Prevalence and antimicrobial susceptibility of Salmonella enteritidis and Salmonella typhimurium isolated from hen eggs and quail eggs in Karaj, Iran.

BACKGROUND AND AIM: Different Salmonella serotypes are considered one of the most important food pathogens in the world. Poultry meat and eggs are the primary carriers of Salmonella in human populations. This study aimed to estimate the Salmonella enteritidis and Salmonella typhimurium contamination rates of retail hen and quail eggs in Karaj, Iran. Moreover, the antimicrobial resistance patterns of the strains were evaluated, and the efficiency of the standard culture method and multiplex polymerase chain reaction (m-PCR) were compared. MATERIALS AND METHODS: In this descriptive cross-sectional study over 1 year (Jan-Dec 2022), 150 commercial and 150 backyard hen eggs and 300 commercial quail eggs, without cracks and fractures, were collected randomly from best selling groceries in Karaj city. All samples were examined for Salmonella contamination independently by standard culture and m-PCR approaches. A standard disc diffusion method was employed to assess the antimicrobial susceptibility of the strains against 18 antimicrobial agents. RESULTS: Out of 300 examined eggs, 2 S. enteritidis strains were isolated from the shell of backyard hen eggs. The same serotype was also detected in the contents of one of these two eggs. One S. typhimurium was isolated from the shell of a commercial hen egg. Overall, the Salmonella contamination of the shell and contents was 1% and 0.3%, respectively. Salmonella was not isolated from the eggshells or the contents of the quail eggs. There was complete agreement between the results of m-PCR and the standard culture methods. Among the 18 tested antibiotics, the highest resistance was recorded for colistin (100%), followed by nalidixic acid (75%). CONCLUSION: As most Salmonella spp. are associated with human food poisoning, continuous surveillance is required to effectively reduce the risk posed by contaminated poultry eggs. Furthermore, mandatory monitoring of antimicrobial use on Iranian poultry farms is recommended.

The optimisation of Salmonella surveillance programmes for pullet and layer farms using local farm density as a risk factor.

Human salmonellosis cases are often caused by Salmonella serovars Enteritidis and Typhimurium and associated with the consumption of eggs and egg products. Many countries therefore implemented general surveillance programmes on pullet and layer farms. The identification of risk factors for Salmonella infection may be used to improve the performance of these surveillance programmes. The aims of this study were therefore to determine 1) whether local farm density is a risk factor for the infection of pullet and layer farms by Salmonella Enteritidis and Typhimurium and 2) whether the sampling effort of surveillance programmes can be reduced by accounting for this risk factor, while still providing sufficient control of these serovars. We assessed the importance of local farm density as a risk factor by fitting transmission kernels to Israeli surveillance data during the period from June 2017 to April 2019. The analysis shows that the risk of infection by serovars Enteritidis and Typhimurium significantly increased if infected farms were present within a radius of approximately 4 km and 0.3 km, respectively. We subsequently optimized a surveillance programme that subdivided layer farms into low and high risk groups based on the local farm density with and allowed the sampling frequency to vary between these groups. In this design, the pullet farms were always sampled one week prior to pullet distribution. Our analysis shows that the risk-based surveillance programme is able to keep the between-farm R0 of serovars Enteritidis and Typhimurium below 1 for all pullet and layer farms, while reducing the sampling effort by 32% compared to the currently implemented surveillance programme in Israel. The results of our study therefore indicate that local farm density is an important risk factor for infection of pullet and layer farms by Salmonella Enteritidis and Typhimurium and can be used to improve the performance of surveillance programmes.

Evolution and genomic profile of Salmonella enterica serovar Gallinarum biovar Pullorum isolates from Brazil.

Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is a pathogenic bacterium that causes Pullorum disease (PD). PD is an acute systemic disease that affects young chickens, causing white diarrhea and high mortality. Although many sanitary programs have been carried out to eradicate S. Pullorum, PD outbreaks have been reported in different types of birds (layers, broilers, breeders) worldwide. This study aimed to evaluate the evolution and genetic characteristics of S. Pullorum isolated from PD in Brazil. Phylogenetic analysis of S. Pullorum genomes sequenced in this study and available genomic databases demonstrated that all isolates from Brazil are from sequence type 92 (ST92) and cluster into two lineages (III and IV). ColpVC, IncFIC(FII), and IncFII(S) were plasmid replicons frequently found in the Brazilian lineages. Two resistance genes (aac(6')-Iaa, conferring resistance to aminoglycoside, disinfecting agents, and antiseptics (mdf(A)) and tetracycline (mdf(A)) were detected frequently. Altogether, these results are important to understand the circulation of S. Pullorum and, consequently, to develop strategies to reduce losses due to PD.

Evolución y perfil genómico de aislados de Salmonella enterica serovar Gallinarum biovar Pullorum de Brasil. Salmonella enterica subespecie enterica serovar Gallinarum biovar Pullorum (S. Pullorum) es una bacteria patógena que causa la enfermedad de Pullorum (EP). La EP es una enfermedad sistémica aguda que afecta a los pollos jóvenes causando diarrea blanca y alta mortalidad. Aunque se han llevado a cabo muchos programas sanitarios para erradicar S. Pullorum, se han informado brotes de EP en diferentes tipos de aves (ponedoras, pollos de engorde, reproductoras) en todo el mundo. Este estudio tuvo como objetivo evaluar la evolución y las características genéticas de S. Pullorum aislado de EP en Brasil. El análisis filogenético de los genomas de S. Pullorum secuenciados en este estudio y las bases de datos genómicas disponibles demostraron que todos los aislamientos de Brasil son del tipo de secuencia 92 (ST92) y se agrupan en dos linajes (III y IV). ColpVC, IncFIC (FII) e IncFII(S) fueron replicones de plásmidos frecuentemente encontrados en los linajes brasileños. Dos genes de resistencia (aac(6')-Iaa, que confiere resistencia a aminoglucósidos, desinfectantes y antisépticos (mdf(A)), y tetraciclina (mdf(A)) fueron detectados con frecuencia. En conjunto, estos resultados son importantes para comprender la circulación de S. Pullorum y, en consecuencia, desarrollar estrategias para reducir las pérdidas por EP.

Prevalence and characterization of non-typhoidal Salmonella in egg from grading and packing plants in Korea.

Egg washing guidelines vary across countries; however, since 2020, Korea has required that all eggs produced from farms with more than 10,000 laying hens must be washed through egg grading and packing (GP) plant. This study investigated the prevalence and characterization of non-typhoidal Salmonella in eggs after washing at GP plants. In total, 16,800 eggs were collected from 60 egg GP plants located inside commercial layer farms, and 840 pooled eggshell and egg contents were tested for Salmonella, respectively. Of the 60 GP plants tested, 11 (18.3%) and 12 (20.0%) plants were positive for Salmonella spp. In the eggshells and egg contents, respectively. In particular, High Salmonella prevalence in the eggshells and egg contents occurred most often in farms with laying hens older than 80 weeks (33.3% and 40.0%, respectively). However, among 840 pooled eggshells and egg content samples, only 19 (2.3%) of each sample type were positive only for non-typhoidal Salmonella spp. The most common Salmonella serovar in both eggshells and egg contents was S. Infantis, which was found in five (8.3%) of 60 GP plants for both samples types. The other Salmonella serovars detected in eggshells were S. Bareilly (5.0%), S. Agona (3.3%), S. Enteritidis (1.7%), and S. Montevideo (1.7%), whereas those detected in egg contents were S. Enteritidis (5.0%), S. Agona (3.3%), S. Newport (3.3%), S. Senftenberg (3.3%), and S. Derby (1.7%). Of the 19 virulence genes tested, 14 genes were detected in all Salmonella. Interestingly, the spvB gene was detected only in S. Enteritidis, and the sefC gene was detected only in S. Enteritidis and S. Senftenberg. Moreover, all S. Infantis isolates showed multidrug resistance (MDR) against five or more classes, and the other serovars only showed MDR against three to four classes or no MDR. These results suggest that comprehensive surveillance and advanced management approaches for egg GP plants are required to minimize egg contamination with non-typhoidal Salmonella.

