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Multidrug resistance (MDR) considered as global crisis facing poultry industry. Migratory birds play very important role in the dissemination of antimicrobial resistant pathogen during their fly way specially to poultry farms. Therefore, 750 samples from migratory birds and 300 samples from broiler chicken farms and its environment were collected during the winter seasons of five years (2019 to 2023). The samples were subjected to the isolation of Salmonella enterica and Escherichia coli with the detection of antimicrobial resistance (phenotypic and genotypic) with insight to the genetic similarity between the isolates from migratory birds and broiler chickens' farms. Different members of Enterobacteriaceae were isolated; Salmonella enterica, Escherichia coli, Citrobacter, Enterobacter, Klebsiella, Proteus, Providencia, Serratia, Hafnia. 298 (28.4%) of S. enterica strains belonging to 27 serovars. S. Typhimurium, S. Kentucky, S. Enteritidis and S. Shangani were the common 4 serotypes between migratory birds and farms. Meanwhile, we found 489 (46.6%) isolates of E. coli belonging to 24 serogroups and O91, O128, O26, O125, O55, O103 and O159 were the common 7serogroups between migratory birds and farms samples. The majority of Salmonella (91.6%; 274 out of 298) and E. coli (92%; 450 out of 489) were MDR. The MDRI range of Salmonella and E. coli was 0.08- 1.The genetic similarity between the isolates of migratory birds and broiler chicken farms were detected by ERICPCR and hot map. This study suggests the continuous applications of surveillance programs for migratory birds and biosecurity measures in poultry farms., (© 2024. The Author(s).)

An increasing number of countries are investigating options to stop the spread of the emerging zoonotic infection Salmonella Dublin (S. Dublin), which mainly spreads among bovines and with cattle manure. Detailed surveillance and cattle movement data from an 11-yr period in Denmark provided an opportunity to gain new knowledge for mitigation options through a combined social network and simulation modeling approach. The analysis revealed similar network trends for noninfected and infected cattle farms despite stringent cattle movement restrictions imposed on infected farms in the national control program. The strongest predictive factor for farms becoming infected was their cattle movement activities in the previous month, with twice the effect of local transmission. The simulation model indicated an endemic S. Dublin occurrence, with peaks in outbreak probabilities and sizes around observed cattle movement activities. Therefore, pre- and postmovement measures within a 1-mo time window may help reduce S. Dublin spread., (The Authors. Published by Elsevier Inc. on behalf of the American Dairy Science Association®. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).)

Background: Although salmonellosis is considered to be a foodborne zoonotic disease, pets can play a significant role in the dissemination of antimicrobial-resistant Salmonella organisms to humans because of close contact with their owners., Objectives: To determine the prevalence, risk factors, virulence factors, serotypes, and antimicrobial resistance profile of Salmonella in pet dogs and cats in Turkey and to assess the public health risk. Furthermore, to perform macroscopic comparison of lactic acid bacteria (LAB) in Salmonella-positive and Salmonella-negative animals., Methods: International Standards Organization (ISO) 6579-1:2017 and Food and Drug Administration (FDA) methods were used to compare the effectiveness of culture methods in the identification of Salmonella in 348 rectal swabs. Positive isolates were serotyped using the slide agglutination method according to the White-Kauffmann-Le Minor scheme and the presence of virulence genes (invA and stn) were evaluated by polymerase chain reaction (PCR). Antimicrobial activity was tested by Kirby-Bauer disk diffusion method according to Clinical and Laboratory Standards Institute (CLSI) guidelines., Results: Salmonella prevalence was 5.73% (9/157) in dogs and 0.0% (0/191) in cats. Eight (8/9) isolates were cultured with the ISO method and 5 (5/9) isolates were cultured with the FDA method. Macroscopic results revealed that Salmonella agents had no effect on LAB. Three different serotypes were detected and all isolates were positive for virulence genes. Antibiotic resistance profiling indicated that 11.1% of the isolates were MDR and the highest resistance was found for ciprofloxacin. MDR-resistant S. Virchow and carbapenem-resistant S. Enteritidis were detected from dog isolates. There was a significant difference between raw meat consumption and Salmonella carriage (p < 0.01)., Conclusions: Dogs could be potential carriers of Salmonella infection. The isolation of Salmonella in healthy dogs instead of dogs suffering from diarrhoea indicates that attention should be paid to asymptomatic carriage. The emergence of resistance among zoonotic Salmonella isolates poses a significant threat to public health., (© 2024 The Author(s). Veterinary Medicine and Science published by John Wiley & Sons Ltd.)

Salmonella Typhimurium is a zoonotic pathogen that poses a major threat to public health. This generalist serotype can be found in many hosts and the environment where varying selection pressures may result in the accumulation of antimicrobial resistance determinants. However, the transmission of this serotype between food-producing hosts, specifically between poultry layer flocks and nearby dairy herds, was never demonstrated. We investigated an outbreak at a dairy in Israel to determine the role of nearby poultry houses to be sources of infection. The 2-month outbreak resulted in a 47% mortality rate among 15 calves born in that period. Routine treatment of fluid therapy, a nonsteroidal anti-inflammatory, and cefquinome was ineffective, and control was achieved by the introduction of vaccination of dry cows against Salmonella (Bovivac S, MSD Animal Health) and a strict colostrum regime. Whole genome sequencing and antimicrobial sensitivity tests were performed on S . Typhimurium strains isolated from the dairy ( n = 4) and strains recovered from poultry layer farms ( n = 10). We identified acquired antimicrobial-resistant genes, including the bla CTX-M-55 gene, conferring resistance to extended-spectrum cephalosporins, which was exclusive to dairy isolates. Genetic similarity with less than five single nucleotide polymorphism differences between dairy and poultry strains suggested a transmission link. This investigation highlights the severe impact of S . Typhimurium on dairy farms and the transmission risk from nearby poultry farms. The accumulation of potentially transferable genes conferring resistance to critically important antimicrobials underscores the increased public health risk associated with S . Typhimurium circulation between animal hosts.IMPORTANCE Salmonella Typhimurium is one of the major causes of food-borne illness globally. Infections may result in severe invasive disease, in which antimicrobial treatment is warranted. Therefore, the emergence of multi-drug-resistant strains poses a significant challenge to successful treatment and is considered one of the major threats to global health. S . Typhimurium can be found in a variety of animal hosts and environments; however, its transmission between food-producing animals, specifically poultry layers flocks and dairy herds, was never studied. Here, we demonstrate the transmission of the pathogen from poultry to a nearby dairy farm. Alarmingly, the multi-drug-resistant strains collected during the outbreak in the dairy had acquired resistance to extended-spectrum cephalosporins, antibiotics critically important in treating Salmonellosis in humans. The findings of the study emphasize the increased risk to public health posed by zoonotic pathogens' circulation between animal hosts., Competing Interests: The authors declare no conflict of interest.

In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0-16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.

Salmonella enterica causes severe food-borne infections through contamination of the food supply chain. Its evolution has been associated with human activities, especially animal husbandry. Advances in intensive farming and global transportation have substantially reshaped the pig industry, but their impact on the evolution of associated zoonotic pathogens such as S. enterica remains unresolved. Here we investigated the population fluctuation, accumulation of antimicrobial resistance genes and international serovar Choleraesuis transmission of nine pig-enriched S. enterica populations comprising more than 9,000 genomes. Most changes were found to be attributable to the developments of the modern pig industry. All pig-enriched salmonellae experienced host transfers in pigs and/or population expansions over the past century, with pigs and pork having become the main sources of S. enterica transmissions to other hosts. Overall, our analysis revealed strong associations between the transmission of pig-enriched salmonellae and the global pork trade., (© 2024. The Author(s).)

