Salmonella spp. transmission in a vertically integrated poultry operation: Clustering and diversity analysis using phenotyping (serotyping, phage typing) and genotyping (MLVA)

Assessment and genomic analysis of Salmonella and Campylobacter from different stages of an integrated no-antibiotics-ever (NAE) broiler complex: a longitudinal study

The objective of this study was to determine prevalence and perform genomic analysis of Salmonella spp. and Campylobacter spp. isolated from different stages of an integrated NAE broiler complex. Environmental samples were screened with 3M-Molecular Detection System (MDS) and MDS positive samples were further processed for confirmation of results and identification. Core genome-based phylogenies were built for both bacteria isolated from this study along with selected NCBI genomes. The odds ratios and 95% confidence limits were compared among stages and sample types (α < 0.05) using multivariable model. Based on MDS results, 4% and 18% of total samples were positive for Salmonella spp. and Campylobacter spp. respectively. The odds of Salmonella detection in hatchery samples were 2.58 times as likely as compared to its detection in production farms' samples (P = 0.151) while the odds of Campylobacter detection in production farms' samples were 32.19 times as likely as its detection in hatchery (P = 0.0015). Similarly, the odds of Campylobacter detection in boot swabs, soil, water, and miscellaneous samples were statistically significant (P < 0.05) as compared with fly paper as reference group. The serovars identified for Salmonella were Typhimurium, Barranquilla, Liverpool, Kentucky, Enteritidis, Luciana, and Rough_O:r:1,5. For Campylobacter, the species identified were Campylobacter jejuni and Campylobacter coli. Phylogeny results show close genetic relatedness among bacterial strains isolated from different locations within the same stage and between different stages. The results show possibility of multiple entry points of such bacteria entering broiler complex and can potentially contaminate the final raw product in the processing plant. It suggests the need for a comprehensive control strategy with strict biosecurity measures and best management practices to minimize or eliminate such pathogens from the poultry food chain.

Comparison of yeast-derived commercial feed additives on Salmonella Enteritidis survival and microbiota populations in rooster cecal in vitro incubations

Yeast-derived products have become more of an interest in the poultry industry as of late because of their use in modulating the gastrointestinal tract (GIT) microbiome to both improve production parameters and prevent infection. This study aimed to evaluate the effects of various yeast-derived products on Salmonella enterica inoculation in un in vitro rooster cecal incubations and associated effects on the cecal microbiome. Cecal contents were obtained from 53-wk old White Leghorn H & N Nick Chick roosters (n = 3) fed a wheat-based, commercial-type basal diet. Cecal contents were diluted 1:3000 in anaerobic dilution solution (ADS) in an anaerobic chamber, with 20 mL aliquoted to each serum bottle. There were three controls (n = 3): basal diet only, diluted cecal contents only, and basal diet and diluted cecal contents; and five treatments containing the basal diet and diluted cecal contents (n = 3): Citristim® (ADM), ImmunoWall® (ICC), Maxi-Gen Plus® (CBS Bio Platforms), Hilyses® (ICC), and Original XPC® (Diamond V). All treatments were applied at a rate of 2.5 kg/tonne or less. All groups were inoculated with a nalidixic acid-resistant strain of Salmonella Enteritidis at 10^7 CFU/mL and incubated at 37 deg C. Samples were collected at 0, 24, and 48 h for S. Enteritidis enumeration and 16S rDNA microbial sequencing. Salmonella data were log-transformed and analyzed in a two-way ANOVA with means separated using Tukey's HSD (P≤0.05). Genomic DNA was extracted, and resulting libraries were prepared and sequenced using an Illumina MiSeq. Sequencing data were analyzed in QIIME2 (2021.4) with diversity metrics (alpha and beta), and an analysis of the composition of microbiomes (ANCOM) was performed. Main effects were considered significant at P≤0.05, with pairwise differences considered significant at Q≤0.05. There was an interaction of treatment and time on the enumeration of Salmonella where treatments of Citristim, Immunowall, Hilyses, and XPC reduced Salmonella by 1 log CFU/mL compared to the controls. At 48 h, each yeast product treatment reduced Salmonella by 3 log CFU/mL compared to the controls. There was no main effect of treatment on the alpha diversity metrics, richness, or evenness (P > 0.05). Treatment affected the beta diversity, abundance, and phylogenetic differences, but there were no pairwise differences (P>0.05, Q>0.05). Using ANCOM at the genus level, the taxa Synergistes, Alloprevotella, Sutterella, and Megasphaera abundance were significantly different (W = 154,147,145,140, respectively). These results demonstrate the potential of these yeast-derived products to reduce foodborne pathogens, such as Salmonella Enteriditis, in vitro, without negatively disrupting the cecal microbiome.

