A comparison between longitudinal shedding patterns of Salmonella Typhimurium and Salmonella Dublin on dairy farms

Semi-Quantitative Biosecurity Assessment Framework Targeting Prevention of the Introduction and Establishment of Salmonella Dublin in Dairy Cattle Herds

An increasing average herd size and complexity in farm structures call for a higher level of biosecurity. It can reduce the risk of introducing and establishing pathogens with multiple-pathway and indirect spread mechanisms, such as Salmonella Dublin, a pathogen with an increasing occurrence in dairy cattle farms across different countries and continents. Therefore, this study aimed to use existing knowledge to develop a framework with a supporting tool allowing for a time-efficient, yet comprehensive, assessment of biosecurity measures that can help prevent the introduction and establishment of S. Dublin in dairy herds. Based on the literature review, a seven-step biosecurity assessment framework was developed and evaluated in collaboration with biosecurity experts. The resulting framework includes a weighted semi-quantitative assessment method with a scoring guide in an electronic supporting tool for 12 biosecurity sections assessed through on-farm observations and farmer interviews. The framework and tool provide a novel approach to comprehensively assess the overall (mainly external) on-farm biosecurity level by a trained biosecurity assessor. They can be used for systematic data collection in epidemiological studies on risk factors for the introduction and establishment of S. Dublin in dairy farms. Preliminary interrater reliability testing indicated moderate reliability between assessors with varying biosecurity skills.

Prevalence and antimicrobial resistance of Salmonella and the enumeration of ESBL E. coli in dairy farms in Hubei Province, China

Dairy cattle and their products have been linked to human outbreaks of Salmonella and Escherichia coli (E. coli). The objective of this study was to estimate the prevalence and antimicrobial resistance of Salmonella and to enumerate Extended-spectrum β-lactamase (ESBL)-producing E. coli in apparently healthy lactating dairy cows in Hubei Province, China. In a cross-sectional study, a total of 291 adult lactating dairy cows from 10 dairy farms were sampled for the detection of Salmonella and ESBL E. coli. Overall, Salmonella was cultured from 15 out of 291 sampled animals (5.2 %; 95 % confidence intervals (CI): 2.9, 8.4), all from two herds with a herd prevalence of 20.0 % (95 % CI: 2.5, 55.6) and the main serotype being S. Dublin. The within-herd prevalence ranged between 0.0 % and 33.3 %. ESBL E. coli was detected by culture in all farms with an animal level prevalence of 59.1 % (95 % CI: 53.2, 64.8) and 116 samples (39.9 %, 95 % CI: 34.2, 45.7) contained ESBL E. coli with a number exceeding 10⁴ CFU/g feces. Sixty percent (9/15) of Salmonella isolates were resistant to ampicillin, however all isolates were sensitive to the other 8 antimicrobials tested. Ninety percent (95 % CI: 84.6, 94.1) of ESBL E. coli contained the resistance gene bla_CTX-M, but no ESBL Salmonella was found. Our findings contribute to the understanding of the prevalence and antimicrobial resistance of Salmonella and the enumeration of ESBL E. coli and will assist in the decision-making for the control of Salmonella in Hubei Province.

Tell me if you prefer bovine or poultry sectors and I'll tell you who you are: Characterization of Salmonella enterica subsp. enterica serovar Mbandaka in France

Introduction

In north-western France, Salmonella enterica susp. enterica serovar Mbandaka (S. Mbandaka) is most frequently isolated from bovine and dairy samples. While this serovar most often results in asymptomatic carriage, for a number of years it has caused episodes of abortions, which have serious economic consequences for the sector. Interestingly, this serovar is also isolated from Gallus gallus in the same geographic zone. Despite its prevalence in bovines in north-western France, S. Mbandaka has not been broadly studied at the genomic level, and its prevalence and host adaptation are still not fully understood.

Methods

In this study, we analyzed the genomic diversity of 304 strains of S. Mbandaka isolated from the bovine and poultry sectors in this area over a period of 5 years. A phylogenetic analysis was carried out and two approaches were followed to identify conserved genes and mutations related to host associations. The first approach targeted the genes compiled in the MEGARESv2, Resfinder, VFDB and SPI databases. Plasmid and phage contents were also investigated. The second approach refers to an in-house algorithm developed for this study that computes sensitivity, specificity, and accuracy of accessory genes and core variants according to predefined genomes groups.

Results and discussion

All the analyzed strains belong to the multi-locus sequence type profile ST413, and the phylogenomic analysis revealed main clustering by host (bovine and poultry), emphasizing the circulation of 12 different major clones, of which seven circulate in poultry and five in the bovine sector in France and a likely food production chain adaptation of these clones. All strains present resistance determinants including heavy metals and biocides that could explain the ability of this serovar to survive and persist in the environment, within herds, and in food processing plants. To explore the wild animal contribution to the spread of this serovar in north-western France, we retrieved S. Mbandaka genomes isolated from wild birds from EnteroBase and included them in the phylogenomic analysis together with our collection. Lastly, screening of accessory genes and major variants allowed us to identify conserved specific mutations characteristic of each major cluster. These mutations could be used to design useful probes for food safety surveillance.