Importance: Salmonella outbreaks linked to poultry meat have been reported continuously worldwide. Therefore, Salmonella contamination of poultry meats in slaughterhouses is one of the critical control points for reducing disease outbreaks in humans., Objective: This study examined the carry-over contamination of Salmonella species through the entire slaughtering process in South Korea., Methods: From 2018 to 2019, 1,097 samples were collected from the nine slaughterhouses distributed nationwide. One hundred and seventeen isolates of Salmonella species were identified using the invA gene-specific polymerase chain reaction, as described previously. The serotype, phylogeny, and antimicrobial resistance of isolates were examined., Results: Among the 117 isolates, 93 were serotyped into Salmonella Mbandaka (n = 36 isolates, 30.8%), Salmonella Thompson (n = 33, 28.2%), and Salmonella Infantis (n = 24, 20.5%). Interestingly, allelic profiling showed that all S . Mbandaka isolates belonged to the lineage of the sequence type (ST) 413, whereas all S . Thompson isolates were ST292. Moreover, almost all S . Thompson isolates (97.0%, 32/33 isolates) belonging to ST292 were multidrug-resistant and possessed the major virulence genes whose products are required for full virulence. Both serotypes were distributed widely throughout the slaughtering process. Pulsed-field gel electrophoretic analysis demonstrated that seven S . Infantis showed 100% identities in their phylogenetic relatedness, indicating that they were sequentially transmitted along the slaughtering processes., Conclusions and Relevance: This study provides more evidence of the carry-over transmission of Salmonella species during the slaughtering processes. ST292 S . Thompson is a potential pathogenic clone of Salmonella species possibly associated with foodborne outbreaks in South Korea., Competing Interests: The authors declare no conflicts of interest., (© 2024 The Korean Society of Veterinary Science.)

The spread of pathogens fundamentally depends on the underlying contacts between individuals. Modeling the dynamics of infectious disease spread through contact networks, however, can be challenging due to limited knowledge of how an infectious disease spreads and its transmission rate. We developed a novel statistical tool, INoDS (Identifying contact Networks of infectious Disease Spread) that estimates the transmission rate of an infectious disease outbreak, establishes epidemiological relevance of a contact network in explaining the observed pattern of infectious disease spread and enables model comparison between different contact network hypotheses. We show that our tool is robust to incomplete data and can be easily applied to datasets where infection timings of individuals are unknown. We tested the reliability of INoDS using simulation experiments of disease spread on a synthetic contact network and find that it is robust to incomplete data and is reliable under different settings of network dynamics and disease contagiousness compared with previous approaches. We demonstrate the applicability of our method in two host-pathogen systems: Crithidia bombi in bumblebee colonies and Salmonella in wild Australian sleepy lizard populations. INoDS thus provides a novel and reliable statistical tool for identifying transmission pathways of infectious disease spread. In addition, application of INoDS extends to understanding the spread of novel or emerging infectious disease, an alternative approach to laboratory transmission experiments, and overcoming common data-collection constraints., Competing Interests: The authors have declared that no competing interests exist.

Food-borne infections with Salmonella are among the most common causes of human diseases worldwide, and infections with the serovar Infantis are becoming increasingly important. So far, diverse phenotypes and genotypes of S . Infantis have been reported. Therefore, the present study aimed to investigate the infection dynamics of two different S . Infantis strains in broilers. For this purpose, 15 birds were infected on day 2 of life with 10 8  CFU/ml of a pESI+ or a pESI- S . Infantis strain, respectively. Ten uninfected birds served as in-contact birds to monitor transmission. In both groups, an increase of infection was observed from 7 days of age onwards, reaching its peak at 28 days. However, the pESI+ strain proved significantly more virulent being re-isolated from most cloacal swabs and organs by direct plating. In contrast, the pESI- strain could be re-isolated from cloacal swabs and caeca only when enrichment was applied. Although the excretion of this strain was limited, the transmission level to in-contact birds was similar to the pESI+ strain. Differences in infection dynamics were also reflected in the antibody response: whereas the pESI+ strain provoked a significant increase in antibodies, antibody levels following infection with the pESI- strain remained in the range of negative control birds. The actual findings provide for the first time evidence of S . Infantis strain-specific infectivity in broilers and confirm previous observations in the field regarding differences in persistence on farms and resistance against disinfectants.

A pandemic of Salmonella enterica serotype Enteritidis emerged in the 1980s due to contaminated poultry products. How Salmonella Enteritidis rapidly swept through continents remains a historical puzzle as the pathogen continues to cause outbreaks and poultry supply becomes globalized. We hypothesize that international trade of infected breeding stocks causes global spread of the pathogen. By integrating over 30,000 Salmonella Enteritidis genomes from 98 countries during 1949-2020 and international trade of live poultry from the 1980s to the late 2010s, we present multifaceted evidence that converges on a high likelihood, global scale, and extended protraction of Salmonella Enteritidis dissemination via centralized sourcing and international trade of breeding stocks. We discovered recent, genetically near-identical isolates from domestically raised poultry in North and South America. We obtained phylodynamic characteristics of global Salmonella Enteritidis populations that lend spatiotemporal support for its dispersal from centralized origins during the pandemic. We identified concordant patterns of international trade of breeding stocks and quantitatively established a driving role of the trade in the geographic dispersal of Salmonella Enteritidis, suggesting that the centralized origins were infected breeding stocks. Here we demonstrate the value of integrative and hypothesis-driven data mining in unravelling otherwise difficult-to-probe pathogen dissemination from hidden origins., (© 2021. The Author(s).)

Salmonella enterica is a major cause of foodborne diseases, and is also an important pathogenic bacterium in poultry industry. Whole genome sequencing (WGS) has become a crucial molecular typing technology used for the surveillance of the pathogenic bacteria. In the present study, we adopted WGS for tracking transmission of S. enterica in the production chain of broiler chickens. A total of 74 S. enterica strains were isolated from the different steps of breeding and slaughtering in a large production enterprise in Sichuan Province, China. The isolation rate of Salmonella was the highest in procedure of defeathering (50.0%) and evisceration (36.7%). Serotype identification showed that 74 Salmonella isolates included 7 serotypes, among which Mbandaka accounted for the highest proportions (35.1%). WGS revealed that 74 strains belonged to 7 different sequence types (STs), as well as 7 different ribosomal STs and 35 core genome STs. cgMLST-based Minimum Spanning Trees and phylogenetic tree based on the SNPs indicated that three serotypes, Mbandaka, Indiana and Kentucky, could be clonally transmitted between broiler farm and slaughterhouse. Heterogeneous resistant phenotypes and genotypes were found in two serotypes, Indiana and Kentucky. Our study indicated WGS in an accurate tool for molecular typing of S. enterica. Routine surveillance of S. enterica in the production chain of broiler chickens is needed., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Due to the recent outbreaks of Salmonella and Escherichia coli in fresh produce in the United States, the transfer of foodborne pathogens between animal feeding operations and fresh produce continues to be a considerable risk. The purpose of this study was to determine if the establishment of a vegetation barrier (VB) on small-scale sustainable farms could prevent the transmission of Salmonella and E. coli to nearby fresh produce fields. A 5-layer VB (31 × 49 m) was constructed between a dairy farm, a poultry farm, and a nearby produce field. Fresh produce (i.e., romaine lettuce and tomato), animal feces, and environmental (i.e., air, soil, and barrier) samples were collected for 15 months from 2018 to 2019. Four replicates of soil and fresh produce samples were taken from three plots located 10 m, 61 m, and 122 m away from the respective animal locations and processed for Salmonella and E. coli. Air and vegetative strip samples were sampled at 15-day intervals. Multiple colonies were processed from each positive sample, and a total of 143 positive Salmonella (n = 15) and E. coli (n = 128) isolates were retrieved from the soil, produce, air, and fecal samples. Interestingly, 18.2% of the Salmonella and E. coli isolates (n = 26) were recovered from fresh produce (n = 9) samples. Surprisingly, Salmonella isolates (n = 9) were only found in fecal (n = 3) samples collected from the dairy pasture. Data analysis suggests that the VB is an effective tool at reducing the transmission of E. coli and Salmonella from animal farms to fresh produce fields. However, based on phenotypic and genotypic testing, it is clear that fecal samples from animal farms are not the only source of pathogen contamination. This indicates that the environment (e.g., soil and wind), as well as the initial setup of the farm (e.g., proximity to service roads and produce plot placement), can contribute to the contamination of fresh produce. Our study recommends the need for more effective bioremediation and prevention control measures to use in conjunction with VBs to reduce pathogen transmission., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The history of pullorum disease is closely intertwined with the history of avian health research and that of the poultry industry. The seriousness of the disease galvanized the attention and brought together, for the first time, the pioneers of poultry health research to work cooperatively on different aspects of the disease. Control of the disease made it possible for intensive poultry production to develop as the basis for the modern poultry industry. During the early 1900s, bacillary white diarrhea (BWD) was a devastating disease of young chickens threatening the developing poultry industry. Dr. Leo F. Rettger isolated and described the bacterial pathogen, Salmonella enterica serotype Pullorum, for the first time in 1900. BWD was renamed pullorum disease in 1929. In subsequent years, Rettger and coworkers were able to reproduce the disease and fulfill Koch's postulates. Rettger et al . also showed that Salmonella Pullorum was vertically transmitted, which was the first time that a pathogen was shown to be vertically transmitted. The development of serologic tests was of crucial importance because it led to the development of effective eradication methods to identify carrier birds and to exclude these birds from the breeder flocks. The negative impact of pullorum disease on the poultry industry ultimately was one of the major reasons that the National Poultry Improvement Plan (NPIP) was developed by scientists, the poultry industry, and the United States Department of Agriculture (USDA). Needless to say, the work of the pioneering researchers formed the basis for the control of the disease. The NPIP started in 1935, with 34 states participating in testing 4 million birds representing 58.2% of the birds hatched. The program rapidly expanded to 47 states by 1948 and tested more than 30 million birds. In 1967, all commercial chicken hatcheries participating in the NPIP were 100% free of pullorum and typhoid disease caused by Salmonella enterica serotype Gallinarum. This historical overview of pullorum disease describes in some detail the progress made, especially during the early years, toward controlling this disease using methodologies that were often very basic but nonetheless effective. One has to admire the ingenuity and persistence of the early researchers leading to their achievements considering the research tools that were available at the time.