Dominant Salmonella Serovars in Australian Broiler Breeder Flocks and Hatcheries: a Longitudinal Study

A longitudinal study was conducted to determine the dominance and prevalence of Salmonella enterica subsp in Australian broiler breeder flocks and hatcheries. Twenty-two flocks (n = 3339 samples) were sampled over 6 time points beginning at placement until week 40. Hatcheries (n = 274 samples) were sampled following removal of chicks hatched from eggs originating from the 22 donor parent flocks. The percent of positive flocks (36%) and frequency of positive samples (15.6%) were highest during rearing at week 7. The frequency of positive samples decreased over the 40 weeks; however, the number of positive flocks remained relatively consistent. Geographical location had a greater influence on Salmonella detection frequency than company sample origin, despite differing management and vaccination protocols within and between companies. Twelve serovars were detected in total. The predominant serovars during rearing were Salmonella Mbandaka (32%), S. Saintpaul (27%), and S. Liverpool (18%). The predominant serovars detected during production were S. Cubana (27%), S. Saintpaul (24%), and S. Havana (13%). Salmonella Typhimurium, S. Ohio, and S. Hessarek were detected in the hatcheries. Of the serovars detected, only S. Typhimurium and S. Ohio were found in both broiler breeder flocks and hatcheries. However, detection did not correspond to the status of the flock eggs feeding into the hatchery. This study provides an up-to-date capture of the current Salmonella serovars circulating in the broiler breeder industry. Continued surveillance within the Australian Chicken Meat industry is imperative to mitigate and reduce the risk of salmonellosis in the community related to chicken meat. IMPORTANCE This study identified prevalent and dominant Salmonella enterica subsp in Australian Broiler Breeder flocks, as well as in hatcheries post chick hatch and removal, from eggs originating from these donor parent flocks. The captured Salmonella data was further compared to the most common Salmonella serovars isolated from broilers, as well as human salmonellosis notification data, which is useful for consideration of the circulating serovars within the chicken meat industry and their significance in public health. As there are multiple entry points for Salmonella during the entire chicken meat production chain that can lead to carcass contamination, it is important to distinguish serovars present between the different stages of vertical integration to implement and enable Salmonella control strategies.

Combined Quantification and Deep Serotyping for Salmonella Risk Profiling in Broiler Flocks