Confounding Role of Salmonella Serotype Dublin Testing Results of Boneless and Ground Beef Purchased for the National School Lunch Program, October 2013 to July 2017

ABSTRACT

The Agricultural Marketing Service procures boneless and ground beef for federal nutrition assistance programs. It tests procured beef for concentrations of standard plate counts (SPCs), coliforms, and Escherichia coli and for the presence of Salmonella and Shiga toxin-producing E. coli. Any lot exceeding predefined critical limits (100,000 CFU g-1 for SPCs, 1,000 CFU g-1 for coliforms, and 500 CFU g-1 for E. coli) or positive for Salmonella or Shiga toxin-producing E. coli is rejected for purchase. Between 1 October 2013 and 31 July 2017, 166,796 boneless beef lots (each approximately 900 kg) and 25,051 ground beef sublots (each approximately 4,500 kg) were produced. Salmonella was detected in 1,955 (1.17%) boneless beef lots and 219 (0.87%) ground beef sublots. Salmonella sample size increased from an individual 25-g sample to a co-enriched 325-g sample on 1 March 2015. Salmonella presence was associated with season (lowest in spring), larger sample size, and increased log SPC in boneless and ground beef. Increased log E. coli was associated with Salmonella presence in boneless beef, but not ground beef. Salmonella Dublin was the most common serotype in boneless beef (743 of 1,407, 52.8%) and ground beef (35 of 171, 20.5%). Salmonella Dublin was generally associated with lower indicator microorganism concentrations compared with other Salmonella serotypes as a group. Relative to other Salmonella, Salmonella Dublin was associated with season (more common in spring) and smaller sample size in boneless and ground beef. Decreased log SPCs and log coliforms were associated with Salmonella Dublin presence in boneless beef, but not in ground beef. Differential associations between Salmonella Dublin and other serotypes with indicator microorganisms were strong enough to cause confounding and suggest that the presence of Salmonella Dublin needs to be accounted for when evaluating indicator performance to assess Salmonella risk in boneless and ground beef.

HIGHLIGHTS

Genomic Investigation of the Emergence of Invasive Multidrug-Resistant Salmonella enterica Serovar Dublin in Humans and Animals in Canada

Salmonella enterica subsp. enterica serovar Dublin is a zoonotic pathogen that often leads to invasive bloodstream infections in humans that are multidrug resistant. Described here are the results of Canadian national surveillance of S Dublin from 2003 to 2015 in humans and bovines, principally collected through the Canadian Integrated Program for Antibiotic Resistance Surveillance (CIPARS). An increase in human infections due to multidrug-resistant (MDR) S Dublin was observed in 2010, many of which were bloodstream infections. Phylogenomic analysis of human and bovine isolates revealed a closely related network that differed by only 0 to 17 single nucleotide variants (SNVs), suggesting some potential transmission between humans and bovines. Phylogenomic comparison of global publicly available sequences of S Dublin showed that Canadian isolates clustered closely with those from the United States. A high correlation between phenotypic and genotypic antimicrobial susceptibility was observed in Canadian isolates. IS26 replication was widespread among U.S. and Canadian isolates and caused the truncation and inactivation of the resistance genes strA and blaTEM-1B A hybrid virulence and MDR plasmid (pN13-01125) isolated from a Canadian S Dublin isolate was searched against NCBI SRA data of bacteria. The pN13-01125 coding sequences were found in 13 Salmonella serovars, but S Dublin appears to be a specific reservoir. In summary, we have observed the rise of invasive MDR S Dublin in humans in Canada and found that they are closely related to bovine isolates and to American isolates in their mobile and chromosomal contents.

Estimating Bacterial Pathogen Levels in New Zealand Bulk Tank Milk

Zoonotic bacteria such as Campylobacter, Listeria, and Shiga toxin-producing Escherichia coli have been found in bulk tank milk in many countries, and the consumption of raw milk has been implicated in outbreaks of disease in New Zealand. Fecal contamination at milking is probably the most common source of pathogenic bacteria in bulk tank milk. Raw milk was collected from 80 New Zealand dairy farms during 2011 and 2012 and tested periodically for Campylobacter, E. coli O157, Listeria monocytogenes, and Salmonella. Milk quality data such as coliform counts, total bacterial counts, and somatic cell counts also were collected. By treating the total bacterial count as a proxy for fecal contamination of milk and utilizing farm and animal level prevalence and shedding rates of each pathogen, a predictive model for the level of pathogenic bacteria in bulk tank raw milk was developed. The model utilizes a mixture distribution to combine the low level of contamination inherent in the milking process with isolated contamination events associated with significantly higher pathogen levels. By simulating the sampling and testing process, the predictive model was validated against the observed prevalence of each pathogen in the survey. The predicted prevalence was similar to the observed prevalence for E. coli O157 and Salmonella, although the predicted prevalence was higher than that observed in samples tested for Campylobacter.