The objective of the present study was to characterize Salmonella enterica serovar Infantis isolated from chicken meat determining their clonal relationships with S. Infantis isolated from children with diarrhea. Fifteen meat-recovered S. Infantis were analyzed. Susceptibility levels to 14 antibacterial agents, the presence of ESBL and that of inducible plasmid-mediated AmpC (i-pAmpC) were determined by phenotypical methods. The presence of ESBL and pAmpC was confirmed by PCR, and detected ESBL-encoding genes were sequenced and their transferability tested by conjugation. The presence of gyrA mutations as well as Class 1 integrons was determined by PCR. Clonal relationships were established by REP-PCR and RAPD. In addition, 25 clinical isolates of S. Infantis were included in clonality studies. All meat-recovered S. Infantis were MDR, showing resistance to ampicillin, nitrofurans and quinolones, while none was resistant to azithromycin, ceftazidime or imipenem. ESBL (bla CTX-M-65 ) and i-pAmpC (bla DHA ) were detected in 2 and 5 isolates respectively (in one case concomitantly), with bla CTX-M-65 being transferable through conjugation. In addition, 1 isolate presented a bla SHV gene. All isolates presented D 87 Y at GyrA, nalidixic acid active efflux pump and a Class 1 integron of ~1000 bp (aadA1). Clonal analysis showed that all isolates were related. Further they were identical to MDR bla CTX-M-65 -producing S. Infantis isolates causing children diarrhea in Lima. The dissemination of MDR bla CTX-M-65 -producing S. Infantis between marketed meat and children highlights a public health problem which needs be controlled at livestock level., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Recent studies have shown that Salmonella shedding status affects sows' microbiota during gestation and that these modifications are reflected in the faecal microbiota of their piglets at weaning. The aims of this study were: (a) to evaluate the persistence, up to the fattening period, of the previously measured link between the microbiota of piglets and their mothers' Salmonella shedding status; and (b) measure the impact of the measured microbiota variations on their Salmonella excretion at this stage. To achieve this, 76 piglets born from 19 sows for which the faecal microbiota was previously documented, were selected in a multisite production system. The faecal matter of these swine was sampled after 4 weeks, at the fattening stage. The Salmonella shedding status and faecal microbiota of these animals were described using bacteriological and 16S rRNA gene amplicon sequencing respectively. The piglet digestive microbiota association with the Salmonella shedding status of their sows did not persist after weaning and did not affect the risk of Salmonella excretion during fattening, while the birth mother still affected the microbiota of the swine at fattening. This supports the interest in sows as a target for potentially transferrable microbiota modifications., (© 2020 The Society for Applied Microbiology.)

Salmonella is a major cause of foodborne disease globally. Pigs can carry and shed non-typhoidal Salmonella (NTS) asymptomatically, representing a significant reservoir for these pathogens. To investigate Salmonella carriage by African domestic pigs, faecal and mesenteric lymph node samples were taken at slaughter in Nairobi, Busia (Kenya) and Chikwawa (Malawi) between October 2016 and May 2017. Selective culture, antisera testing and whole genome sequencing were performed on samples from 647 pigs; the prevalence of NTS carriage was 12.7% in Busia, 9.1% in Nairobi and 24.6% in Chikwawa. Two isolates of S. Typhimurium ST313 were isolated, but were more closely related to ST313 isolates associated with gastroenteritis in the UK than bloodstream infection in Africa. The discovery of porcine NTS carriage in Kenya and Malawi reveals potential for zoonotic transmission of diarrhoeal strains to humans in these countries, but not for transmission of clades specifically associated with invasive NTS disease in Africa., Competing Interests: The authors have declared that no competing interests exist.

The transmission of Salmonella to humans via contaminated eggs is an international public health concern. S. Enteritidis is deposited inside eggs after colonizing reproductive tissues of infected hens. Diverse housing facility characteristics and flock management practices influence Salmonella persistence and transmission in poultry, but the food safety consequences of different housing systems for laying hens remain unresolved. The present study compared the horizontal transmission of infection and invasion of internal organs during the first 2 wk after experimental S. Enteritidis and S. Kentucky infection of laying hens in indoor cage-free housing. Groups of 72 hens were housed in isolation rooms simulating commercial cage-free barns, and 1/3 of the hens in each room were orally inoculated with either S. Enteritidis (2 rooms) or S. Kentucky (2 rooms). At 6 d and 12 d postinoculation, 12 inoculated and 24 contact-exposed hens in each room were euthanized, and samples of liver, spleen, ovary, oviduct, and intestinal tract were removed for bacteriologic culturing. All orally inoculated hens were positive for intestinal colonization by S. Enteritidis at 6 d postinfection, and 70.8% of contact-exposed hens had become colonized by 12 d. S. Enteritidis was isolated from 100% of livers and 50.0% of ovaries from inoculated birds at 6 d and from 41.7% of livers and 10.4% of ovaries from contact-exposed birds at 12 d. The majority of both orally inoculated and contact-exposed hens were positive for intestinal colonization by S. Kentucky at 6 d, but S. Kentucky was found in other internal organs of both inoculated and contact-exposed hens significantly (P < 0.05) less often than S. Enteritidis at both sampling intervals. These results indicate that Salmonella infection can spread rapidly and extensively among hens in cage-free indoor housing, including a high frequency of internal organ involvement for invasive S. Enteritidis., (Copyright © 2020. Published by Elsevier Inc.)

This study presents a new method for detection of between-herd livestock movements to facilitate disease tracing and more accurately describe network behaviour of relevance for spread of infectious diseases, including within-livestock business risk-carrying contacts that are not necessarily recorded anywhere. The study introduces and substantiates the concept of grouping livestock herds into business-units based on ownership and location in the tracing analysis of animal movement-based contact networks. To test the utility of this approach, whole core genome sequencing of 196 Salmonella Dublin isolates stored from previous surveillance and project activities was combined with information on cattle movements recorded in the Danish Cattle Database between 1997 and 2017. The aim was to investigate alternative explanations for S. Dublin circulation in groups of herds connected by ownership, but without complete records of livestock movements. The EpiContactTrace R-package was used to trace the contact networks between businesses and compare the network characteristics of businesses sharing strains of S. Dublin with different levels of genetic relatedness. The ownership-only definition proved to be an unreliable grouping approach for large businesses, which could have internal distances larger than 250 km and therefore do not represent useful epidemiological units. Therefore, the grouping was refined using spatial analysis. More than 90% of final business units formed were composed of one single cattle property, whereas multi-property businesses could reach up to eight properties in a given year, with up to 15 cattle herds having been part of the same business through the study period. Results showed markedly higher probabilities of introduction of infectious animals between proposed businesses from which the same clone of S. Dublin had been isolated, when compared to businesses with non-related strains, thus substantiating the business-unit as an important epidemiological feature to consider in contact network analysis and tracing of infection routes. However, this approach may overestimate real-life contacts between cattle properties and putatively overestimate the degree of risk-contacts within each business, since it is based solely on information about property ownership and location. This does not consider administrative and individual farmers behaviours that essentially keep two properties separated. Despite this, we conclude that defining epidemiological units based on businesses is a promising approach for future disease tracing tasks., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Salmonella enterica serotype Typhimurium (S. Typhimurium) is a leading cause of gastroenteritis and bacteraemia worldwide, and a model organism for the study of host-pathogen interactions. Two S. Typhimurium strains (SL1344 and ATCC14028) are widely used to study host-pathogen interactions, yet genotypic variation results in strains with diverse host range, pathogenicity and risk to food safety. The population structure of diverse strains of S. Typhimurium revealed a major phylogroup of predominantly sequence type 19 (ST19) and a minor phylogroup of ST36. The major phylogroup had a population structure with two high order clades (α and β) and multiple subclades on extended internal branches, that exhibited distinct signatures of host adaptation and anthropogenic selection. Clade α contained a number of subclades composed of strains from well characterized epidemics in domesticated animals, while clade β contained multiple subclades associated with wild avian species. The contrasting epidemiology of strains in clade α and β was reflected by the distinct distribution of antimicrobial resistance (AMR) genes, accumulation of hypothetically disrupted coding sequences (HDCS), and signatures of functional diversification. These observations were consistent with elevated anthropogenic selection of clade α lineages from adaptation to circulation in populations of domesticated livestock, and the predisposition of clade β lineages to undergo adaptation to an invasive lifestyle by a process of convergent evolution with of host adapted Salmonella serotypes. Gene flux was predominantly driven by acquisition and recombination of prophage and associated cargo genes, with only occasional loss of these elements. The acquisition of large chromosomally-encoded genetic islands was limited, but notably, a feature of two recent pandemic clones (DT104 and monophasic S. Typhimurium ST34) of clade α (SGI-1 and SGI-4)., Competing Interests: The authors have declared that no competing interests exist.