Despite a reduction of Salmonella contamination on final poultry products, the level of human salmonellosis cases attributed to poultry has remained unchanged over the last few years. There needs to be improved effort to target serovars which may survive antimicrobial interventions and cause illness, as well as to focus on lessening the amount of contamination entering the processing plant. Advances in molecular enumeration approaches allow for the rapid detection and quantification of Salmonella in pre- and postharvest samples, which can be combined with deep serotyping to properly assess the risk affiliated with a poultry flock. In this study, we collected a total of 160 boot sock samples from 20 broiler farms across four different integrators with different antibiotic management programs. Overall, Salmonella was found in 85% (68/80) of the houses, with each farm having at least one Salmonella-positive house. The average Salmonella quantity across all four complexes was 3.6 log10 CFU/sample. Eleven different serovars were identified through deep serotyping, including all three key performance indicators (KPIs; serovars Enteritidis, Infantis, and Typhimurium) defined by the U.S. Department of Agriculture-Food Safety and Inspection Service (USDA-FSIS). There were eight multidrug resistant isolates identified in this study, and seven which were serovar Infantis. We generated risk scores for each flock based on the presence or absence of KPIs, the relative abundance of each serovar as calculated with CRISPR-SeroSeq (serotyping by sequencing the clustered regularly interspaced palindromic repeats), and the quantity of Salmonella organisms detected. The work presented here provides a framework to develop directed processing approaches and highlights the limitations of conventional Salmonella sampling and culturing methods. IMPORTANCE Nearly one in five foodborne Salmonella illnesses are derived from chicken, making it the largest single food category to cause salmonellosis and indicating a need for effective pathogen mitigation. Although industry has successfully reduced Salmonella incidence in poultry products, there has not been a concurrent reduction in human salmonellosis linked to chicken consumption. New efforts are focused on improved control at preharvest, which requires improved Salmonella surveillance. Here, we present a high-resolution surveillance approach that combines quantity and identity of Salmonella in broiler flocks prior to processing which will further support improved Salmonella controls in poultry. We developed a framework for this approach, indicating that it is possible and important to harness deep serotyping and molecular enumeration to inform on-farm management practices and to minimize risk of cross-contamination between flocks at processing. Additionally, this framework could be adapted to Salmonella surveillance in other food animal production systems.

Antimicrobial Resistance and Genomic Characterization of Salmonella Infantis from Different Sources

The epidemiology of Salmonella Infantis is complex in terms of its distribution and transmission. The continuous collection and analysis of updated data on the prevalence and antimicrobic resistance are essential. The present work aimed to investigate the antimicrobial resistance and the correlation among S. Infantis isolates from different sources through the multiple-locus variable-number of tandem repeat (VNTR) analysis (MLVA). A total of 562 Salmonella strains isolated from 2018 to 2020 from poultry, humans, swine, water buffalo, mussels, cattle, and wild boar were serotyped, and 185 S. Infantis strains (32.92%) were identified. S. Infantis was commonly isolated in poultry and, to a lesser extent, in other sources. The isolates were tested against 12 antimicrobials, and a high prevalence of resistant strains was recorded. S. Infantis showed high resistance against fluoroquinolones, ampicillin, and tetracycline, which are commonly used in human and veterinary medicine. From all S. Infantis isolates, five VNTR loci were amplified. The use of MLVA was not sufficient to understand the complexity of the epidemiological relationships between S. Infantis strains. In conclusion, an alternative methodology to investigate genetic similarities and differences among S. Infantis strains is needed.

Assessing evidence of a potential Salmonella transmission across the poultry food chain

Enhanced Salmonella surveillance programmes in poultry were implemented in all European Member States, with minimum prevalence targets for a list of targeted serotypes to safeguard food and public health. Based on the Belgian Salmonella surveillance programme and focusing on poultry, the overarching aim of this study was to highlight possible Salmonella transmissions across the food chain (FC). For this purpose, firstly, the prevalence patterns of Salmonella (targeted and the most prevalent non-targeted) serotypes along the FC were described over time. Secondly, the effectiveness of the control measures against vertical transmission (breeders to 1-day-old broiler and layer chicks) was indirectly assessed by looking into the odds of targeted serotypes detection. Thirdly, it was appraised if Salmonella prevalence can significantly increase during broilers and layers production. In addition, it was tested if being tested negative at the end of production in broilers when tested positive at the entrance is serotype dependent (targeted vs. non-targeted serotypes). Results showed that, firstly, the prevalence patterns of the listed serotypes were inconstant over time and across the FC. Secondly, the odds of Salmonella targeted serotype detection in 1-day-old broiler and in 1-day-old layer flocks were lower than in breeder flocks while, thirdly, infection during broiler and layer production can lead to significant increase in positivity in subsequent samples. Finally, being infected by a targeted or by non-targeted serotype at the entrance of the flock poorly reflects the Salmonella status at the end of production. Note that this study did not make a distinction between the different sources of contamination and the effects of sampling methods and isolation methods should be subject to further investigation.

