Prevalence and Antimicrobial Resistance of Salmonella Dublin and Thermotolerant Campylobacter in Liver from Veal Calves in Québec, Canada.

Salmonella Dublin and Campylobacter spp. are two foodborne pathogens of importance. A small number of studies reported that consumption of veal liver was associated with an increased risk of human illness from these two pathogens. To better characterize the risk of exposure from liver, a cross-sectional study was conducted to estimate the prevalence of white veal calf liver contamination with these two pathogens and to characterize the antimicrobial non-susceptibility patterns of isolates. Veal liver samples were collected at two slaughterhouses in Quebec, Canada, in 2016 and 2017. Samples were submitted for polymerase chain reaction (PCR) screening followed by culture of Salmonella and thermotolerant Campylobacter. Isolates were tested for antimicrobial susceptibility using broth microdilution. Salmonella Dublin was the only serotype cultured from 3.6% (95% confidence interval [CI]: 0.0-7.9) of 560 liver samples. Among them and for technical reasons, 498 were tested by PCR for Campylobacter. The prevalence of PCR-positive livers was estimated to be 65.8% (95% CI: 58.7-72.9) for Campylobacter jejuni and 7.0% (95% CI: 3.9-10.1%) for Campylobacter coli. Fourteen Salmonella Dublin isolates were submitted for antimicrobial resistance (AMR) testing; all were non-susceptible to at least eight antimicrobials from six different classes. Most (81.4%) of the 188 C. jejuni isolates submitted for AMR testing were non-susceptible to tetracycline, and 23.0% of isolates were non-susceptible to nalidixic acid and ciprofloxacin. Of the seven C. coli isolates, four were multidrug resistant. This study highlights the importance of veal liver as a potential source of exposure to multidrug-resistant Salmonella Dublin and thermotolerant Campylobacter spp.

Comparison of microbiota of recycled manure solids and straw bedding used in dairy farms in eastern Canada.

Recycled manure solids (RMS) bedding is an alternative bedding option that is growing in popularity on Canadian dairy farms. However, the microbiological characteristics and production of RMS bedding are poorly documented under on-farm conditions in eastern Canada. This bedding could support the presence of pathogens and could have an effect on cow and human health. The aim of this study was to describe the RMS microbiota when used under dairy cows and compare it with straw bedding. Unused and used bedding from 27 RMS and 61 straw-bedded dairy farms were collected and compared using 16S amplicon sequencing, bacterial counts, and Salmonella spp. and Listeria monocytogenes detection. Microbiota composition of unused RMS and unused straw were different. After use, both bedding microbiota were similar in their bacterial composition, structure, and diversity. Unused RMS generally contained higher bacterial counts than did unused straw, except for Klebsiella spp. counts. Salmonella spp. and L. monocytogenes were more frequently detected in unused RMS (Salmonella spp.: 11%; L. monocytogenes: 30%), than in unused straw (Salmonella spp.: 0%; L. monocytogenes: 11%). Finally, 2 RMS production systems (extraction of the liquid fraction followed by maturation in an opened or enclosed container vs. in a heap) did not influence the microbiota richness and bacteria distribution (α-diversity), but did influence the microbiota structure (ß-diversity). In conclusion, animal and human pathogens were found in greater numbers and more frequently in unused RMS than unused straw, and this could eventually affect dairy cow or human health.

Putative antigenic proteins identified by comparative and subtractive reverse vaccinology in necrotic enteritis-causing Clostridium perfringens isolated from broiler chickens.

BACKGROUND: Avian necrotic enteritis (NE) caused by Clostridium perfringens is a disease with a major economic impact, generating losses estimated to 6 billion of dollars annually for the poultry industry worldwide. The incidence of the disease is particularly on the rise in broiler chicken flocks eliminating the preventive use of antibiotics. To date, no alternative allows for the efficient prevention of NE and a control of the disease using a vaccinal strategy would be mostly prized. For this purpose, comparative and subtractive reverse vaccinology identifying putative immunogenic bacterial surface proteins is one of the most promising approaches. RESULTS: A comparative genomic study was performed on 16 C. perfringens strains isolated from healthy broiler chickens and from broilers affected with necrotic enteritis. Results showed that the analyzed genomes were composed of 155,700 distinct proteins from which 13% were identified as extracellular, 65% as cytoplasmic and 22% as part of the bacterial membrane. The evaluation of the immunogenicity of these proteins was determined using the prediction software VaxiJen®. CONCLUSIONS: For the most part, proteins with the highest scores were associated with an extracellular localisation. For all the proteins analyzed, the combination of both the immunogenicity score and the localisation prediction led to the selection of 12 candidate proteins that were mostly annotated as hypothetical proteins. We describe 6 potential candidates of higher interest due to their antigenic potential, their extracellular localisation, and their possible role in virulence of C. perfringens.

