples) from 15 BPS (4·6 % of total sampled BPS) were found positive forSalmonella. Positive samples were found in poultry (chickens and ducks), swine and environmental sources. Molecular prediction of serovars onSalmonellaisolated showed 52·0% ofS.Typhimurium, 16·0% ofS.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 toSalmonellaspp. This is the first evidence of serovars ofSalmonellaspp. 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 ofSalmonellaserovars potentially hazardous to public health.

Objective The purpose of this study was to detect the presence of circulating Salmonella spp. on backyard production systems (BPS) with poultry or swine breeding in central Chile Introduction Characteristics and conditions of backyard production systems (BPS) transform them into potential maintainers of priority zoonotic agents, like Salmonella spp., highly important agent because of its impact in animal and public health (1). Methods A stratified and proportional random sampling approach was performed (2), based on 15 provinces from the study area (regions of Valparaiso, Metropolitana and LGB O’Higgins). 329 BPS sampled (equivalent to 1,744 samples). Stool content inoculated in test tubes with peptone water (APT, Difco®) supplemented with Novobiocin (Sigma®), incubated for 18 to 24 hours at 37° C. Subcultured on modify semisolid Rappaport Vassiliadis (MSRV, Oxoid®) agar supplemented with Novobiocin, incubated for 24 to 48 hours at 41.5° C. Samples compatible with growth and/or diffusion were sub-cultured by exhaustion on Xylose Lysine Deoxychocolate (XLD, Difco®) agar and then incubated for 24 hours at 37° C (3). Confirmation made by conventional PCR for invA genes (4). Serotypes were predicted using a combination of PCR and sequencing, aimed directly at genes coding for O, H1 and H2 antigens (5). Results 1,744 samples were collected belonging to the 329 BPS. 15 positive BPS (4.6%) detected. Serotypes detected correspond to Salmonella Typhimurium (21.7%), followed by Salmonella Enteritidis (13.0%) and Salmonella Infantis (13.0%), Salmonella Hadar or Istanbul (8.7%), Salmonella [z42] or Tenessee (4.4%), Salmonella Kentucky (4.4) and unknown (34.8%) (Table 1). Conclusions This is the first evidence of serotypes of Salmonella spp. circulating at a regional level in BPS from central Chile. A relevant pathogen for public health.

Foodborne pathogens cause an important public health burden, which is estimated in 600 million cases and more than 400,000 deaths, globally every year. The most susceptible populations, such as children under the age of five, the elderly and immunocompromised, account for the majority of the deaths. Food safety incidents, outbreaks, sporadic cases, and recalls have recognized economic impact, estimated at 7 billion every year in the US. Food safety has become a priority, and the implementation of preventive controls and monitoring systems has raised the development of new tools to detect and prevent pathogens in the food chain. Detection tools have evolved quickly, from rapid testing methods to application of genomics and metagenomics. Importantly, to reduce food safety hazards at food processing, the food chain needs to be seen from farm to fork. This review summarized the main findings discussed during the 2016 OECD-sponsored symposium on food safety. These include i) trends in food safety that embrace the need to implement new tools in detection and prevention, ii) the very rapid evolution of technologies to detect foodborne pathogens, iii) holistic approaches to prevent pathogens require a whole chain approach, and iv) key pillars to facilitate global implementations of new tools in food safety.

Salmonella Infantis is considered in recent years an emerging Salmonella serovar, as it has been associated with several outbreaks and multidrug resistance phenotypes. Phages appear as a possible alternative strategy to control Salmonella Infantis (SI). The aims of this work were to characterize two phages of the Felixounavirus genus, isolated using the same strain of SI, and to expose them to interact in challenge assays to identify genetic and phenotypic changes generated from these interactions. These two phages have a shared nucleotide identity of 97% and are differentiated by their host range: one phage has a wide host range (lysing 14 serovars), and the other has a narrow host range (lysing 6 serovars). During the 12 h challenge we compared: (1) optical density of SI, (2) proportion of SI survivors from phage-infected cultures, and (3) phage titer. Isolates obtained through the assays were evaluated by efficiency of plating (EOP) and by host-range characterization. Genomic modifications were characterized by evaluation of single nucleotide polymorphisms (SNPs). The optical density (600 nm) of phage-infected SI decreased, as compared to the uninfected control, by an average of 0.7 for SI infected with the wide-host-range (WHR) phage and by 0.3 for SI infected with the narrow-host-range (NHR) phage. WHR phage reached higher phage titer (7 &times, 1011 PFU/mL), and a lower proportion of SI survivor was obtained from the challenge assay. In SI that interacted with phages, we identified SNPs in two genes (rfaK and rfaB), which are both involved in lipopolysaccharide (LPS) polymerization. Therefore, mutations that could impact potential phage receptors on the host surface were selected by lytic phage exposure. This work demonstrates that the interaction of Salmonella phages (WHR and NHR) with SI for 12 h in vitro leads to emergence of new phenotypic and genotypic traits in both phage and host. This information is crucial for the rational design of phage-based control strategies.