Observations on the distribution and control of Salmonella in commercial broiler hatcheries in Great Britain

Salmonella can enter hatcheries via contaminated eggs and other breaches of biosecurity. The study examined the prevalence and distribution of Salmonella in commercial hatcheries and assessed the effects of providing advice on Salmonella control. Intensive swab sampling was performed throughout 23 broiler hatcheries in Great Britain (GB). Swabs were cultured using a modified ISO6579:2017 method. After each visit, tailored advice on biosecurity and cleaning and disinfection procedures was provided to the hatchery managers. Repeat sampling was carried out in 10 of the 23 hatcheries. Salmonella prevalence ranged between 0% and 33.5%, with the chick handling areas, hatcher areas, macerator area, tray wash/storage areas, external areas and other waste handling areas being more contaminated than the setter areas. Salmonella Senftenberg and Salmonella 13,23:i:‐ were the most commonly isolated serovars. There was a reduction in Salmonella prevalence at the second visit in eight out of 10 premises, but prevalence values had increased again in all of the improved hatcheries that were visited a third time. One hatchery harboured a difficult‐to‐control resident Salmonella 13,23:i:‐ strain and was visited six times; by the final visit, Salmonella prevalence was 2.3%, reduced from a high of 23.1%. In conclusion, the study found low‐level Salmonella contamination in some GB broiler hatcheries, with certain hatcheries being more severely affected. Furthermore, it was shown that Salmonella typically is difficult to eradicate from contaminated hatcheries, but substantial reductions in prevalence are possible with improvements to biosecurity, cleaning and disinfection.

In-depth farm investigations and an exploratory risk factor analysis for the presence of Salmonella on broiler farms in Great Britain

Salmonella is a major cause of foodborne illness across Europe but there has been little recent research on its control in broiler production in Great Britain. Investigations of Salmonella presence on 20 broiler farms and a separate exploratory risk factor analysis involving 36 Salmonella-positive farms and 22 Salmonella-negative farms were carried out to investigate Salmonella contamination and control on broiler farms in Great Britain. Sources of Salmonella persistence on farm and potential risk factors for on-farm contamination were identified, enabling provision of up-to-date advice on Salmonella control to farmers. Twenty broiler farms across England and Wales were intensively sampled over time. Most farms were included in the study after routine testing as part of the Salmonella National Control Programmes (NCPs) identified regulated Salmonella serovars or potential associations with outbreak cases of significance for human health. Across all farms and visits, the highest proportion of Salmonella-positive samples were from areas exterior to broiler houses compared to anterooms or house interiors. Exterior Salmonella-positive samples were primarily collected from the immediate areas around the houses, with the highest proportions being from drainage, farm tracks/driveways, and pooled water. Elimination of Salmonella was variable but was most successful inside affected houses (compared to exterior areas) and for regulated Salmonella serovars under the Salmonella NCPs and high priority Salmonella strains with multi-drug resistances. It is likely that the financial and reputational concerns associated with regulated Salmonella serovars and those of greater public health significance underlie the reason that these serovars were more effectively controlled at farm level, as effective elimination of Salmonella can involve a considerable investment in infrastructure, time and resources. Without perceived direct benefits in eliminating non-regulated Salmonella serovars at farm level it can be challenging to maintain the required motivation and investment. A separate farm-level risk factor analysis was carried out using data collected from 58 broiler farms representing six GB broiler companies. Risk of testing positive for Salmonella via NCP sampling in the previous year was greater in the absence of house-specific anterooms and if at least some poultry houses were surrounded by soil/grass compared to if all were surrounded by concrete or a mixture of concrete and stones/gravel. Odds of testing positive for Salmonella in the previous year was also greater for farms whose maximum holding capacity was >100,000 birds, and farms where the usual number of visitors per day was 0-1 compared to 2-3. The analysis was exploratory and caution is required with interpretation, but results provide preliminary insight into aspects of farm management that may be important, practicable targets for Salmonella control on broiler farms in GB.

