Characterization of Salmonella species from poultry slaughterhouses in South Korea: carry-over transmission of Salmonella Thompson ST292 in slaughtering process.

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.

Investigation of prevalence and antimicrobial resistance of Salmonella in pet dogs and cats in Turkey.

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.

Accumulation of resistance genes in Salmonella Typhimurium transmitted between poultry and dairy farms increases the risk to public health.

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 blaCTX-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.IMPORTANCESalmonella 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.

Centralized industrialization of pork in Europe and America contributes to the global spread of Salmonella enterica.

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.

Revealing mechanisms of infectious disease spread through empirical contact networks.

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.

Pullorum Disease: Evolution of the Eradication Strategy.

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.

Artículo histórico­Pulorosis: Evolución de las estrategias de erradicación La historia de la pulorosis está estrechamente relacionada con la historia de la investigación en salud aviar y de la industria avícola. La severidad de la enfermedad despertó la atención y reunió, por primera vez a los pioneros de la investigación en salud avícola para trabajar de manera cooperativa en diferentes aspectos de la enfermedad. El control de la enfermedad hizo posible que la producción avícola intensiva se desarrollara como base de la industria avícola moderna. A principios de la década de los 1900, la diarrea blanca bacilar (con las siglas en inglés BWD) era una enfermedad devastadora de pollos jóvenes que amenazaba la industria avícola en desarrollo. El Dr. Leo F. Rettger aisló y describió el patógeno bacteriano, Salmonella enterica serotipo Pullorum, por primera vez en 1900. La diarrea blanca bacilar pasó a llamarse pulorosis (pullorum disease) en 1929. En los años siguientes, Rettger y sus colaboradores pudieron reproducir la enfermedad y cumplir los postulados de Koch. Rettger y col. también mostraron que Salmonella Pullorum se transmitía verticalmente, y fue la primera vez que se demostró que un patógeno se transmitía verticalmente. El desarrollo de pruebas serológicas fue de crucial importancia porque condujo al desarrollo de métodos de erradicación efectivos para identificar aves portadoras y eliminar a estas aves de las parvadas reproductoras. El impacto negativo de la pulorosis en la industria avícola fue, en última instancia, una de las principales razones por las que los científicos, la industria avícola y el Departamento de Agricultura de los Estados Unidos (USDA) desarrollaron el Plan Nacional de Mejoramiento Avícola (NPIP). Es importante decir que el trabajo de los investigadores pioneros formó la base para el control de la enfermedad. El Plan Nacional de Mejoramiento Avícola comenzó en año 1935, con 34 estados participando en el análisis de 4 millones de aves que representaban el 58.2% de las aves producidas. El programa se expandió rápidamente a 47 estados en 1948 y evaluó a más de 30 millones de aves. En 1967, todas las plantas incubadoras de pollos comerciales que participaban en el Plan Nacional de Mejoramiento Avícola estaban 100% libres de pulorosis y tifoidea aviar causada por Salmonella enterica serotipo Gallinarum. Esta reseña histórica de la pulorosis describe con cierto detalle el progreso realizado, especialmente durante los primeros años, hacia el control de esta enfermedad utilizando metodologías que a menudo eran muy básicas no obstante efectivas. Es admirable el ingenio y la persistencia de los primeros investigadores que los llevaron a sus logros considerando las herramientas de investigación que estaban disponibles en ese momento.

Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks.

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.

Infection dynamics of Salmonella Infantis strains displaying different genetic backgrounds - with or without pESI-like plasmid - vary considerably.

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 108 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.

Tracking Salmonella enterica by whole genome sequencing of isolates recovered from broiler chickens in a poultry production system.

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.

The effect of vegetation barriers at reducing the transmission of Salmonella and Escherichia coli from animal operations to fresh produce.

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.

Dissemination of a multidrug resistant CTX-M-65 producer Salmonella enterica serovar Infantis clone between marketed chicken meat and children.

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 (blaCTX-M-65) and i-pAmpC (blaDHA) were detected in 2 and 5 isolates respectively (in one case concomitantly), with blaCTX-M-65 being transferable through conjugation. In addition, 1 isolate presented a blaSHV gene. All isolates presented D87Y 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 blaCTX-M-65-producing S. Infantis isolates causing children diarrhea in Lima. The dissemination of MDR blaCTX-M-65-producing S. Infantis between marketed meat and children highlights a public health problem which needs be controlled at livestock level.

Sows affect their piglets' faecal microbiota until fattening but not their Salmonella enterica shedding status.

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.

Research Note: Horizontal transmission and internal organ colonization by Salmonella Enteritidis and Salmonella Kentucky in experimentally infected laying hens in indoor cage-free housing.

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.

Salmonella identified in pigs in Kenya and Malawi reveals the potential for zoonotic transmission in emerging pork markets.

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.

Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation.

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 ß) 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 ß contained multiple subclades associated with wild avian species. The contrasting epidemiology of strains in clade α and ß 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 ß 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).

Emergence of a Novel Salmonella enterica Serotype Reading Clonal Group Is Linked to Its Expansion in Commercial Turkey Production, Resulting in Unanticipated Human Illness in North America.

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.

The Expanded Role of Roof-Rats (Rattus rattus) in Salmonella spp. Contamination of a Commercial Layer Farm in East Japan.

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.

Analyses of prevalence and molecular typing of Salmonella in the goose production chain.

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.

Research Note: Evaluation of several inoculation procedures for colonization of day-old broiler chicks with Salmonella Heidelberg.

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 106 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 106 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.