Expert Elicitation to Estimate the Relative Risk of Food Safety Criteria Included in the Establishment-Based Risk Assessment Model for Canadian Hatcheries.

The Canadian Food Inspection Agency is developing an Establishment-based Risk Assessment model for Hatcheries to allocate inspection resources according to the food safety risk associated with each hatchery falling under its jurisdiction. In a previous study, 29 factors contributing to the food safety risk of hatcheries were identified and grouped into three clusters (inherent risk, risk mitigation, and compliance) and assessment criteria were defined. The objective of the current study was to estimate the relative risk (RR) of these criteria. Two rounds of expert elicitations were conducted to allow 13 Canadian experts to estimate the RR of each criterion (n = 96) based on its potential impact on human health, with a specific focus on Salmonella spp. This process also aimed to estimate the maximum increase or decrease in the overall food safety risk of a hatchery when considering multiple criteria belonging to a specific cluster and to assess the risk attribution of Salmonella spp. at the hatchery and bird-type levels. Results showed that the respondent profile had no influence on the importance given to a majority of criteria. Uniformity of answers among experts improved from the first to the second round. Overall, 62.5%, 32.3%, and 5.2% of the criteria were attributed to an RR that was less than 2, between 2 and 3, and greater than 3, respectively. Mixing eggs from different supply flocks when placed into the same hatching unit, hatching multiple species, and importing eggs with unknown quality status were identified as having the highest contribution to a hatchery's inherent risk. Requiring information on the foodborne pathogen status of supplying flocks and the occurrence of regulatory enforcement actions were the most impactful risk mitigation and compliance factors, respectively. The median RR value assigned to each criterion and cluster will be used to build this new model.

Genomic characterization of Listeria monocytogenes isolates reveals that their persistence in a pig slaughterhouse is linked to the presence of benzalkonium chloride resistance genes.

BACKGROUND: The aim of this study was to characterize the genomes of 30 Listeria monocytogenes isolates collected at a pig slaughterhouse to determine the molecular basis for their persistence. RESULTS: Comparison of the 30 L. monocytogenes genomes showed that successive isolates (i.e., persistent types) recovered from thew sampling site could be linked on the basis of single nucleotide variants confined to prophage regions. In addition, our study revealed the presence among these strains of the bcrABC cassette which is known to produce efflux pump-mediated benzalkonium chloride resistance, and which may account for the persistence of these isolates in the slaughterhouse environment. The presence of the bcrABC cassette was confirmed by WGS and PCR and the resistance phenotype was determined by measuring minimum inhibitory concentrations. Furthermore, the BC-resistant strains were found to produce lower amounts of biofilm in the presence of sublethal concentrations of BC. CONCLUSIONS: High resolution SNP-based typing and determination of the bcrABC cassette may provide a means of distinguishing between resident and sporadic L. monocytogenes isolates, and this in turn will support better management of this pathogen in the food industry.

Overlooked sources of Salmonella contamination in the pig production network: Slaughterhouse yard pathways and mudguards and carpets from transport trucks.

This report describes various Salmonella serovars which were found on often overlooked locations in a pig farm/slaughterhouse interface. These include slaughterhouse yard pathways and mudguards and carpets of transport trucks arriving at and departing from production sites.

Sources négligées de contamination par Salmonella dans un réseau de production de porcs: les voies de circulation de l'abattoir et les garde-boues et les tapis de cabine des camions de transport. Nous montrons ici que Salmonella, l'agent causal de la salmonellose, peut être trouvé sur des sites très inhabituels et négligés dans l'interface ferme porcine/abattoir: les voies de circulation de la cour d'abattoir, et les garde-boues et tapis des camions de transport qui arrivent et partent vers les sites de production.(Traduit par les auteurs).