Two separate human outbreaks of Salmonella enterica serotype Reading occurred between 2017 and 2019 in the United States and Canada, and both outbreaks were linked to the consumption of raw turkey products. In this study, a comprehensive genomic investigation was conducted to reconstruct the evolutionary history of S. Reading from turkeys and to determine the genomic context of outbreaks involving this infrequently isolated Salmonella serotype. A total of 988 isolates of U.S. origin were examined using whole-genome-based approaches, including current and historical isolates from humans, meat, and live food animals. Broadly, isolates clustered into three major clades, with one apparently highly adapted turkey clade. Within the turkey clade, isolates clustered into three subclades, including an "emergent" clade that contained only isolates dated 2016 or later, with many of the isolates from these outbreaks. Genomic differences were identified between emergent and other turkey subclades, suggesting that the apparent success of currently circulating subclades is, in part, attributable to plasmid acquisitions conferring antimicrobial resistance, gain of phage-like sequences with cargo virulence factors, and mutations in systems that may be involved in beta-glucuronidase activity and resistance towards colicins. U.S. and Canadian outbreak isolates were found interspersed throughout the emergent subclade and the other circulating subclade. The emergence of a novel S Reading turkey subclade, coinciding temporally with expansion in commercial turkey production and with U.S. and Canadian human outbreaks, indicates that emergent strains with higher potential for niche success were likely vertically transferred and rapidly disseminated from a common source. IMPORTANCE Increasingly, outbreak investigations involving foodborne pathogens are difficult due to the interconnectedness of food animal production and distribution, and homogeneous nature of industry integration, necessitating high-resolution genomic investigations to determine their basis. Fortunately, surveillance and whole-genome sequencing, combined with the public availability of these data, enable comprehensive queries to determine underlying causes of such outbreaks. Utilizing this pipeline, it was determined that a novel clone of Salmonella Reading has emerged that coincided with increased abundance in raw turkey products and two outbreaks of human illness in North America. The rapid dissemination of this highly adapted and conserved clone indicates that it was likely obtained from a common source and rapidly disseminated across turkey production. Key genomic changes may have contributed to its apparent continued success in commercial turkeys and ability to cause illness in humans., (Copyright © 2020 Miller et al.)

Background: Salmonella is a zoonotic bacterium transmitted through the food chain and is an important cause of disease in humans. The current study is aimed to characterize Salmonella isolates from broiler breeder chickens farms using, polymerase chain reaction (PCR) and sequencing analysis of representative isolates., Methods: S. Kentucky (n=11), S. Enteritidis (n=4), S. Typhimurium (n=3), S. Breanderp (n=1), and Sand S. Newport (n=1), were identified from chicken farms. Antimicrobial sensitivity test among the strains were investigated using 13 antibacterial discs. The amplified fragments of fliC and sefA genes were used to characterize S. Kentucky, S. Enteritidis and S. Typhimurium strains. Sequence analysis of the amplified PCR products for Salmonella Kentucky, Enteritidis and Typhimurium were carried out., Results: Antimicrobial sensitivity testing revealed that 95% of the isolates were resistant to penicillin, 85% to norfloxacin and colistin sulfate (each), 75% to gentamicin, 70% to nalidixic acid and 60% to flumequine. The obtained sequences revealed the close identity of the isolated strains with other Salmonella reference strains in different countries., Conclusion: Analysis of the selected salmonellae confirm the report of Salmonella Enteritidis, Salmonella Typhimurium and Salmonella Kentucky circulation among broiler breeder flocks and the need to determine antibacterial susceptibility pattern regularly to detect multidrug-resistant salmonellae. The present study reports the circulation of Salmonella Kentucky, Enteritidis and Typhimurium among broiler breeder farms in Egypt. Emergency control of salmonellae is a global public health concern., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

This study investigated the prevalence of Salmonella and the molecular typing of all isolates in a goose production chain including hatchery, farm, slaughterhouse, and market. A total of 350 Salmonella isolates was detected from 1,030 samples, and 13 serotypes were recovered. The highest Salmonella contamination frequency was observed at the hatchery, which 51.8% (188/363) of samples were Salmonella positive. S. Potsdam and S. Typhimurium were the 2 most common serotypes. S. Potsdam was most frequently found in the hatchery, while S. Typhimurium was widely distributed in the goose production chain. In general, the antibiotic resistance of Salmonella isolates is low, which isolates from the market is comparatively higher than from other production links indicating a possibility of Salmonella cross-contamination in the market. By the multilocus sequence typing (MLST) analysis, 7 different ST types were identified. ST2039 was the most common ST type, which was mostly found from S. Potsdam isolates in hatchery indicating that S. Potsdam might have been long existed in hatchery. The pulsed-field gel electrophoresis (PFGE) analysis of S. Potsdam indicated that S. Potsdam could be transmitted along the production chain. The PFGE analysis of S. Typhimurium showed that PFGE pattern 29 (PF29) was distributed in hatchery, and also in farm and from humans indicating the risk of S. Typhimurium transmitting to humans by the food supply chain. Our study provided the evidence of Salmonella cross-contamination in the slaughterhouse and the retail market of goose production chain, and specific serotypes existed for a long time at a particular production link. The spread of Salmonella along the production chain, might cause harm to humans through cross-contamination. Further studies would be needed to control the Salmonella contamination in hatchery and prevent the transmission of the pathogen during the goose production., (Copyright © 2019. Published by Elsevier Inc.)

Rodents serve as amplifiers of Salmonella infections in poultry flocks and can serve as a source of Salmonella contamination in the environment even after thorough cleaning and disinfection. This study aims to determine the dynamics of Salmonella occurrence in rodents and its relation to Salmonella contamination in the layer farm environment, including air dusts and eggs. From 2008 to 2017, roof rats ( Rattus rattus ), environmental swabs, air dusts, and eggs were collected from an intensive commercial layer farm in East Japan and were tested for Salmonella spp. using standard procedures. In roof rat samples, the Salmonella isolation rate was reached at 10% (95% confidence interval [CI] 8.1-21.9) in which Salmonella Corvallis, Salmonella Infantis, Salmonella Potsdam, and Salmonella Mbandaka were the frequent isolates from the cecal portion of the intestines. On the other hand, the prevalence rate of Salmonella in environmental swabs was at 5.1% (95% CI 2.2-7.4) while air dusts were at 0.9% (95% CI 0.2-1.8). It was observed that the prevalence of predominant Salmonella serotypes shifted over time; in roof rats, it was noted that Salmonella Potsdam gradually replaced Salmonella Infantis. In environmental swabs and eggs, Salmonella Corvallis and Salmonella Potsdam increased significantly while Salmonella Infantis became less frequent. In air dusts, Salmonella Corvallis was observed to decrease and Salmonella Potsdam became more common. Based on our findings, the role of roof rats in the epidemiology of Salmonella in layer farms was expanded from being a reservoir and an amplifier host into a shifting vessel of the most predominant serotypes.

