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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Vertical transmission of Salmonella Enteritidis with heterogeneous antimicrobial resistance from breeding chickens to commercial chickens in China.

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 blaCTX-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.

Combining Salmonella Dublin genome information and contact-tracing to substantiate a new approach for improved detection of infectious transmission routes in cattle populations.

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.

Genetic diversity of Salmonella enterica recovered from chickens farms and its potential transmission to human.

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.

A within-flock model of Salmonella Heidelberg transmission in broiler chickens.

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.

An investigation of Salmonella Fluntern illnesses linked to leopard geckos-United States, 2018.

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.