Dynamics of Virus Distribution in a Defined Swine Production Network Using Enteric Viruses as Molecular Markers.

Modern swine production systems represent complex and dynamic networks involving numerous stakeholders. For instance, livestock transporters carry live animals between fattening sites, abattoirs, and other premises on a daily basis. This interconnected system may increase the risk of microbial spread within and between networks, although little information is available in that regard. In the present study, a swine network composed of 10 finishing farms, one abattoir, and three types of stakeholders (veterinarians, livestock transporters, and nutritional technicians) in Quebec, Canada, was selected to investigate specific vectors and reservoirs of enteric viruses. Environmental samples were collected from the premises over a 12-month period. Samples were screened using targeted reverse transcription-PCR and sequencing of two selected viral markers, group A rotaviruses (RVA) and porcine astroviruses (PoAstV), both prevalent and genetically heterogeneous swine enteric viruses. The results revealed frequent contamination of farm sites (21.4 to 100%), livestock transporter vehicles (30.6 to 68.8%) and, most importantly, the abattoir yard (46.7 to 94.1%), depending on the sample types. Although high levels of strain diversity for both viruses were found, identical PoAstV and RVA strains were detected in specific samples from farms, the abattoir yard, and the livestock transporter vehicle, suggesting interconnections between these premises and transporters. Overall, the results from this study underscore the potential role of abattoirs and livestock transport as a reservoir and transmission route for enteric viruses within and between animal production networks, respectively. IMPORTANCE: Using rotaviruses and astroviruses as markers of enteric contamination in a swine network has revealed the potential role of abattoirs and livestock transporters as a reservoir and vectors of enteric pathogens. The results from this study highlight the importance of tightening biosecurity measures. For instance, implementing sanitary vacancy between animal batches and emphasizing washing, disinfection, and drying procedures on farms and for transportation vehicles, as well as giving limited access and circulation of vehicles throughout the production premises, are some examples of measures that should be applied properly. The results also emphasize the need to closely monitor the dynamics of enteric contamination in the swine industry in order to better understand and potentially prevent the spread of infectious diseases. This is especially relevant when a virulent and economically damaging agent is involved, as seen with the recent introduction of the porcine epidemic diarrhea virus in the country.

Extensive characterization of Campylobacter jejuni chicken isolates to uncover genes involved in the ability to compete for gut colonization.

BACKGROUND: Campylobacter jejuni is responsible for human foodborne enteritis. This bacterium is a remarkable colonizer of the chicken gut, with some strains outcompeting others for colonization. To better understand this phenomenon, the objective of this study was to extensively characterize the phenotypic performance of C. jejuni chicken strains and associate their gut colonizing ability with specific genes. RESULTS: C. jejuni isolates (n = 45) previously analyzed for the presence of chicken colonization associated genes were further characterized for phenotypic properties influencing colonization: autoagglutination and chemotaxis as well as adhesion to and invasion of primary chicken caecal cells. This allowed strains to be ranked according to their in vitro performance. After their in vitro capacity to outcompete was demonstrated in vivo, strains were then typed by comparative genomic fingerprinting (CGF). In vitro phenotypical properties displayed a linear variability among the tested strains. Strains possessing higher scores for phenotypical properties were able to outcompete others during chicken colonization trials. When the gene content of strains was compared, some were associated with different phenotypical scores and thus with different outcompeting capacities. Use of CGF profiles showed an extensive genetic variability among the studied strains and suggested that the outcompeting capacity is not predictable by CGF profile. CONCLUSION: This study revealed a wide array of phenotypes present in C. jejuni strains, even though they were all recovered from chicken caecum. Each strain was classified according to its in vitro competitive potential and its capacity to compete for chicken gut colonization was associated with specific genes. This study also exposed the disparity existing between genetic typing and phenotypical behavior of C. jejuni strains.

Genetic diversity of group A rotavirus in swine in Canada.