Before starting a study with many birds, it helps to know the method of chick inoculation. The objective was to compare 3 methods of Salmonella challenge (oral gavage [OR], intracloacal inoculation [IC], and seeder bird [SB]). Day-old broiler chicks (n = 100) were inoculated with 10 6 colony forming units (CFU) per chick of a marker strain of Salmonella Heidelberg (SH) with each route of inoculation. Chicks (n = 25) inoculated by each route were placed in floor pens on fresh pine shavings litter. For the seeder batch, 5 colonized chicks, each orally gavaged with 10 6  CFUs, were placed with 20 pen mates. Two weeks after inoculation, 10 birds from each pen and the 5 inoculated seeder birds were euthanized, the ceca were aseptically removed and macerated with a rubber mallet and weighed, and 3 times (w/v) buffered peptone was added and stomached for 60 s. Serial dilutions were made and plated onto Brilliant Green Sulfa plates containing 200 ppm nalidixic acid. Plates were incubated along with the stomached ceca for 24 h at 37°C. If no colonies appeared on the plates, an additional plate was streaked from the preenriched bag and incubated for 24 h at 37°C. In addition to all seeder birds being positive, the number of SH-positive birds out of 20 sampled in each group was 13, 17, and 7 for OR, IC, and SB, respectively. The level of SH per g of ceca and cecal contents was log (SE) 3.0 (0.7), 2.0 (0.4), and 2.6 (0.4) for OR, IC, and SB, respectively. After enrichment, the number of colonized birds out of 20 was 18, 20, and 10 for OR, IC, and SB, respectively. In conclusion, this study suggests that IC is the method to use to ensure most of the challenged birds are colonized. However, if you prefer to have a smaller percentage of the birds colonized with higher levels, then OR might be better., (Copyright © 2019. Published by Elsevier Inc.)

As part of the development of a quantitative microbial risk assessment (QMRA) model of third-generation cephalosporins (3GC)-resistant Salmonella Heidelberg, a compartmental (SEIR) model for S. Heidelberg transmission within a typical Canadian commercial broiler chicken flock was developed. The model was constructed to estimate the within-flock prevalence and the bacterial concentration in the barn environment at pre-harvest, and to assess the effect of selected control measures. The baseline scenario predicted an average within-flock prevalence of 23.5 % (95 % tolerance interval: 15.7-31.4) and an average bacterial concentration of 3.579 (0-4.294) log CFU/g of feces in the barn environment at pre-harvest (on the day the flock is sent to slaughter). Because vertical introduction of S. Heidelberg into the barn was already uncommon in the baseline scenario, vaccination of broiler parent flocks appeared to have a negligible effect, while vaccination of broiler chicken flocks substantially reduced the bacterial concentration at pre-harvest. Cleaning and disinfection between batches markedly reduced the within-flock prevalence at pre-harvest, but the effect on bacterial concentration was limited outside of the beginning of the production period. Extending downtime between batches by 7 days had little effect on within-flock prevalence or bacterial concentration of S. Heidelberg when compared to the baseline scenario. This study provides a basis to describe S. Heidelberg dynamics within a broiler chicken flock and to predict the within-flock prevalence and bacterial concentration at pre-harvest, and includes a description of the limitations and data gaps. The results of these analyses and associated uncertainties are critical information for populating QMRA models of the downstream impacts on public health from on-farm and other food-chain practices. Specifically, the study findings will be integrated into a broader farm-to-fork QMRA model to support the risk-based control of S. Heidelberg resistant to 3GC in broiler chicken in Canada., (Crown Copyright © 2019. Published by Elsevier B.V. All rights reserved.)

Human salmonellosis caused by the consumption of eggs and chicken meat contaminated with Salmonella Enteritidis has become a continuing public health concern worldwide. In this study we adopted whole genome sequencing (WGS) to determine the genetic relationship and antimicrobial resistance of S. enterica strains isolated from a poultry breeding enterprise that consists of one breeding chicken farm, one egg hatchery and one commercial chicken farm. A total of 148 S. enterica including 147 S. Enteritidis strains were isolated from 2100 fecal swab samples, with 16 (5.3 %, 16/300) from breeding chicken farm, 38 (4.2 %, 38/900) from egg hatchery and 94 (10.4 %, 94/900) from commercial chicken farm. WGS revealed that all 147 S. Enteritidis strains belonged to ST11, and further divided into 4 different ribosomal STs and 64 core genome STs. Single nucleotide polymorphism typing suggested the presence of the vertical transmission of S. Enteritidis from breeding chicken to commercial chicken. Three different antimicrobial-resistant plasmids including one bla CTX-M-14 -carrying plasmid and two virulence-resistance plasmids were characterized, resulting in the heterogeneous antimicrobial resistance of clonally related S. Enteritidis strains. Routine surveillance in breeding chicken farms is conducive to the control of S. Enteritidis from farm to fork., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Reptile contact can result in zoonotic non-typhoidal salmonellosis. In April 2018, Oregon Public Health Division contacted CDC about a cluster of four Salmonella serovar Fluntern (SF) illnesses in four states (OR, CA, IA, NY); patients reported contact with geckos, a popular reptile pet. PulseNet, the national molecular subtyping network of food-borne disease surveillance, subsequently identified additional SF clinical isolates. Twelve cases in 11 states were identified; median age was 5 years (range: <1-58 years). Three patients were hospitalized; no deaths were reported. Of those with exposure information (n = 10), all reported reptile exposure; 9 (90%) specified contact with leopard geckos. No common source of geckos was identified from reported purchase locations. Los Angeles County (LAC) health officials isolated SF from one patient's leopard gecko. Five reptile/gecko isolates were identified from the USDA National Veterinary Services Laboratories (NVSL) from 2015 to 2018. Five countries responded to an Epidemic Intelligence Information System post by PulseNet; reptile isolate sequence data were received from Czech Republic. A clinical case from England was identified through the National Center for Biotechnology Information pathogen detection pipeline; the patient did not report contact with leopard geckos. Whole genome sequencing analysis revealed substantial genetic diversity between clinical and animal isolates; however, gecko and clinical isolates from LAC were highly related (1 allele difference). This investigation linking SF illnesses to leopard geckos highlights an important public health risk from pets. A better understanding of how geckos are distributed by the pet industry in the United States could improve traceability to points of origin and mitigate Salmonella transmission at gecko breeders. Earlier NVSL reports of SF isolates from geckos suggest the risk of human SF infection from geckos is not new. This investigation demonstrates a need to educate gecko breeders, retailers and gecko owners about the continued Salmonella infection risk from pet geckos., (© 2019 Blackwell Verlag GmbH.)

Salmonella is an established pathogen of the members of the kingdom Animalia. Reports indicate that the association of Salmonella with fresh, edible plant products occurs at the pre-harvest state, i.e. in the field. In this study, we follow the interaction of Salmonella Typhimurium with the model plant Arabidopsis thaliana to understand the process of migration in soil. Plant factors like root exudates serve as chemo-attractants. Our ex situ experiments allowed us to track Salmonella from its free-living state to the endophytic state. We found that genes encoding two-component systems and proteins producing extracellular polymeric substances are essential for Salmonella to adhere to the soil and roots. To understand the trans-kingdom flow of Salmonella, we fed the contaminated plants to mice and observed that it invades and colonizes liver and spleen. To complete the disease cycle, we re-established the infection in plant by mixing the potting mixture with the fecal matter collected from the diseased animals. Our experiments revealed a cross-kingdom invasion by the pathogen via passage through a murine intermediate, a mechanism for its persistence in the soil and invasion in a non-canonical host. These results form a basis to break the life-cycle of Salmonella before it reaches its animal host and thus reduce Salmonella contamination of food products., (© FEMS 2019.)

In 2016, an outbreak of Salmonella Typhimurium (STm) with multilocus variable-number tandem repeat analysis (MLVA) profiles historically associated with passerine birds (2-[11-15]-[3-4]-NA-212) occurred among passerines, cats and humans in Sweden. Our retrospective observational study investigated the outbreak and revisited historical data from 2009-16 to identify seasonality, phylogeography and other characteristics of this STm variant. Outbreak isolates were analysed by whole-genome single nucleotide polymorphism (SNP) typing. The number of notified cases of passerine-associated STm among passerines, cats and humans per month and county, and their MLVA profiles, were compared to birdwatchers' counts of passerines. Seasonal trend decomposition and correlation analysis was performed. Outbreak isolates did not cluster by host on SNP level. Passerine-associated STm was seasonal for birds, cats and humans, with a peak in March. Cases and counts of passerines at bird feeders varied between years. The incidence of passerine-associated STm infections in humans was higher in the boreal north compared with the southern and capital regions, consistent with passerine population densities. Seasonal mass migration of passerines appears to cause STm outbreaks among cats certain years in Sweden, most likely via predation on weakened birds. Outbreaks among humans can follow, presumably caused by contact with cats or environmental contamination.