Emergence of Salmonella Infantis carrying the pESI megaplasmid in commercial farms of five major integrated broiler operations in Korea.

Considering Salmonella transmission occurs through several routes in integrated broiler operations, control of nontyphoidal Salmonella in commercial farms is essential. This study aimed to compare the distribution of persistent Salmonella serovars in environments and dead chickens between 5 major integrated broiler operations in Korea. The prevalence of Salmonella-positive farms in dust prior to placement by operations was 0 to 25%, but the prevalence in dust and feces at the time of depletion was increased to 16.7 to 41.7% and 16.7 to 66.7%, respectively. Moreover, the prevalence of farms with Salmonella in chickens that died within 1 week old and at 4 to 5 weeks old ranged from 8.3 to 58.3% and 16.7 to 41.7%, respectively. The prevalence of Salmonella enterica serovar Infantis-positive farms in dust prior to placement and in chickens that died within 1 week old was 5.2 and 3.4%, respectively, but the prevalence in dust and feces at the time of depletion and in chickens that died at 4 to 5 weeks old was significantly increased to 27.6, 41.4, and 20.7%, respectively (P < 0.05). Interestingly, the plasmid of emerging S. Infantis (pESI) was only identified in S. Infantis, and the prevalence of multidrug-resistance was significantly higher in pESI-positive S. Infantis (99.2%) than in pESI-negative S. Infantis (6.7%) (P < 0.05). The distribution of pulsotypes between pESI-positive and pESI-negative S. Infantis were varied, but a majority of S. Infantis were clustered only 2 pulsotypes. Moreover, pESI-positive S. Infantis harbored more virulence factors than pESI-negative S. Infantis. This study is the first report on characteristics of S. Infantis carrying the pESI plasmid in commercial broiler farms in Korea.

Phenotypic and genetic characterization of antimicrobial resistance in Salmonella enterica serovar Choleraesuis isolates from humans and animals in Spain from 2006 to 2021.

OBJECTIVES: While an increase in the levels of MDR in Salmonella enterica sevorar Choleraesuis has been reported in Europe, little is known about the situation in Spain. Therefore, we first aimed to assess the phenotypic resistance profile and to determine the presence of genetic determinants of resistance of S. Choleraesuis isolates collected in animal and human. Our second objective was to identify and characterize clusters of highly related isolates. METHODS: We analysed 50 human and 45 animal isolates retrieved from 2006 to 2021 using the disc diffusion method and performed WGS followed by analyses of genetic determinants and phylogenetic analysis. RESULTS: All isolates were of ST145 and corresponded to the variant Kunzendorf. Swine isolates harboured a significantly higher number of antimicrobial resistance genes than human isolates, and often carried plasmid replicons of the IncHI2/IncHI2A type (42% of all animal isolates). In addition, we identified several MDR S. Choleraesuis strains circulating in humans and swine between 2006 and 2021. The phylogenetic analyses identified four clades associated with specific patterns of resistance genes and plasmid replicons. The clades also included isolates that differed in terms of year and region of isolation as well as host of origin. CONCLUSIONS: This One Health approach highlights that reducing human MDR S. Choleraesuis infections may require the adoption of strategies that not only seek to prevent cases in humans but also to characterize and reduce the infection burden in swine.

Microdiversity of Salmonella Kentucky During Long-Term Colonization of a Dairy Herd.