Bovine salmonellosis in northeast of Iran: frequency, genetic fingerprinting and antimicrobial resistance patterns of Salmonella spp

OBJECTIVE

To evaluate serovar and antimicrobial resistance patterns of Salmonella spp isolated from healthy, diseased and necropsied cows and calves in this observational study.

METHODS

Nineteen isolates recovered from feces and tissues of salmonellosis-affected animals of two commercial farms in north-east of Iran. In second part of the study, the two farms were sampled 4 times with an interval of 2 month. The samples included calves' feces, adult cows' feces, feeds, water, milk filters, and milk fed to calves. Five Salmonella were isolated from 332 fecal samples collected from calves and peri-parturient cows. No Salmonella was recovered from water, feed, milk filers and milk fed to calves.

RESULTS

Salmonella Typhimurium was the most frequently isolate among all sero-groups. S. Dublin was only accounted for 8% (two out of 24) of isolates. Isolated Salmonella strains were used for the ERIC PCR DNA fingerprinting assay. Our results grouped Salmonella isolates into 3 clusters, suggesting that specific genotypes were responsible for each sero-group of Salmonella. The results also revealed diversity among Salmonella isolates in cluster III (sero-group B). Eighteen out of 19 Salmonella spp. were resistant to oxytetracycline. Five isolates out of 19 showed more than one drug resistance. Multi-drug resistance was seen only among Salmonella Typhimurium isolates. Enrofloxacin was the most susceptible antibiotic against all isolates in this study.

CONCLUSION

The emergence of multiple antibiotic-resistant strains of Salmonella Typhimurium should be of great concern to the public. No correlation between ERIC fingerprinting and resistance patterns of Salmonella isolates was found, which indicates resistance to antimicrobial agents was not related to specific genetic background.

Amelioration of salmonellosis in pre-weaned dairy calves fed Saccharomyces cerevisiae fermentation products in feed and milk replacer

Salmonellosis is an insidious and potentially epidemic problem in pre-weaned dairy calves. Managing this disease, or any other diarrheal disease, is a financial burden to producers. Calf mortalities and medicinal treatments are overt costs of salmonellosis, while hidden costs include hampered weight gains and persistent intestinal colonization of the pathogen. In this study, we examined the anti-Salmonella effects of Saccharomyces cerevisiae fermentation products (SCFP) incorporated into both the milk replacer and the starter grain. In a blinded study, 2-8 day-old calves were fed SCFP (n=20 calves) or an SCFP-free Control (n=20 calves) for two weeks before and three weeks after experimental challenge with Salmonella enterica serotype Typhimurium. Following the challenge, calves were monitored for clinical signs and parameters associated with salmonellosis. Calves were then euthanized and examined for rumen development and intestinal Salmonella colonization. When compared to calves that received milk replacer and feed lacking SCFP, calves fed SCFP had fewer bouts of diarrhea and fever. Rumens from these calves were more developed, as measured by the length of papillae, which is consistent with the enhanced weight gain observed in this treatment group. Additionally, Salmonella intestinal colonization was reduced in SCFP-fed calves and Salmonella fecal shedding disappeared at an earlier stage in these calves. This study revealed that the combination of two proprietary S. cerevisiae fermentation products provide marked benefit for preventing the negative effects of salmonellosis in pre-weaned dairy calves, while also boosting productivity. The mechanism of action needs to be clarified, but it may be related to the observed decrease in colonization by the pathogen and increase in rumen development.

Salmonella enterica serovar Stanley intrauterine infection in a stillborn calf - case report

The aim of this study was to report the response to a bacterial intrauterine infection in a calf. A stillborn calf, dam’s blood and amniotic fluid were submitted for examination. Necropsy of the calf was performed and IgG1, IgG2, IgM, IL-6 in the calf’s serum, Il-6 in the dam’s serum, and amniotic fluid were estimated. During necropsy, fluid in pleural and peritoneal cavities stained with haemoglobin and diagonal fissures in the aortic arch endothelium were found.Salmonella entericaserovar Stanley was isolated from the spleen, lungs and abomasal fluid.Histopathological examination revealed: inflammatory infiltration and haemorrhages in lungs and small perivascular haemorrhages in the frontal cortex and near the lateral ventricles of the white matter, focal gliosis in the frontal cortex, and neuronal atrophy of the dentate gyrus with diffuse glial cells proliferation in the brain. The concentration of IgG1in the calf’s serum was increased and IL-6 was detected in both the dam’s blood and amniotic fluid. Necropsy, bacterial culture and immunological findings in the stillborn calf confirmed the intrauterine infectionwithSalmonellaStanley as the cause of death. Meanwhile, neonatal diarrhoea (incidence 46%) with high mortality (54%) occurred on the same farm. From diarrhoeic calves,SalmonellaTyphimurium andS.Enteritidis were isolated. Based on available literature this is the first evidence ofSalmonella entericaserovar Stanley isolation from a stillborn calf.