Group A rotaviruses (RVA) in pigs have been poorly investigated in Canada. In a continued effort to fill this gap, ten finisher swine farms in Quebec, Canada, were sampled over a nine-month period. The presence of RVA was detected in healthy pigs on all farms investigated during the entire sampling period. The genotypes detected included G2, G5, G9 and G11; P[6], P[7], P[13], P[27] and P[34]; and I5 and I14. The predominant types were G2, P[13] and I5, which is different from previous global reports. Various fomites were consistently contaminated by RVA, suggesting that a resident viral flora remains in the farm environment and may play a role in the infection of incoming pigs. The results also suggest temporal or geographical specificities regarding strain distribution on pig farms.

Essential oils mix effect on chicks ileal and caecal microbiota modulation: a metagenomics sequencing approach.

Introduction: Microbiota plays a pivotal role in promoting the health and wellbeing of poultry. Essential oils (EOs) serve as an alternative solution for modulating poultry microbiota. This study aimed to investigate, using amplicon sequencing, the effect of a complex and well-defined combination of EOs feed supplement on both ileal and caecal broiler microbiota, within the context of Salmonella and Campylobacter intestinal colonization. Material and methods: For this experiment, 150-day-old Ross chicks were randomly allocated to two groups: T+ (feed supplementation with EO mix 500 g/t) and T- (non-supplemented). At day 7, 30 birds from each group were orally inoculated with 106 CFU/bird of a Salmonella enteritidis and transferred to the second room, forming the following groups: TS+ (30 challenged birds receiving infeed EO mix at 500g/t) and TS- (30 challenged birds receiving a non-supplemented control feed). At day 14, the remaining birds in the first room were orally inoculated with 103 CFU/bird of two strains of Campylobacter jejuni, resulting in the formation of groups T+C+ and T-C+. Birds were sacrificed at day 7, D10, D14, D17, and D21. Ileal and caecal microbiota samples were analyzed using Illumina MiSeq sequencing. At D7 and D14, ileal alpha diversity was higher for treated birds (p <0.05). Results and discussion: No significant differences between groups were observed in caecal alpha diversity (p>0.05). The ileal beta diversity exhibited differences between groups at D7 (p < 0.008), D10 (p = 0.029), D14 (p = 0.001) and D17 (p = 0.018), but not at D21 (p = 0.54). For all time points, the analysis indicated that 6 biomarkers were negatively impacted, while 10 biomarkers were positively impacted. Sellimonas and Weissella returned the lowest (negative) and highest (positive) coefficient, respectively. At each time point, treatments influenced caecal microbiota beta diversity (p < 0.001); 31 genera were associated with T+: 10 Ruminoccocaceae genera were alternatively more abundant and less abundant from D7, 7 Lachnospiraceae genera were alternatively more and less abundant from D10, 6 Oscillospiraceae genera were variable depending on the date and 4 Enterobacteriaceae differed from D7. During all the experiment, Campylobacter decreased in treated birds (p < 0.05). This study showed that EO mix modulates ileal and caecal microbiota composition both before and during challenge conditions, increasing alpha diversity, especially in ileum during the early stages of chick life.

Distribution of colonization and antimicrobial resistance genes in Campylobacter jejuni isolated from chicken.

Campylobacter jejuni is an important worldwide foodborne pathogen commonly found as a commensal organism in poultry that can reach high numbers within the gut after colonization. Although information regarding some genes involved in colonization is available, little is known about their distribution in strains isolated specifically from chickens and whether there is a linkage between antimicrobial resistance (AMR) and colonization genes. To assess the distribution and relevance of genes associated with chicken colonization and AMR, a C. jejuni microarray was created to detect 254 genes of interest in colonization and AMR including variants. DNA derived from chicken-specific Campylobacter isolates collected in 2003 (n=29) and 2008 (n=28) was hybridized to the microarray and compared. Hybridization results showed variable colonization-associated gene presence. Acquired AMR genes were low in prevalence whereas chemotaxis receptors, arsenic resistance genes, as well as genes from the cell envelope and flagella functional groups were highly variable in their presence. Strains clustered into two groups, each linked to different control strains, 81116 and NCTC11168. Clustering was found to be independent of collection time. We also show that AMR weakly associated with the CJ0628 and arsR genes. Although other studies have implicated numerous genes associated with C. jejuni chicken colonization, our data on chicken-specific isolates suggest the opposite. The enormous variability in presumed colonization gene prevalence in our chicken isolates suggests that many are of lesser importance than previously thought. Alternatively, this also suggests that combinations of genes may be required for natural colonization of chicken intestines.