Salmonella enterica subsp. enterica serovar Kentucky was repeatedly isolated from a commercial dairy herd that was enrolled in a longitudinal study where feces of asymptomatic dairy cattle were sampled intensively over an 8-year period. The genomes of 5 Salmonella Kentucky isolates recovered from the farm 2 years before the onset of the long-term colonization event and 13 isolates collected during the period of endemicity were sequenced. A phylogenetic analysis inferred that the Salmonella Kentucky strains from the farm were distinct from poultry strains collected from the same region, and three subclades (K, A1, and A2) were identified among the farm isolates, each appearing at different times during the study. Based on the phylogenetic analysis, three separate lineages of highly similar Salmonella Kentucky were present in succession on the farm. Genomic heterogeneity between the clades helped identify regions, most notably transcriptional regulators, of the Salmonella Kentucky genome that may be involved in competition among highly similar strains. Notably, a region annotated as a hemolysin expression modulating protein (Hha) was identified in a putative plasmid region of strains that colonized a large portion of cows in the herd, suggesting that it may play a role in asymptomatic persistence within the bovine intestine. A cell culture assay of isolates from the three clades with bovine epithelial cells demonstrated a trend of decreased invasiveness of Salmonella Kentucky isolates over time, suggesting that clade-specific interactions with the animals on the farm may have played a role in the dynamics of strain succession. Results of this analysis further demonstrate an underappreciated level of genomic diversity within strains of the same Salmonella serovar, particularly those isolated during a long-term period of asymptomatic colonization within a single dairy herd.

Bayesian evaluation of meat juice ELISA for detecting Salmonella in slaughtered pigs without specifying a cut-off.

BACKGROUND: Consumption of pork and pork products is a major source of human infection with Salmonella. Salmonella is typically subclinical in pigs, making it difficult to identify infected pigs. Therefore, effective surveillance of Salmonella in pigs critically relies on good knowledge on how well the diagnostic tests used perform. A test that has been used in several countries for Salmonella monitoring is serological testing of meat juice using an ELISA (MJ ELISA) to detect antibodies against Salmonella. This MJ ELISA data could be used to estimate infection prevalence and trends. However, as the MJ ELISA output is a sample-to-positive (S/P) ratio, which is a continuous outcome rather than a binary (positive/negative) result, the interpretation of this data depends upon a chosen cut-off. AIM: To apply Bayesian latent class models (BLCMs) to estimate diagnostic accuracy of the MJ ELISA test values in the absence of a gold standard without needing to apply a cut-off. METHODS AND RESULTS: BLCMs were fitted to data from a UK abattoir survey carried out in 2006 in order to estimate the diagnostic accuracy of MJ ELISA with respect to the prevalence of active Salmonella infection. This survey consisted of a MJ ELISA applied in parallel with the bacteriological testing of caecal contents, carcass swabs and lymph nodes (n = 625). A BLCM was also fitted to the same data but with dichotomisation of the MJ ELISA results, in order to compare with the model using continuous outcomes. Estimates were obtained for sensitivity and specificity of the ELISA over a range of S/P values and for the bacteriological tests and were found to be similar between the models using continuous and dichotomous ELISA outcomes. CONCLUSION: The Bayesian method without specifying a cut-off does allow prevalence to be inferred without specifying a cut-off for the ELISA. The study results will be useful for estimating infection prevalence from serological surveillance data.

Antimicrobial resistance in multistate outbreaks of nontyphoidal Salmonella infections linked to animal contact-United States, 2015-2018.

Animal contact is an established risk factor for nontyphoidal Salmonella infections and outbreaks. During 2015-2018, the U.S. Centers for Disease Control and Prevention (CDC) and other U.S. public health laboratories began implementing whole-genome sequencing (WGS) of Salmonella isolates. WGS was used to supplement the traditional methods of pulsed-field gel electrophoresis for isolate subtyping, outbreak detection, and antimicrobial susceptibility testing (AST) for the detection of resistance. We characterized the epidemiology and antimicrobial resistance (AMR) of multistate salmonellosis outbreaks linked to animal contact during this time period. An isolate was considered resistant if AST yielded a resistant (or intermediate, for ciprofloxacin) interpretation to any antimicrobial tested by the CDC or if WGS showed a resistance determinant in its genome for one of these agents. We identified 31 outbreaks linked to contact with poultry (n = 23), reptiles (n = 6), dairy calves (n = 1), and guinea pigs (n = 1). Of the 26 outbreaks with resistance data available, we identified antimicrobial resistance in at least one isolate from 20 outbreaks (77%). Of 1,309 isolates with resistance information, 247 (19%) were resistant to ≥1 antimicrobial, and 134 (10%) were multidrug-resistant to antimicrobials from ≥3 antimicrobial classes. The use of resistance data predicted from WGS increased the number of isolates with resistance information available fivefold compared with AST, and 28 of 43 total resistance patterns were identified exclusively by WGS; concordance was high (>99%) for resistance determined by AST and WGS. The use of predicted resistance from WGS enhanced the characterization of the resistance profiles of outbreaks linked to animal contact by providing resistance information for more isolates.