Isolation and antimicrobial resistance of motile Salmonella enterica from the poultry hatchery environment

Salmonella is a globally distributed major food-borne pathogen and poultry is one of the predominant sources of salmonellosis in humans. To investigate the presence of motile Salmonella in the poultry hatchery environment, we collected 97 fluff samples from four selected broiler breeder chicken hatcheries from Chattogram, Bangladesh during July-December 2015. To isolate motile Salmonella enterica, we used conventional bacteriological techniques followed by serological verification using anti-Salmonella Poly A-E serum and species confirmation by conventional PCR assay. Antimicrobial susceptibility testing by Kirby-Bauer disc diffusion method for 10 commonly used antibiotics was performed on all isolates. Isolates displaying phenotypic resistance to ampicillin were tested by PCR for bla_TEM gene, whereas those resistant to tetracycline were tested for the presence of tetA, tetB and tetC genes. A total of 24 samples (24.7%; 95% CI: 16.5-34.5, N = 97) from 3 hatcheries were positive for motile Salmonella. Of them, 21 (87.5%) and 12 (50.0%) were resistant to ampicillin and tetracycline, respectively, 9 (37.5%) to nalidixic acid and sulphamethoxazole/trimethoprim. No resistance was detected to ceftriaxone, cefoxitin, gentamicin, neomycin, ciprofloxacin and colistin. Ten (42%) of 24 isolates from 2 hatcheries were multi-drug resistant (i.e. resistant to ≥ 3 antimicrobial classes). Six of 21 ampicillin resistant isolates contained bla_TEM gene and 10 of 12 tetracycline resistant isolates contained tetA gene. This study highlights the circulation of multi-drug resistant motile Salmonella in the hatchery environment for the first time in Bangladesh. Further epidemiological and molecular studies are therefore needed to identify the serotypes and source of the bacteria in hatcheries.

Molecular Epidemiology of Salmonellosis in Florida, USA, 2017-2018

The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose “combination approach” comprising “HC5 clustering,” as efficient tool to trigger Salmonella outbreak investigations, and “SNP-based analysis,” for higher resolution phylogeny to confirm an outbreak. We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017–2018. Several clusters of closely related isolates (0–4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks.

Molecular characterization and antimicrobial resistance profiles of Salmonella Heidelberg isolates from poultry

In the last 10 years, Salmonella Heidelberg has been extensively isolated from poultry in several countries. In this context, molecular characterization is essential to understand whether the strains have entered the farms from a single or several sources. Thus, the aim of this study was to determine the genetic relationship and antimicrobial susceptibility of S. Heidelberg strains isolated between 2011 and 2012 from broiler farms belonging to three integrated poultry companies located in Argentina. The genetic relatedness of the S. Heidelberg isolates was determined by pulsed-field gel electrophoresis (PFGE), and resistance to 21 antimicrobials was determined by the disc diffusion method. The isolates were assigned to four PFGE patterns. Most of the strains showed 100% similarity and belonged to the same integrated poultry company. This PFGE pattern was also prevalent in S. Heidelberg strains isolated from humans in several provinces of Argentina, which suggests an epidemiological association between human and poultry strains. All the isolates were classified as multidrug-resistant (MDR), and no clear relationship was observed between PFGE and resistance patterns. S. Heidelberg strains may circulate among farms from the same integrated company due to common sources of contamination. To guarantee the safety of the poultry product for the consumers, holistic approaches including surveillance of Salmonella throughout the production chain together with control measures are crucial.