Objectives: Salmonella is the most important causes of foodborne illness especially from poultry and poultry products. So the aim of this study was to carryout phenotypic characterization, antimicrobials susceptibility pattern and risk factors of Salmonella isolates from farms and markets eggs, cloacae swabs of chickens and stool of egg collectors. A cross-sectional study was conducted from January 2018 to September 2018. Samples were, processed; Salmonella was isolated, phenotypically identified by OmniLog and antimicrobials susceptibility were carried out., Result: Over all; 11 (2.65%) of Salmonella enterica were phenotypically characterized out of 415 samples from farms egg content (n = 83), farms eggshell (n = 83), cloacae (n = 83), market eggshell (n = 83) and market egg contents (n = 83) with 2.4%, 0%, 2.4%, 4.8% and 3.6% prevalence, respectively. Out of isolates, 8 (72.72%) displayed multidrug resistance. All isolates showed susceptibility to Gentamicin, Kanamycin and Streptomycin. Lack of separating cracked eggs, washing hand, eggs stay longer unsold, and mixing excreta with feed were associated risk factors for Salmonella presence (P-value < 0.05). The presence of drug resistant Salmonella enterica within egg/and chicken can pose serious health problem. Good hygienic practices are important to reduce risk factors of Salmonella contamination.

Field studies on Salmonella infection in suckling piglets are scarce due to the intrinsic difficulties of collecting proper samples (i.e. tonsils or mesenteric lymph nodes), and most of them rely on the analysis of rectal swabs that limit their accuracy. We used 495 slaughtered 4-weeks-old male piglets intended for human consumption from 5 Salmonella-seropositive breeding farms to collect gastrointestinal packages and perform a thorough detection of Salmonella on mesenteric lymph nodes and intestinal content. The overall prevalence of both infection and shedding was high (≈ 36%) indicating that piglets played an active role in Salmonella maintenance in the farms. Major serotypes found in piglets included 4,[5],12:i: (35.4%), Rissen (17.1%), Derby (10.9%) and Bovismorbificans (10.3%). In most of the infected animals (72.8%) the same serotype was found in mesenteric lymph nodes and feces. Significant higher ELISA OD% values were found in meat juice samples from non-infected piglets compared to infected ones (median OD% of 12.0 and 17.3, respectively; P = 0.002) suggesting some protective effect of sow's colostrum. Salmonella was also isolated from feces from weaned sows contemporary of the slaughtered piglets, and 89% of the serotypes identified in sows were also detected in piglets. Pulsed field gel electrophoresis analyses showed that 75% of the piglet isolates that were compared to those of sows were related to them, suggesting the circulation of Salmonella strains between sows and piglets. It appears that improving piglet colostrum intake along with the reduction of the shedding in sows may favor the control of Salmonella infection in breeding farms.

Salmonella Kentucky is among the most frequently isolated S. enterica serovars from food animals in the United States. Recent research on isolates recovered from these animals suggests there may be geographic and host specificity signatures associated with S. Kentucky strains. However, the sources and genomic features of human clinical S. Kentucky isolated in the United States remain poorly described. To investigate the characteristics of clinical S. Kentucky and the possible sources of these infections, the genomes of all S. Kentucky isolates recovered from human clinical cases in the State of Maryland between 2011 and 2015 (n = 12) were sequenced and compared to a database of 525 previously sequenced S. Kentucky genomes representing 12 sequence types (ST) collected from multiple sources on several continents. Of the 12 human clinical S. Kentucky isolates from Maryland, nine were ST198, two were ST152, and one was ST314. Forty-one per cent of isolates were recovered from patients reporting recent international travel and 58% of isolates encoded genomic characteristics similar to those originating outside of the United States. Of the five isolates not associated with international travel, three encoded antibiotic resistance genes conferring resistance to tetracycline or aminoglycosides, while two others only encoded the cryptic aac(6')-Iaa gene. Five isolates recovered from individuals with international travel histories (ST198) and two for which travel was not recorded (ST198) encoded genes conferring resistance to between 4 and 7 classes of antibiotics. Seven ST198 genomes encoded the Salmonella Genomic Island 1 and substitutions in the gyrA and parC genes known to confer resistance to ciprofloxacin. Case report data on food consumption and travel were, for the most part, consistent with the inferred S. Kentucky phylogeny. Results of this study indicate that the majority of S. Kentucky infections in Maryland are caused by ST198 which may originate outside of North America., (Published 2019. This article is a U.S. Government work and is in the public domain in the USA.)

The role of free-ranging wildlife in the epidemiology of enteropathogens causing clinical illness in humans and domestic animals is unclear. Salmonella enterica and anti-microbial resistant bacteria have been detected in the faeces of raccoons (Procyon lotor), but little is known about the carriage of these bacteria in other sympatric meso-mammals. Our objectives were to: (a) report the prevalence of Salmonella and associated anti-microbial resistance, Campylobacter spp, Clostridium difficile, and anti-microbial resistant Escherichia coli in the faeces of striped skunks (Mephitis mephitis) and Virginia opossums (Didelphis virginiana) in southern Ontario; and (b) compare the prevalence of these bacteria in the faeces of these meso-mammal hosts with raccoons from a previously reported study. Faecal swabs were collected from striped skunks and Virginia opossums on five swine farms and five conservation areas from 2011 to 2013. Salmonella was detected in 41% (9/22) and 5% (5/95) of faecal swabs from Virginia opossums and striped skunks, respectively. None of the Salmonella serovars carried resistance to anti-microbials. The prevalence of Campylobacter spp., C. difficile, and anti-microbial resistant E. coli ranged from 6% to 22% in striped skunk and Virginia opossums. Using exact logistic regression, Salmonella was significantly more likely to be detected in faecal swabs of Virginia opossums than skunks and significantly less likely in faecal swabs from skunks than raccoons from a previously reported study. In addition, Campylobacter spp. was significantly more likely to be detected in raccoons than opossums. Salmonella Give was detected in 8/9 (89%) of Salmonella-positive Virginia opossum faecal swabs. Our results suggest that striped skunks and Virginia opossums have the potential to carry pathogenic enteric bacteria in their faeces. The high prevalence of Salmonella Give in Virginia opossum faecal swabs in this study as well as its common occurrence in other Virginia opossum studies throughout North America suggests Virginia opossums may be reservoirs of this serovar., (© 2019 Blackwell Verlag GmbH.)

Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum ( S Pullorum) is the etiological agent of pullorum disease, causing white diarrhea with high mortality in chickens. There are many unsolved issues surrounding the epidemiology of S Pullorum, including its origin and transmission history as well as the discordance between its phenotypic heterogeneity and genetic monomorphism. In this paper, we report the results of whole-genome sequencing of a panel of 97 S Pullorum strains isolated between 1962 and 2014 from four countries across three continents. We utilized 6,795 core genome single nucleotide polymorphisms (SNPs) to reconstruct a phylogenetic tree within a spatiotemporal Bayesian framework, estimating that the most recent common ancestor of S Pullorum emerged in ∼914 CE (95% confidence interval [95%CI], 565 to 1273 CE). The extant S Pullorum strains can be divided into four distinct lineages, each of which is significantly associated with geographical distribution. The intercontinental transmissions of lineages III and IV can be traced to the mid-19th century and are probably related to the "Hen Fever" prevalent at that time. Further genomic analysis indicated that the loss or pseudogenization of functional genes involved in metabolism and virulence in S Pullorum has been ongoing since before and after divergence from the ancestor. In contrast, multiple prophages and plasmids have been acquired by S Pullorum, and these have endowed it with new characteristics, especially the multidrug resistance conferred by two large plasmids in lineage I. The results of this study provide insight into the evolution of S Pullorum and prove the efficiency of whole-genome sequencing in epidemiological surveillance of pullorum disease. IMPORTANCE Pullorum disease, an acute poultry septicemia caused by Salmonella Gallinarum biovar Pullorum, is fatal for young chickens and is a heavy burden on poultry industry. The pathogen is rare in most developed countries but still extremely difficult to eliminate in China. Efficient epidemiological surveillance necessitates clarifying the origin of the isolates from different regions and their phylogenic relationships. Genomic epidemiological analysis of 97 S Pullorum strains was carried out to reconstruct the phylogeny and transmission history of S Pullorum. Further analysis demonstrated that functional gene loss and acquisition occurred simultaneously throughout the evolution of S Pullorum, both of which reflected adaptation to the changing environment. The result of our study will be helpful in surveillance and prevention of pullorum disease., (Copyright © 2019 Hu et al.)