A Salmonella Pullorum outbreak with neurological signs in adult layers and outbreak investigation using whole genome sequencing.

RESEARCH HIGHLIGHTS: Cerebral granulomas are associated with nervous signs in Salmonella Pullorum outbreak.Bone marrow is also a recommended tissue for isolation of Salmonella Pullorum.Rapid plate agglutination test detects Pullorum antibodies in a vaccinated flock.Phylogenetic analysis showed clonality of isolates within the outbreak.

Frequency of isolation and phenotypic antimicrobial resistance of fecal Salmonella enterica recovered from dairy cattle in Canada.

Salmonellosis is one of the leading causes of gastrointestinal infections in humans. In Canada, it is estimated that approximately 87,500 cases of salmonellosis occur every year in humans, resulting in 17 deaths. In the United States, it is estimated that 26,500 hospitalizations and 420 deaths occur every year. In dairy cattle, infections caused by nontyphoidal Salmonella enterica can cause mild to severe disease, including enteritis, pneumonia, and septicemia. Our study objectives were to determine the proportion of fecal samples positive for Salmonella in dairy cattle in Canada and determine the resistance pattern of these isolates. We used data collected through the Canadian Dairy Network for Antimicrobial Stewardship and Resistance (CaDNetASR). Pooled fecal samples from preweaning calves, postweaning heifers, lactating cows, and manure storage were cultured for Salmonella, and the isolates were identified using matrix-assisted laser desorption/ionization-time of flight mass spectrometry. Antimicrobial susceptibilities were determined using the minimum inhibitory concentration test, and resistance interpretation was made according to the Clinical and Laboratory Standards Institute. A 2-level, multivariable logistic regression model was built to determine the probability of recovering Salmonella from a sample, accounting for province, year, and sample source. The proportion of farms with at least one positive sample were 12% (17/140), 19% (28/144), and 17% (24/144) for the sampling years 2019, 2020, and 2021, respectively. Out of the 113 Salmonella isolates, 23 different serovars were identified. The occurrence of Salmonella appeared to be clustered by farms and provinces. The most common serovars identified were Infantis (14%) and Typhimurium (14%). Overall, 21% (24/113) of the Salmonella isolates were resistant to at least one antimicrobial. Resistance to tetracycline was commonly observed (17%); however, very limited resistance to category I antimicrobials (categorization according to Health Canada that includes third-generation cephalosporins, fluoroquinolones, polymyxins, and carbapenems) was observed, with one isolate resistant to amoxicillin and clavulanic acid. The proportion of Salmonella isolates resistant to 2 and 3 antimicrobial classes was 3.5% and 8.8%, respectively. Our study provided valuable information on the proportion of fecal samples positive for Salmonella, the serovars identified, and the associated resistance patterns across CaDNetASR herds, at regional and national levels.

Serotype and anti-microbial resistance trends among bovine Salmonella isolates from samples submitted to a veterinary diagnostic laboratory in central New York, 2007-2021.