Intestinal Colonization of Campylobacter jejuni and Its Hepatic Dissemination Are Associated with Local and Systemic Immune Responses in Broiler Chickens.

Campylobacter jejuni is an important foodborne pathogen. Despite the lack of clinical signs associated with its colonization in poultry, it has been reported to interact with the intestinal immune system. However, little is known about the interaction between C. jejuni and the chicken immune system, especially in the context of hepatic dissemination. Therefore, to follow up on our previous study showing intestinal colonization and hepatic spread of C. jejuni, cecal tonsils and liver samples were collected from these birds to determine the mRNA levels of chemokines and cytokines. Serum samples were also collected to determine serum amyloid A (SAA) concentrations and specific IgY titers. Lack of Th17 induction was observed in the cecal tonsils of only the liver-contaminated groups. This hepatic dissemination was accompanied by innate, Th1 and Th2 immune responses in livers, as well as an increase in SAA concentrations and specific IgY levels in sera. Campylobacter appears to be able to restrain the induction of the chicken gut immunity in particular conditions, possibly enhancing its hepatic dissemination and thus eliciting systemic immune responses. Although Campylobacter is often recognized as a commensal-like bacterium in chickens, it seems to modulate the gut immune system and induce systemic immunity.

A short-term bioreactor assay to assess the effect of essential oils on a microbiota derived from piglet's intestinal content.

BACKGROUND: Modulating the microbiota is an emerging way to improve pig health. In-vitro bioreactor systems can be used to reproduce intestinal microbiota to study modulating avenues. In this study, a continuous feeding system to support a microbiota derived from piglet colonic contents, over 72 h, was developed. The microbiota from piglets was collected and used as inoculum. The culture media was derived from an artificial digestion of piglet feed. The microbiota diversity in time, the reproducibility between replicates and the diversity of the bioreactor microbiota compared to the inoculum was assessed. Essential oils were used as a proof of concept to assess the in vitro microbiota modulation. The microbiota diversity was assessed by 16S rRNA amplicon sequencing. Quantitative PCR was also used for total bacteria, lactobacilli and Enterobacteria. RESULTS: At the start of the assay, the bioreactor microbiota diversity was similar to the inoculum. Time and replication affected the bioreactor microbiota diversity. Between 48 and 72 h, no statistical variation of the microbiota diversity was observable. After a 48 h running period, thymol and carvacrol were added at 200 ppm or 1000 ppm for 24 h. No microbiota modification was observed by sequencing. Quantitative PCR results showed a significant growth of lactobacilli when thymol was used at 1000 ppm, where only a trend was observed with the 16S analysis. CONCLUSIONS: This study presents a bioreactor assay that can be used as a tool for rapid screening of additives and suggests that the effects of essential oils on the microbiota are subtle, acting against a few bacterial genera.

Slight Temperature Deviation during a 56-Day Storage Period Does Not Affect the Microbiota of Fresh Vacuum-Packed Pork Loins.

It is profitable to export fresh meat overseas, where it is often regarded as a premium commodity. Meeting this demand for fresh meat, however, necessitates long export times, during which uncontrolled temperature increases can affect the microbiological quality of the meat and thereby, reduce shelf life or compromise food safety. To study the impact of temperature deviations on microbial community composition and diversity, we used 16S rRNA gene sequencing for Listeria monocytogenes and Salmonella spp. detection to describe the surface microbiota of eight batches of vacuum-packed loins stored at -1.5 °C (control) for 56 days and subjected to a 2 °C or 10 °C temperature deviation for a few hours (mimicking problems regularly encountered in the industry) at day 15 or 29. The presence of pathogens was negligible. The applied temperature deviations were not associated with different microbiota. Sequencing analysis showed the presence of Yersinia, an unexpected pathogen, and relative abundance increased in the groups subjected to temperature deviations. Over time, Lactobacillales_unclassified genus became the main constituent of the microbiota of vacuum-packed pork loins. Although the microbiota of the eight batches appeared similar at the beginning of storage, differences were revealed after 56 days, suggesting unequal aging of the microbiota.

Monophasic Variant of Salmonella Typhimurium Infection Affects the Serum Metabolome in Swine.