Multi-drug resistant (MDR) non-typhoidal Salmonella (NTS) is increasingly common worldwide. While food animals are thought to contribute to the growing antimicrobial resistance (AMR) problem, limited data is documenting this relationship, especially in low and middle-income countries (LMIC). Herein, we aimed to assess the role of non-clinical NTS of bovine origin as reservoirs of AMR genes of human clinical significance. We evaluated the phenotypic and genotypic AMR profiles in a set of 44 bovine-associated NTS. For comparative purposes, we also included genotypic AMR data of additional isolates from Mexico (n = 1,067) that are publicly available. The most frequent AMR phenotypes in our isolates involved tetracycline (40/44), trimethoprim-sulfamethoxazole (26/44), chloramphenicol (19/44), ampicillin (18/44), streptomycin (16/44), and carbenicillin (13/44), while nearly 70% of the strains were MDR. These phenotypes were correlated with a widespread distribution of AMR genes (i.e. tetA, aadA, dfrA12, dfrA17, sul1, sul2, bla-TEM-1, blaCARB-2) against multiple antibiotic classes, with some of them contributed by plasmids and/or class-1 integrons. We observed different AMR genotypes for betalactams and tetracycline resistance, providing evidence of convergent evolution and adaptive AMR. The probability of MDR genotype occurrence was higher in meat-associated isolates than in those from other sources (odds ratio 11.2, 95% confidence interval 4.5-27.9, P < 0.0001). The study shows that beef cattle are a significant source of MDR NTS in Mexico, highlighting the role of animal production on the emergence and spread of MDR Salmonella in LMIC.

Dermanyssus gallinae (Mesostigmata: Dermanyssidae, De Geer, 1778) is an ectoparasite of poultry, suspected to play a role as a vector of Salmonella enterica subsp. enterica ser. Gallinarum. Despite an association between them being reported, the actual dynamics in field remain unclear. Therefore, the present study aimed to confirm the interactions among mites, pathogen and chickens. The study was carried out in an industrial poultry farm infested by D. gallinae, during an outbreak of fowl typhoid. The presence of S. Gallinarum in mites was assessed and quantified by a semi-nested polymerase chain reaction (PCR) and real-time PCR, respectively, in mites collected during two subsequent productive cycles and the sanitary break. The anti-group D Salmonella antibodies were quantified by an enzyme-linked immunosorbent assay. During the outbreak and the sanitary break, S. Gallinarum was constantly present in mites. In the second cycle, scattered positivity was observed, although hens did not exhibit signs of fowl typhoid, as a result of the vaccination with BIO-VAC SGP695 (Fatro, Ozzano Emilia Bo, Italy). The data strongly suggest that D. gallinae acts as reservoir of S. Gallinarum, thus allowing the pathogen to persist in farms. Furthermore, the present study has highlighted the interactions among D. gallinae, S. Gallinarum and hens with respect to enhancing the mite-mediated circulation of S. Gallinarum in an infested poultry farm., (© 2018 The Royal Entomological Society.)

Salmonella enterica serovar Wangata (S. Wangata) is an important cause of endemic salmonellosis in Australia, with human infections occurring from undefined sources. This investigation sought to examine possible environmental and zoonotic sources for human infections with S. Wangata in north-eastern New South Wales (NSW), Australia. The investigation adopted a One Health approach and was comprised of three complimentary components: a case-control study examining human risk factors; environmental and animal sampling; and genomic analysis of human, animal and environmental isolates. Forty-eight human S. Wangata cases were interviewed during a 6-month period from November 2016 to April 2017, together with 55 Salmonella Typhimurium (S. Typhimurium) controls and 130 neighbourhood controls. Indirect contact with bats/flying foxes (S. Typhimurium controls (adjusted odds ratio (aOR) 2.63, 95% confidence interval (CI) 1.06-6.48)) (neighbourhood controls (aOR 8.33, 95% CI 2.58-26.83)), wild frogs (aOR 3.65, 95% CI 1.32-10.07) and wild birds (aOR 6.93, 95% CI 2.29-21.00) were statistically associated with illness in multivariable analyses. S. Wangata was detected in dog faeces, wildlife scats and a compost specimen collected from the outdoor environments of cases' residences. In addition, S. Wangata was detected in the faeces of wild birds and sea turtles in the investigation area. Genomic analysis revealed that S. Wangata isolates were relatively clonal. Our findings suggest that S. Wangata is present in the environment and may have a reservoir in wildlife populations in north-eastern NSW. Further investigation is required to better understand the occurrence of Salmonella in wildlife groups and to identify possible transmission pathways for human infections.

Conversion of natural habitats into urban landscapes can expose wildlife to novel pathogens and alter pathogen transmission pathways. Because transmission is difficult to quantify for many wildlife pathogens, mathematical models paired with field observations can help select among competing transmission pathways that might operate in urban landscapes. Here we develop a mathematical model for the enteric bacteria Salmonella enterica in urban-foraging white ibis ( Eudocimus albus) in south Florida as a case study to determine (i) the relative importance of contact-based versus environmental transmission among ibis and (ii) whether transmission can be supported by ibis alone or requires external sources of infection. We use biannual field prevalence data to restrict model outputs generated from a Latin hypercube sample of parameter space and select among competing transmission scenarios. We find the most support for transmission from environmental uptake rather than between-host contact and that ibis-ibis transmission alone could maintain low infection prevalence. Our analysis provides the first parameter estimates for Salmonella shedding and uptake in a wild bird and provides a key starting point for predicting how ibis response to urbanization alters their exposure to a multi-host zoonotic enteric pathogen. More broadly, our study provides an analytical roadmap to assess transmission pathways of multi-host wildlife pathogens in the face of scarce infection data.

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., (© 2018 Blackwell Verlag GmbH.)

Foodborne outbreaks caused by Salmonella are often attributed to the pork consumption. Salmonella contamination of retail pork is directly linked to the Salmonella prevalence on farm. In UK, approximately 40% of breeding pigs are kept outdoors. Aim of this study was to investigate the role of wild birds in the epidemiology of Salmonella in one outdoor pig farm. Three sampling visits were carried out at monthly intervals to an outdoor farm consisting of two fields, one left empty of pigs for more than 2 years (field A) while the second (field B) was occupied by pigs during the first visit only. Faeces from wild bird droppings, environmental samples and pig faeces were tested for Salmonella. Salmonella spp. was isolated from environmental samples also in field A that had not been occupied by pigs more than 2 years. Interestingly, the wild bird population accessing the fields increased considerably once the pigs had left the farm and the proportion of Salmonella positive wild bird droppings increased over time with 7.4%, 15.8% and 44.3% at the first, second and third visit, respectively. The levels of Salmonella identified in some of the wild bird droppings were unusually high (10 5 -10 6 CFU/g) suggesting that Salmonella was actively replicating in the gastrointestinal tract of these birds. Monophasic Salmonella Typhimurium DT193 was the predominant serotype isolated in pigs as well as in wild bird droppings and the environment, suggesting that the pigs were the original source of infection, as this serovar is typically associated with pigs., (Crown Copyright © 2018. Published by Elsevier B.V. All rights reserved.)