AIMS: Salmonella enterica is a leading cause of acute enteritis in people, and dairy cattle are an important reservoir of this pathogen. The objective of this study was to analyse serotype and anti-microbial resistance trends of Salmonella isolated from dairy cattle in the United States between 2007 and 2021. METHODS AND RESULTS: We collected data for bovine Salmonella isolates obtained from samples submitted to Cornell University's Animal Health Diagnostic Center (AHDC). We analysed 5114 isolates for serotype trends, and a subset of 2521 isolates tested for anti-microbial susceptibility were analysed for resistance trends. The most frequently identified serotypes were Salmonella Cerro, Dublin, Typhimurium, Montevideo, 4,[5],12:i:-, and Newport. Among these serotypes, a Cochran-Armitage trend test determined there was a significant increase in the proportion of isolates serotyped as Salmonella Dublin (p < 0.0001) and Montevideo (p < 0.0001) over time. There was a significant decrease in the proportion of isolates serotyped as Salmonella Cerro (p < 0.0001), Typhimurium (p < 0.0001), and Newport (p < 0.0001). For the anti-microbial resistance (AMR) analysis, we found an overall increase in the proportion of multi-drug-resistant isolates over time (p = 0.009). There was a significant increase in the proportion of isolates resistant to ampicillin (p = 0.007), florfenicol (p = 0.0002), and ceftiofur (p < 0.0001) and a marginal increase in resistance to enrofloxacin (p = 0.05). There was a significant decrease in the proportion of isolates resistant to spectinomycin (p = 0.0002), trimethoprim/sulphamethoxazole (p = 0.01), sulphadimethoxine (p = 0.003), neomycin (p < 0.0001), and gentamicin (p = 0.0002). CONCLUSIONS: Our results provide evidence of an increase in resistance to key anti-microbial agents, although the observed trends were driven by the sharp increase in the proportion of Salmonella Dublin isolates over time.

Phenotypic and genotypic characterization of antibiotic-resistant Salmonella isolated from humans, aquaculture, and poultry in Sri Lanka: A retrospective study.

BACKGROUND: In Sri Lanka, foodborne diseases caused by nontyphoidal Salmonella are of increasing concern. We therefore aimed to characterize the dominant Salmonella serovars in humans, poultry, and aquaculture through a One Health approach. METHODS: We collected isolates from different sectors, confirmed their identities using PCR, screened their antibiotic resistance profiles, and determined their antibiotic resistance genes based on whole-genome sequencing. RESULTS: Of the 75 Salmonella isolates identified, the majority of serotypes were unidentified. Both Salmonella enterica serovar Enteritidis (S. Enteritidis) and Salmonella enterica serovar Typhimurium (S. Typhimurium) could be isolated from human sources and were also found prevalent in the poultry sector. ST36, ST11 and ST1541 were the dominant serotypes of S. Typhimurium and S. Enteritidis, respectively. Alarmingly, 4% (1/25) of poultry Salmonella isolates were resistant to ciprofloxacin, suggesting an emergence of this phenotype. Moreover, virulence genes were very diverse among S. Enteritidis and S. Typhimurium isolates. CONCLUSIONS: With the diversity of unidentified serotypes found and the detection of emerging resistances, our study highlights the importance of a One Health approach to monitoring antibiotic resistance. For public health initiatives in Sri Lanka to be successful in mitigating salmonellosis, all three sectors - humans, aquaculture, and poultry - must be tackled concomitantly in a coordinated manner under the One Health approach because antibiotic resistance genes, and even specific sequence types, may be able to spread across the aforementioned sectors. We anticipate that our results will inform public health policies in Sri Lanka to tackle foodborne illnesses.

The Importance of Hazard Analysis by Critical Control Point for Effective Pathogen Control in Animal Feed: Assessment of Salmonella Control in Feed Production in Sweden, 1982-2005.

This study is the first to show that Hazard Analysis by Critical Control Point (HACCP)-based monitoring can be an effective tool for ensuring Salmonella-safe feed, by virtually eliminating feedborne Salmonella infection even in broiler production. Data from the control of Salmonella in feed and food animal production during 1982-2005, showed that conventional endpoint testing in feed mills did not ensure a Salmonella-safe feed, and in one feed mill failed to detect Salmonella contamination, resulting in the feed infecting 80 out of 197 (40.6%) recipient broiler flocks. Following implementation in 1991 of a HACCP-based control in feed mills, the annual number of samples tested at specified critical control points during a 15-year period increased from ∼4400 to 10,000, while the proportion of Salmonella-contaminated samples decreased from 2.0% to 0.3%. Thus, introduction of HACCP was followed by a dramatic decrease, from 40 to <5, in the annual number of Salmonella-infected broiler flocks identified by preslaughter monitoring. Incidence has generally remained at that low level, despite production since 1980 increasing from 39 to 112 million chickens per year. Feed mills start using soymeal with an unsafe Salmonella status and possibly with a suboptimal HACCP control, increased their level of Salmonella-contaminated HACCP samples, and their feed subsequently infected 78 swine-producing herds. The results also show that the HACCP concept can be an effective tool to supply feed mills with Salmonella-safe feed ingredients as demonstrated for a soybean crushing plant, which produced Salmonella-safe soymeal over a 19-year period despite frequent (34%) and highly varied (92 different serovars) Salmonella contamination in samples from incoming soybean. Similar results are reported for a plant producing rapeseed meal. It is emphasized that the achievements described through use of the HACCP required interventions of relevant preventive biosecurity measures and corrective actions when the HACCP-based monitoring identified Salmonella contamination.