Salmonella Contamination of Broiler Chicken Carcasses at Critical Steps of the Slaughter Process and in the Environment of Two Slaughter Plants: Prevalence, Genetic Profiles, and Association with the Final Carcass Status

ABSTRACT

Salmonella is a foodborne pathogen commonly associated with poultry products. The aims of this work were to (i) estimate the impact of critical steps of the slaughter process on Salmonella detection from broiler chicken carcasses in two commercial poultry slaughter plants in Quebec, Canada; (ii) investigate the presence of Salmonella in the slaughter plant environment; (iii) describe, using a high-resolution melting (HRM) approach, the HRM Salmonella profiles and serotypes present on carcasses and in the slaughter plant environment; and (iv) evaluate whether the HRM flock status after chilling could be predicted by the flock status at previous steps of the slaughter process, the status of previous flocks, or the status of the processing environment, for the same HRM profile. Eight visits were conducted in each slaughter plant over a 6-month period. In total, 379 carcass rinsates from 79 flocks were collected at five critical steps of the slaughter process. Environmental samples were also collected from seven critical sites in each slaughter plant. The bleeding step was the most contaminated, with >92% positive carcasses. A decrease of the contamination along the slaughtering process was noted, with carcasses sampled after dry-air chilling showing ≤2.5% Salmonella prevalence. The most frequently isolated serotypes were Salmonella Heidelberg, Kentucky, and Schwarzengrund. The detection of the Salmonella Heidelberg 1-1-1 HRM profile on carcasses after chilling was significantly associated with its detection at previous steps of the slaughter process and in previously slaughtered flocks from other farms during a same sampling day. Results highlight the importance of the chilling step in the control of Salmonella on broiler chicken carcasses and the need to further describe and compare the competitive advantage of Salmonella serotypes to survive processing. The current study also illustrates the usefulness of HRM typing in investigating Salmonella contamination along the slaughter process.

HIGHLIGHTS

Field investigations of multidrug-resistant Salmonella Infantis epidemic strain incursions into broiler flocks in England and Wales

Salmonella Infantis is a major public health concern and has become established in the broiler sector in some European countries, as well as globally, and is frequently multidrug resistant (MDR). Three broiler farms in England and Wales, which had incursions of MDR S. Infantis between 2013 and 2017, were investigated longitudinally. The company feed mill and two associated hatcheries were intensively sampled. Following each visit, advice on cleaning, disinfection and other control measures for Salmonella was given to help eliminate S. Infantis from the premises. Four samples collected from inside the broiler houses after cleaning and disinfection were Salmonella-positive, indicating cleaning and disinfection within houses was generally effective. However, the exterior of persistently infected houses remained substantially contaminated and feeding systems could not be sampled. Clearance of S. Infantis from affected houses requires additional attention to decontamination of these aspects. Sixty S. Infantis isolates were tested for antimicrobial susceptibility by disk diffusion tests. All isolates were MDR, with resistance to at least nalidixic acid (Na), tetracycline (T), compound sulphonamide (Su), streptomycin (S) and furazolidone. This is a similar resistance pattern to the previously identified MDR (NaSSuT) clone in some European countries. The study shows that to remove S. Infantis from premises effectively, a combined approach to poultry houses and the surrounding farm environment is necessary. A revised cleaning and disinfection programme was developed that was associated with the clearance of MDR S. Infantis from persistently infected and newly infected broiler flocks, and UK livestock remains free of MDR S. Infantis. RESEARCH HIGHLIGHTS Standard cleaning and disinfection protocols did not completely eliminate infection. A revised cleaning and disinfection programme was developed. Disinfecting feeder lines and external areas was key to eliminating S. Infantis. Identified similar antimicrobial resistance pattern to MDR epidemic S. Infantis.