Nontyphoidal Salmonella (NTS), particularly Salmonella enterica serovar Typhimurium, is among the leading etiologic agents of bacterial enterocolitis globally and a well-characterized cause of invasive disease (iNTS) in sub-Saharan Africa. In contrast, S  Typhimurium is poorly defined in Southeast Asia, a known hot spot for zoonotic disease with a recently described burden of iNTS disease. Here, we aimed to add insight into the epidemiology and potential impact of zoonotic transfer and antimicrobial resistance (AMR) in S  Typhimurium associated with iNTS and enterocolitis in Vietnam. We performed whole-genome sequencing and phylogenetic reconstruction on 85 human (enterocolitis, carriage, and iNTS) and 113 animal S  Typhimurium isolates isolated in Vietnam. We found limited evidence for the zoonotic transmission of S  Typhimurium. However, we describe a chain of events where a pandemic monophasic variant of S  Typhimurium (serovar I:4,[5],12:i:- sequence type 34 [ST34]) has been introduced into Vietnam, reacquired a phase 2 flagellum, and acquired an IncHI2 multidrug-resistant plasmid. Notably, these novel biphasic ST34 S  Typhimurium variants were significantly associated with iNTS in Vietnamese HIV-infected patients. Our study represents the first characterization of novel iNTS organisms isolated outside sub-Saharan Africa and outlines a new pathway for the emergence of alternative Salmonella variants into susceptible human populations. IMPORTANCE Salmonella Typhimurium is a major diarrheal pathogen and associated with invasive nontyphoid Salmonella (iNTS) disease in vulnerable populations. We present the first characterization of iNTS organisms in Southeast Asia and describe a different evolutionary trajectory from that of organisms causing iNTS in sub-Saharan Africa. In Vietnam, the globally distributed monophasic variant of Salmonella Typhimurium, the serovar I:4,[5],12:i:- ST34 clone, has reacquired a phase 2 flagellum and gained a multidrug-resistant plasmid to become associated with iNTS disease in HIV-infected patients. We document distinct communities of S Typhimurium and I:4,[5],12:i:- in animals and humans in Vietnam, despite the greater mixing of these host populations here. These data highlight the importance of whole-genome sequencing surveillance in a One Health context in understanding the evolution and spread of resistant bacterial infections., (Copyright © 2018 Mather et al.)

Salmonella remains one of the most prevalent zoonoses worldwide. Although salmonellosis is commonly associated with the consumption of contaminated food, it has been estimated that up to 11% of Salmonella infections overall are acquired from direct or indirect contact with animals, including reptiles. In 2016, an outbreak of Salmonella Enteritidis involving multiple cases, especially children, associated with reptile contact and contaminated feeder mice was reported in the United Kingdom. The aim of this study was to investigate Salmonella external and internal contamination of stored commercial frozen feeder mice used to feed reptiles and obtained from the same supplier involved in the outbreak. In this study a total of 295 mice were tested (60 pinkies, 60 fuzzies, 60 small, 60 large, and 55 extra large). In this study, both external (integument) and internal (selected organs) contamination were evaluated. Salmonella Enteritidis PT8 and PT13 were isolated from 28.8% (n = 17) of the 59 batches tested, with the exception of the large mice category. Positive mice were mostly contaminated externally (92.3% vs. 26.9% for carcass wash and viscera, respectively). All isolates were sensitive to all 16 antimicrobials tested. The high level of external contamination of the rodent carcasses might have played a role in the human outbreak in 2016. Reptile owner management of the rodent carcasses at home could be an important source of salmonellosis outbreaks. Collaboration among public health officials, pet industry, veterinarians, and reptile owners is needed to help prevent the risk of salmonellosis associated with animal-based food intended for reptiles.

A total of 201 wild geckos from the region of Mekong Delta, Vietnam were collected to determine the viable number and survival period of Salmonella in their feces. Of the 101 samples examined, 24 (23.8%) were Salmonella positive. These 24 geckos excreted Salmonella in their feces in a range of 1 to 8.6 log CFU/g with a mean of 4.5 ± 3.2 log CFU/g. Among the Salmonella serovars, Salmonella Weltevreden was the most predominant serovar (37.5%). Moreover, Salmonella could survive for 6 weeks in gecko feces at room temperature in Vietnam. These results indicate that the wild gecko seems to play an important role as a reservoir for Salmonella and a source of Salmonella infection in humans in Southeast Asian countries.

The number of outbreaks of Salmonella infections linked to live poultry contact increased from 1990 to 2016. In 2016, the number of human illnesses linked to live poultry was the highest reported, with more than 900 cases, including 209 hospitalizations and three deaths. Live poultry harboring Salmonella typically appear healthy but can intermittently shed bacteria in their droppings, contaminating their feathers, beaks, and the areas where they live and roam. Thus, both direct contact with poultry and indirect contact with anything in areas where animals live and roam can result in human Salmonella infection. To prevent Salmonella infections linked to live poultry, a One Health approach for control and prevention is required. This approach unifies animal and human health needs and takes into account the environments at the hatcheries where poultry are produced, the agricultural retail stores where poultry are sold, and the customers who own and raise poultry. Agricultural retail stores are the main point of sale for backyard poultry in the U.S. Therefore, stores can play a vital role in preventing infections by sourcing poultry from hatcheries that take steps to reduce Salmonella in the environment, by displaying poultry in areas that can be easily cleaned, and by using barriers that allow customers to view, but not touch, poultry from a distance. Retail store employees also have a role in preventing illnesses and contamination after the sale by educating customers about appropriate housing for live poultry in outdoor coops, barns, or other designated areas., (Copyright© by the American Society of Agricultural Engineers.)

In December 2012, an increase in human Salmonella Typhimurium cases was identified in the province of Ontario, Canada launching an outbreak investigation. The outbreak spanned 3 years (2012-2014), with 134 cases reported from five Canadian provinces. There was a substantial burden of illness among children: 45% of cases were children 12 years old or under, and 23% of cases were under 5 years old. Epidemiologic, traceback and laboratory findings linked this outbreak to feeder rodents (used to feed snakes) supplied by a network of rodent breeders in Ontario. Cases likely acquired their illness through either direct or indirect contact with feeder rodents. This investigation not only contributes to the weight of evidence on the risk that feeder rodents pose, but also underscores the importance of investigating indirect animal contact and associated risks, especially for high-risk individuals., (© 2018 Her Majesty the Queen in Right of Canada Zoonoses Public Health © 2018 Blackwell Verlag GmbH Reproduced with the permission of the Minister of Public Health Agency of Canada.)

To better understand factors influencing infectious agent dispersal within a livestock population information is needed on the nature and frequency of contacts between farm enterprises. This study uses social network analysis to describe the contact network within a vertically integrated broiler poultry enterprise to identify the potential horizontal and vertical transmission pathways for Salmonella spp. Nodes (farms, sheds, production facilities) were identified and the daily movement of commodities (eggs, birds, feed, litter) and people between nodes were extracted from routinely kept farm records. Three time periods were examined in detail, 1- and 8- and 17-weeks of the production cycle and contact networks were described for all movements, and by commodity and production type. All nodes were linked by at least one movement during the study period but network density was low indicating that all potential pathways between nodes did not exist. Salmonella spp. transmission via vertical or horizontal pathways can only occur along directed pathways when those pathways are present. Only two locations (breeder or feed nodes) were identified where the transmission of a single Salmonella spp. clone could theoretically percolate through the network to the broiler or processing nodes. Only the feed transmission pathway directly connected all parts of the network., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

In the United Kingdom a serological Salmonella surveillance scheme was run in pigs up to 2012. Farms that maintained a low seroprevalence (<10%) were recognised as "Platinum" pig farms. The aim of this study was to investigate the occurrence and distribution of Salmonella in three farms (17P, 18P and 46P) that had lost their "Platinum" status. Four visits to each farm were made over a period of 15 months. The sampling was carried out by collecting pooled pen floor faecal swab and environmental samples. All samples were tested for Salmonella by a modification of ISO6579 Annex D, and serovars were determined for all isolates. The Salmonella prevalence peaked in the Summer/Autumn months and all farms were still positive at the end of the study. The overall sample prevalence was higher in farm 17P (46%) and 18P (35%) than 46P (19%). Monophasic S. Typhimurium (mST) represented 77.8% of the Salmonella isolates, mainly from farms 17P and 46P. The mST isolated at the initial visit may have been introduced via other livestock present on farm or introduction into the herd of infected animals. The results of this study suggest that incursion of mST was likely to be the main cause of the loss of "Platinum" status and confirm that mST can persist in pigs and their environment., (Copyright © 2017. Published by Elsevier Ltd.)

Salmonella infections in pigs are in most cases asymptomatic, posing a risk of salmonellosis for pork consumers. Salmonella can transmit to pigs from various sources, including contaminated feed. We present an approach for quantifying the risk to pigs from contaminations in the feed chain, based on a Bayesian model. The model relies on Salmonella surveillance data and other information from surveys, reports, registries, statistics, legislation and literature regarding feed production and pig farming. Uncertainties were probabilistically quantified by synthesizing evidence from the available information over a categorically structured flow chain of ingredients mixed for feeds served to pigs. Model based probability for infection from feeds together with Salmonella subtyping data, were used to estimate the proportion of Salmonella infections in pigs attributable to feed. The results can be further used in assessments considering the human health risk linked to animal feed via livestock. The presented methods can be used to predict the effect of changes in the feed chain, and they are generally applicable to other animals and pathogens., (Copyright © 2017 Elsevier Ltd. All rights reserved.)