Salmonella is the most relevant foodborne zoonotic agent found in swine, and its presence in French herds is significant. Its carriage is asymptomatic, which makes it difficult to detect during rearing, thus increasing the risk of its presence on pork meat. Studies have shown that enteric infection in animals could be associated with changes in the serum metabolome composition, through the immune response or changes in the digestive microbiota composition. We hypothesized that these changes in the serum metabolome composition could be used as markers for the detection of asymptomatic animals infected by Salmonella. Using untargeted analysis by liquid chromatography coupled with mass spectrometry, we showed that significant differences in the composition of the serum metabolome could be detected between infected or noninfected animals both 1 and 21 days after experimental infection. This serum metabolome composition significantly changed during the 21 days postinfection in the infected animal groups, suggesting an evolution of the impact of infection with time. Despite this evolution, differences in the serum metabolome composition persisted between infected and noninfected animals 21 days after the initial infection. We also showed a possible difference between high-shedding and low-shedding animals 21 days postinfection. Finally, some of the variations in the metabolome were found to be significantly associated with variations of specific members of the fecal microbiota. Thus, excreting and asymptomatic animals, but also high-shedding animals, could be identified on the basis of their serum metabolome composition.

Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse.

The microorganisms found on fresh, raw meat cuts at a slaughterhouse can influence the meat's safety and spoilage patterns along further stages of processing. However, little is known about the general microbial ecology of the production environment of slaughterhouses. We used 16s rRNA sequencing and diversity analysis to characterize the microbiota heterogeneity on conveyor belt surfaces in the cutting room of a swine slaughterhouse from different production lines (each associated with a particular piece/cut of meat). Variation of the microbiota over a period of time (six visits) was also evaluated. Significant differences of alpha and beta diversity were found between the different visits and between the different production lines. Bacterial genera indicative of each visit and production line were also identified. We then created random forest models that, based on the microbiota of each sample, allowed us to predict with 94% accuracy to which visit a sample belonged and to predict with 88% accuracy from which production line it was taken. Our results suggest a possible influence of meat cut on processing surface microbiotas, which could lead to better prevention, surveillance, and control of microbial contamination of meat during processing.

First Expert Elicitation of Knowledge on Possible Drivers of Observed Increasing Human Cases of Tick-Borne Encephalitis in Europe.

Tick-borne encephalitis (TBE) is a viral disease endemic in Eurasia. The virus is mainly transmitted to humans via ticks and occasionally via the consumption of unpasteurized milk products. The European Centre for Disease Prevention and Control reported an increase in TBE incidence over the past years in Europe as well as the emergence of the disease in new areas. To better understand this phenomenon, we investigated the drivers of TBE emergence and increase in incidence in humans through an expert knowledge elicitation. We listed 59 possible drivers grouped in eight domains and elicited forty European experts to: (i) allocate a score per driver, (ii) weight this score within each domain, and (iii) weight the different domains and attribute an uncertainty level per domain. An overall weighted score per driver was calculated, and drivers with comparable scores were grouped into three terminal nodes using a regression tree analysis. The drivers with the highest scores were: (i) changes in human behavior/activities; (ii) changes in eating habits or consumer demand; (iii) changes in the landscape; (iv) influence of humidity on the survival and transmission of the pathogen; (v) difficulty to control reservoir(s) and/or vector(s); (vi) influence of temperature on virus survival and transmission; (vii) number of wildlife compartments/groups acting as reservoirs or amplifying hosts; (viii) increase of autochthonous wild mammals; and (ix) number of tick species vectors and their distribution. Our results support researchers in prioritizing studies targeting the most relevant drivers of emergence and increasing TBE incidence.

Co-Occurrence of L. monocytogenes with Other Bacterial Genera and Bacterial Diversity on Cleaned Conveyor Surfaces in a Swine Slaughterhouse.