Salmonella Bacteriophage Diversity According to Most Prevalent Salmonella Serovars in Layer and Broiler Poultry Farms from Eastern Spain

The exploration of novel nonantibiotic interventions in the field, such as the use of bacteriophages, is necessary to avoid the presence of Salmonella. Bacteriophages are a group of viruses widely distributed in nature, strictly associated with the prokaryotic cell. Researchers have demonstrated the success of phage therapy in reducing Salmonella counts in poultry products. However, the impact that phage concentration in the environment may have against certain Salmonella serovars is not well understood. Therefore, the aim of this study was to assess Salmonella phage prevalence in commercial poultry farms in terms of the production type: layers or broilers. The most prevalent Salmonella serovars isolated in poultry production were used for phage isolation. Salmonella specific phages were isolated from 141 layer and broiler farms located in the Valencia region during 2019. Analysis of the samples revealed that 100% presented Salmonella phages, the most prevalent being against serovar S. Enteritidis (93%), followed by S. Virchow (59%), S. Typhimurium (55%), S. Infantis (52%) and S. Ohio (51%). These results indicate that poultry farms could represent an important source of Salmonella phages. Nevertheless, further studies are needed to assess the epidemiology of phages against other serovars present in other countries and their diversity from the point of view of molecular studies.

Genetic diversity of clinical Salmonella enterica serovar Typhimurium in a university hospital of south Tunisia, 2000-2013

Typhimurium is one of the main Salmonella serovar responsible for non-typhoidal gastro-enteritis in Tunisia. Here, we aimed to assess the genetic diversity of 88 clinical Salmonella Typhimurium strains recovered during 14 years from 2000 to 2013. Phage typing, CRISPR polymorphisms (CRISPOL), pulsed-field gel electrophoresis (PFGE), multi-locus variable-number tandem repeat analysis (MLVA) and Whole genome sequencing (WGS) were used to study the relatedness and spatio-temporal evolution of Salmonella Typhimurium populations (Typhimurium (n = 81), monophasic (n = 3) and nonmotile (n = 4) variants). Seven-locus MLST from whole genome assemblies showed that all isolates, except one, belonged to ST19. The isolates were divided into 10 definitive phage (DT) types, dominated by DT104-L (39.8%), DT41 (14.8%), DT116 (11.4%) and DT120 (5.7%). Fifty-seven MLVA patterns (DI, 0.978) were obtained compared to 11 different CRISPOL types and 15 PFGE types (DI,0.845). For cgMLST analysis, 20 profiles were found. A total of 3056 SNPs were identified from the whole genome of the 88 Salmonella Typhimurium isolates. These SNPs resolved these isolates into 86 SNP haplotypes. The phylogeny result allocated most Salmonella Typhimurium isolates into four distinct clades and seven subclades. Genetic diversity between the four clades ranged in the order of 249 to 720 nucleotide changes. The prevalent phage type DT104L formed a major clade on the phylogenetic tree. Pairwise SNP differences between the strains of this clade ranged between 0 and 59. SNP-based WGS typing seems to be the most valuable molecular markers for studying the evolutionary relationships of homogeneous serovar Typhimurium isolates.

Spatial Distribution of Salmonella enterica in Poultry Shed Environments Observed by Intensive Longitudinal Environmental Sampling