Accuracy of testing strategies using antibody-ELISA tests on repeated bulk tank milk samples and/or sera of individual animals for predicting herd status for Salmonella dublin in dairy cattle.

There is currently no perfect test for determining herd-level status for Salmonella Dublin in dairy cattle herds. Our objectives were to evaluate the accuracy, predictive ability, and misclassification cost term of different testing scenarios using repeated measurements for establishing the S. Dublin herd status. Diagnostic strategies investigated used repeated bulk tank milk antibody-ELISA tests, repeated rounds of blood antibody-ELISA tests on non-lactating animals or a combination of both approaches. Two populations hypothesized to have different S. Dublin prevalences were included: (i) a convenience sample of 302 herds with unknown history of infection; and (ii) a cohort of 58 herds that previously tested positive to S. Dublin. Bulk milk samples were collected monthly for 6-7 months and serum were obtained from 10 young animals on two occasions, at the beginning and end of bulk milk sampling period. A series of Bayesian latent class models for two populations and comparing two tests were used to compare bulk milk-based to serum-based strategies. Moreover, Monte Carlo simulations were used to compared diagnostic strategies combining both types of samples. For each diagnostic strategy, we estimated the predictive values using two theoretical prevalences (0.05 and 0.25). Misclassification cost term was also estimated for each strategy using these two prevalences and a few relevant false-negative to false-positive cost ratios. When used for screening a population with an expected low prevalence of disease, for instance for screening herds with no clinical signs and no previous S. Dublin history, a diagnostic strategy consisting of two visits at 6 months interval, and with herd considered positive if bulk milk PP% ≥ 35 and/or ≥ 1/10 animals are positive on one or both visits could be used to confidently rule-out S. Dublin infection (median negative predictive value of 0.99; 95% Bayesian credible intervals, 95BCI: 0.98, 1.0). With this approach, however, positive results should later be confirmed with more specific tests to confirm whether S. Dublin is truly present (median positive predictive value of 0.36; 95BCI: 0.22, 0.57). The same diagnostic strategy could also be used confidently to reassess the S. Dublin status in herds with a previous S. Dublin history. When use for such a purpose, the predictive value of a positive result could be greatly improved, from 0.78 (95BCI: 0.65, 0.90) to 0.99 (95BCI: 0.94, 1.0) by requiring ≥ 1 positive result on both visits, rather than at any of the two visits.

The advantage of intergenic regions as genomic features for machine-learning-based host attribution of Salmonella Typhimurium from the USA.