Bacterial pathogens, such as Listeria monocytogenes, can show resistance to disinfection and persistence on working surfaces, permitting them to survive and contaminate food products. Persistence-a complex phenomenon involving interactions between many bacteria within a biofilm-is modulated by in situ characteristics. This study aimed to describe, in silico, the microbiota identified in a swine slaughterhouse after sanitation procedures to better understand the presence of L. monocytogenes on these surfaces. Molecular tools for characterization of microbial communities were used to assess the relative contribution of different bacteria resulting from this phenomenon, and the 16S rRNA sequencing method was used on samples from meat conveyor belt surfaces collected on four sampling visits to study the co-occurrence between L. monocytogenes and other bacteria. From the background microbiota, a total of six genera were found to be negatively correlated with Listeria spp., suggesting Listeria growth inhibition, competition, or at least an absence of shared habitats. Based on these results, a complete scenario of interactions of Listeria with components of background microbiota was established. This work contributes to identifying avenues that could prevent the growth and persistence of L. monocytogenes on food-processing surfaces.

Observations supporting hypothetical commensalism and competition between two Campylobacter jejuni strains colonizing the broiler chicken gut.

Campylobacter jejuni is the most prevalent bacterial foodborne pathogen in humans. Given the wide genetic diversity of C. jejuni strains found in poultry production, a better understanding of the relationships between these strains within chickens could lead to better control of this pathogen on farms. In this study, 14-day old broiler chickens were inoculated with two C. jejuni strains (103 or 107 CFU of D2008b and 103 CFU of G2008b, alone or together) that were previously characterized in vitro and that showed an opposite potential to compete for gut colonization in broilers. Liver samples and ileal and cecal contents were collected and used to count total C. jejuni and to quantify the presence of each strain using a strain specific qPCR or PCR approach. Ileal tissue samples were also collected to analyze the relative expression level of tight junction proteins. While a 103 CFU inoculum of D2008b alone was not sufficient to induce intestinal colonization, this strain benefited from the G2008b colonization for its establishment in the gut and its extraintestinal spread. When the inoculum of D2008b was increased to 107 CFU - leading to its intestinal and hepatic colonization - a dominance of G2008b was measured in the gut and D2008b was found earlier in the liver for birds inoculated by both strains. In addition, a transcript level decrease of JAM2, CLDN5 and CLDN10 at 7 dpi and a transcript level increase of ZO1, JAM2, OCLN, CLDN10 were observed at 21 dpi for groups of birds having livers contaminated by C. jejuni. These discoveries suggest that C. jejuni would alter the intestinal barrier function probably to facilitate the hepatic dissemination. By in vitro co-culture assay, a growth arrest of D2008b was observed in the presence of G2008b after 48 h of culture. Based on these results, commensalism and competition seem to occur between both C. jejuni strains, and the dynamics of C. jejuni intestinal colonization and liver spread in broilers appear to be strain dependent. Further in vivo experimentations should be conducted to elucidate the mechanisms of commensalism and competition between strains in order to develop adequate on-farm control strategies.

The swine enteric virome in a commercial production system and its association with neonatal diarrhea.

Swine are an important food source worldwide and producers may not always be aware of the variety of the pathogens infecting their herds, particularly viruses. In this study, 12 enteric viruses were monitored in a total of 181 diarrheic and healthy piglets; namely porcine astrovirus groups 1-5 (poAstV1-5), rotavirus A and C (RVA-RVC), caliciviruses (CaVs), porcine kobuvirus (PoK), hepatitis E virus (HEV), and torque teno sus virus 1 and k2 (TTsuV1-k2). All animals were sampled before 3 weeks of age, and then at 5, 12 and 20 weeks of age. In addition to the 12 targeted viruses, the virome of 12 piglets at 4 different life stages was characterized using a high-throughput sequencing approach. The presence of CaV (sapovirus), poAstV-3 or poAstV-5 was found to be a risk factor for neonatal diarrhea. Co-infections with RVC and poAstV-2, poAstV-3, and poAstV-4 and CaV co-infected with PoK or poAstV-4 were also found to be risk factors for diarrhea in piglets. RVC, PoK, poAstV-3 and poAstV-4 were the most prevalent viruses in piglets below 3 weeks of age. PoAstV-2, poAstV-4, TTsuV1 and TTsuVk2 were found to be the most prevalent viruses infecting piglets of 20 weeks of age. The enteric virome composition varied between healthy and diarrheic piglets. The alpha and beta diversity of the enteric viromes varied from under 3 weeks of age to 20 weeks and was mainly supported by phages. Overall, this study sheds new light on enteric virome dynamics and the virome's relationship with neonatal diarrhea.