Detection of salmonellae within poultry environments is an important component of many food safety programs, but sampling approaches vary greatly and may not enable the detection of salmonellae when bacteria are present at a low prevalence or concentration. Intensive longitudinal sampling within caged sheds enabled us to undertake a longitudinal analysis of the spatial distribution of salmonellae in caged shed environments. Both the number of samples collected and location of sample collection within a poultry shed were important to ensure the best chance of detecting Salmonella spp. Differences in the within-shed spatial distribution of Salmonella enterica subspecies enterica serovar Typhimurium [χ2(27, 1,538) = 54.4; P < 0.001] and Salmonella enterica subspecies enterica serovar Infantis [χ2(27, 1,538) = 79.8; P < 0.0001] were identified. More than one Salmonella enterica serovar was detected in each shed on the same sampling occasion; 5% of all samples contained more than one serovar. Samples collected on the north side of the shed (odds ratio [OR], 1.77; 95% confidence interval [CI], 1.17-2.68), on the sheltered side of the shed (OR, 1.90; 95% CI, 1.26-2.89), and during winter (OR, 48.41; 95% CI, 23.56-104.19) were more likely to be positive for salmonellae. The within-shed differences observed in the both the sample prevalence and spatial location of the serovar detected indicate that there are important shed microenvironmental factors that influence the survival and/or distribution of salmonellae. These factors should be taken into consideration when environmental surveillance is undertaken for salmonellae in flocks housed in cage sheds.IMPORTANCE Routine epidemiological surveillance for salmonellae in poultry relies initially on environmental sampling. Intensive, spatially homogenous sampling, as conducted within this study, confirmed that the sampling methodology conducted within a poultry environment is a nontrivial part of sampling design. The frequency of sampling is especially important when the prevalence of Salmonella spp. is low. These factors must be taken into consideration in the design of studies for the detection of salmonellae in poultry sheds.

Traditional Salmonella Typhimurium typing tools (phage typing and MLVA) are sufficient to resolve well-defined outbreak events only

Between 1991 and 2014 the per capita notification rate of salmonellosis in Australia increased from 31.9 to 69.7 cases per 100,000 people. Salmonella Typhimurium accounted for nearly half the human cases until the end of 2014. In this study, we used cluster analysis tools to compare S. Typhimurium isolates from a chicken-meat study with those reported to the National Enteric Pathogen Surveillance System (NEPSS) from the coincident human and non-human populations. There was limited phage type diversity within all populations and a lack of specificity of MLVA profiling within phage types. The chicken-meat study isolates were not significantly clustered with the human cases and at least 7 non-human sources, based on typing profiles (PT/MLVA combination), could be implicated as a source of human cases during the same period. In the absence of a strong surveillance system representative of all putative sources, MLVA and phage typing alone or in combination are insufficient to identify the source of human cases.

Salmonella control in poultry flocks and its public health impact

An increase in confirmed human salmonellosis cases in the EU after 2014 triggered investigation of contributory factors and control options in poultry production. Reconsideration of the five current target serovars for breeding hens showed that there is justification for retaining Salmonella Enteritidis, Salmonella Typhimurium (including monophasic variants) and Salmonella Infantis, while Salmonella Virchow and Salmonella Hadar could be replaced by Salmonella Kentucky and either Salmonella Heidelberg, Salmonella Thompson or a variable serovar in national prevalence targets. However, a target that incorporates all serovars is expected to be more effective as the most relevant serovars in breeding flocks vary between Member State (MS) and over time. Achievement of a 1% target for the current target serovars in laying hen flocks is estimated to be reduced by 254,400 CrI95[98,540; 602,700] compared to the situation in 2016. This translates to a reduction of 53.4% CrI95[39.1; 65.7] considering the layer-associated human salmonellosis true cases and 6.2% considering the overall human salmonellosis true cases in the 23 MSs included in attribution modelling. A review of risk factors for Salmonella in laying hens revealed that overall evidence points to a lower occurrence in non-cage compared to cage systems. A conclusion on the effect of outdoor access or impact of the shift from conventional to enriched cages could not be reached. A similar review for broiler chickens concluded that the evidence that outdoor access affects the occurrence of Salmonella is inconclusive. There is conclusive evidence that an increased stocking density, larger farms and stress result in increased occurrence, persistence and spread of Salmonella in laying hen flocks. Based on scientific evidence, an impact of Salmonella control programmes, apart from general hygiene procedures, on the prevalence of Campylobacter in broiler flocks at the holding and on broiler meat at the end of the slaughter process is not expected.