Salmonella enterica is a taxonomically diverse pathogen with over 2600 serovars associated with a wide variety of animal hosts including humans, other mammals, birds and reptiles. Some serovars are host-specific or host-restricted and cause disease in distinct host species, while others, such as serovar S. Typhimurium (STm), are generalists and have the potential to colonize a wide variety of species. However, even within generalist serovars such as STm it is becoming clear that pathovariants exist that differ in tropism and virulence. Identifying the genetic factors underlying host specificity is complex, but the availability of thousands of genome sequences and advances in machine learning have made it possible to build specific host prediction models to aid outbreak control and predict the human pathogenic potential of isolates from animals and other reservoirs. We have advanced this area by building host-association prediction models trained on a wide range of genomic features and compared them with predictions based on nearest-neighbour phylogeny. SNPs, protein variants (PVs), antimicrobial resistance (AMR) profiles and intergenic regions (IGRs) were extracted from 3883 high-quality STm assemblies collected from humans, swine, bovine and poultry in the USA, and used to construct Random Forest (RF) machine learning models. An additional 244 recent STm assemblies from farm animals were used as a test set for further validation. The models based on PVs and IGRs had the best performance in terms of predicting the host of origin of isolates and outperformed nearest-neighbour phylogenetic host prediction as well as models based on SNPs or AMR data. However, the models did not yield reliable predictions when tested with isolates that were phylogenetically distinct from the training set. The IGR and PV models were often able to differentiate human isolates in clusters where the majority of isolates were from a single animal source. Notably, IGRs were the feature with the best performance across multiple models which may be due to IGRs acting as both a representation of their flanking genes, equivalent to PVs, while also capturing genomic regulatory variation, such as altered promoter regions. The IGR and PV models predict that ~45 % of the human infections with STm in the USA originate from bovine, ~40 % from poultry and ~14.5 % from swine, although sequences of isolates from other sources were not used for training. In summary, the research demonstrates a significant gain in accuracy for models with IGRs and PVs as features compared to SNP-based and core genome phylogeny predictions when applied within the existing population structure. This article contains data hosted by Microreact.

Human Salmonellosis Outbreak Linked to Salmonella Typhimurium Epidemic in Wild Songbirds, United States, 2020-2021.

Salmonella infection causes epidemic death in wild songbirds, with potential to spread to humans. In February 2021, public health officials in Oregon and Washington, USA, isolated a strain of Salmonella enterica serovar Typhimurium from humans and a wild songbird. Investigation by public health partners ultimately identified 30 illnesses in 12 states linked to an epidemic of Salmonella Typhimurium in songbirds. We report a multistate outbreak of human salmonellosis associated with songbirds, resulting from direct handling of sick and dead birds or indirect contact with contaminated birdfeeders. Companion animals might have contributed to the spread of Salmonella between songbirds and patients; the outbreak strain was detected in 1 ill dog, and a cat became ill after contact with a wild bird. This outbreak highlights a One Health issue where actions like regular cleaning of birdfeeders might reduce the health risk to wildlife, companion animals, and humans.

[Influence of breed and herd size on the intra-herd prevalence of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) in sheep]. / Einfluss von Rasse und Herdengröße auf die Intraherdenprävalenz von Salmonella enterica subspecies diarizonae Serovar 61: k: 1, 5, (7) bei Schafen.

SUBJECT AND AIM: At present, only little information is available on the within-flock prevalence of Salmonella enterica subspecies diarizonae serovar 61: k: 1, 5, (7) (SASd) in sheep flocks in Germany as well as their possible influencing factors. The aim of the study was to investigate relationships between flock size, breed and within-flock prevalence. MATERIAL AND METHODS: A total of 1610 clinically healthy ewes from 14 sheep flocks of 9 different breeds aged 2 to 12 years were microbiologically tested for SASd by nasal swab and fecal samples. Linear multivariable models were used to analyse the associations between within-flock prevalence and farm factors (flock size, breed) or detection frequencies in fecal or nasal swabs. RESULTS: SASd was detected in all sheep flocks examined, with 75% of adults having at least one positive nasal or fecal result. In comparison to the 11 flocks in which commercial breeds were kept, the 3 flocks of landraces had a lower apparent within-flock prevalence (p=0.01). No association with herd size was evident. With respect to the age of the ewes, there was a negative relationship (p=0.05) with the frequency of detection of SASd in the nasal swab but not in the fecal swab. The health status and fertility performance of the flocks were in line with a normal range for commercial sheep flocks, with lambing losses of 5% to 10% and lambing scores of 130% to 158%. CONCLUSIONS: Despite the high prevalence of SASd infections particularly within commercial breeds, there was no evidence of a relevant risk to sheep health. Compared with commercial breed flocks, a lower spread of SASd within flocks keeping landraces was evident. CLINICAL RELEVANCE: Despite a high prevalence, infections with SASd are very unlikely to lead to clinical symptoms or disease. Regulation and monitoring of SASd in sheep are of low priority for animal health authorities.