Genomic and phenotypic comparison of two variants of multidrug-resistant Salmonella enterica serovar Heidelberg isolated during the 2015-2017 multi-state outbreak in cattle

Salmonella enterica subspecies enterica serovar Heidelberg (Salmonella Heidelberg) has caused several multistate foodborne outbreaks in the United States, largely associated with the consumption of poultry. However, a 2015-2017 multidrug-resistant (MDR) Salmonella Heidelberg outbreak was linked to contact with dairy beef calves. Traceback investigations revealed calves infected with outbreak strains of Salmonella Heidelberg exhibited symptoms of disease frequently followed by death from septicemia. To investigate virulence characteristics of Salmonella Heidelberg as a pathogen in bovine, two variants with distinct pulse-field gel electrophoresis (PFGE) patterns that differed in morbidity and mortality during the multistate outbreak were genotypically and phenotypically characterized and compared. Strain SX 245 with PFGE pattern JF6X01.0523 was identified as a dominant and highly pathogenic variant causing high morbidity and mortality in affected calves, whereas strain SX 244 with PFGE pattern JF6X01.0590 was classified as a low pathogenic variant causing less morbidity and mortality. Comparison of whole-genome sequences determined that SX 245 lacked ~200 genes present in SX 244, including genes associated with the IncI1 plasmid and phages; SX 244 lacked eight genes present in SX 245 including a second YdiV Anti-FlhC(2)FlhD(4) factor, a lysin motif domain containing protein, and a pentapeptide repeat protein. RNA-sequencing revealed fimbriae-related, flagella-related, and chemotaxis genes had increased expression in SX 245 compared to SX 244. Furthermore, SX 245 displayed higher invasion of human and bovine epithelial cells than SX 244. These data suggest that the presence and up-regulation of genes involved in type 1 fimbriae production, flagellar regulation and biogenesis, and chemotaxis may play a role in the increased pathogenicity and host range expansion of the Salmonella Heidelberg isolates involved in the bovine-related outbreak.

Investigation of brix refractometry for estimating bovine colostrum immunoglobulin G concentration

Many dairy operations uses a Brix refractometer to assess the quality of first-milking colostrum. This study investigated whether a digital Brix refractometer could be used in a model to predict colostrum IgG concentration and whether more than one %Brix threshold could be used for different colostrum IgG concentrations. Colostrum from 182 animals was tested using a digital Brix refractometer and by single radial immunodiffusion. Statistical analysis, using simple linear regression to relate %Brix results with corresponding colostral IgG concentration, and receiver operating characteristic (ROC) analysis were used to identify %Brix cutoffs that had no false positive results. Colostral IgG concentrations from digital Brix refractometry had a R2 value of 0.818 and a S-value of 21.7 g/L. The large S-value shows that a digital Brix refractometer should not be used in a model to predict colostrum IgG concentration. However, %Brix scores of 19.0, 22.0, 25.0 and 30.0 percent can be used to estimate minimum colostral IgG concentrations of 25, 50, 75 and 100 g/L. These four cutoffs can be used to strategically feed smaller volumes of colostrum to newborn calves. Smaller volumes may reduce unwanted side effects and shorten the time interval in which calves refuse to nurse, while still delivering an adequate mass of IgG to have successful transfer of passive immunity.

Survival of bovine-associated serotypes of Salmonella enterica in bedding sand

Cattle persistently infected with bovine-adapted serotypes of Salmonella enterica are an important animal health and food safety issue. One possible mechanism by which infection is sustained in a dairy herd is by survival of Salmonella in sand used as bedding material. In this study we assessed the survival of 10⁷ to 10⁸ cfu bovine-associated serotypes of Salmonella enterica (sv. Cerro, Dublin, and Heidelberg) in sterile sand, recycled bedding sand, and gray water collected from a Wisconsin dairy farm. All 3 serotypes persisted at relatively high numbers (>10⁶ cfu/g) for at least 28 d in sterile sand, with Salmonella sv. Dublin decreasing less than 1 log₁₀ over 70 d. To our surprise, when low numbers of Salmonella sv. Dublin (10³ cfu) were inoculated into sterile sand, the organism multiplied within 3 d to approximately 10⁶ cfu/g sand and persisted at that level for 28 d. When we inoculated Salmonella sv. Dublin into recycled bedding sand or sand taken directly from cow pens, we observed a significant decrease in colony-forming units by d 7. In contrast, we observed a significant increase in colony-forming units when Salmonella sv. Dublin was inoculated into gray water from the sand recycling system. These data demonstrate that Salmonella can persist for extended periods of time in bedding sand, although this is limited to some extent by the native microbiota in recycled bedding sand.

Prevalence and Sources of Salmonella Lymph Node Infection in Special-Fed Veal Calves

ABSTRACT

Peripheral lymph nodes (LNs) have been implicated as potential contaminants of ground beef, yet the source and timing of Salmonella LN infection in cattle is still unclear, limiting targeted intervention. The aim of this study was to leverage the vertical integration of special-fed veal production to identify preharvest environmental exposures, specifically in livestock trailers and harvest facility holding pens where calves spend 30 min to 4 h, that result in Salmonella LN infection. Ten cohorts of 80 to 82 veal calves were followed through the harvest process, and environmental samples were collected in barns, trailers, and holding pens. Mesenteric LNs from 35 calves were collected at harvest, and 25 prefemoral LNs per cohort were pooled. Within the same cohort, for 12 samples for which the serovar of the environmental and calf LN Salmonella isolates matched, the isolates were submitted for whole genome sequencing to determine whether environmental exposure resulted in LN infection. Cohort-level Salmonella mesenteric LN prevalence ranged from 0% (0 of 35 samples) to 80% (28 of 35 samples), and pooled prefemoral LNs were positive for Salmonella in 3 of the 10 cohorts. Salmonella prevalence in samples from barns, livestock trailers, and harvest facility holding pens was 22% (13 of 60 samples), 74% (59 of 80 samples), and 93% (74 of 80 samples), respectively. Some environmental and LN isolates were multidrug resistant. Four instances of Salmonella transmission from trailers and/or holding pens to calf LNs were supported by sequence data. Salmonella serovars Agona, Give, and Muenster were identified in transmission events. One instance of transmission from the livestock trailer, two instances from holding pens, and one instance from either trailer or holding pens were observed. Further research is needed to evaluate the extent of environmental Salmonella transmission in cattle and to determine whether targeted interventions in trailers or holding pens could reduce novel Salmonella LN infection in veal calves before harvest.

HIGHLIGHTS

Outbreak of Multidrug-Resistant Salmonella Heidelberg Infections Linked to Dairy Calf Exposure, United States, 2015-2018

In August 2016, the Wisconsin Department of Health Services notified the U.S. Centers for Disease Control and Prevention of multidrug-resistant (MDR) Salmonella enterica serovar Heidelberg infections in people who reported contact with dairy calves. Federal and state partners investigated this to identify the source and scope of the outbreak and to prevent further illnesses. Cases were defined as human Salmonella Heidelberg infection caused by a strain that had one of seven pulsed-field gel electrophoresis (PFGE) patterns or was related by whole genome sequencing (WGS), with illness onset from January 1, 2015, through July 2, 2018. Patient exposure and calf purchase information was collected and analyzed; calves were traced back from the point of purchase. Isolates obtained from animal and environmental samples collected on-farm were supplied by veterinary diagnostic laboratories and compared with patient isolates using PFGE and WGS. Antimicrobial susceptibility testing by standardized broth microdilution was performed. Sixty-eight patients from 17 states were identified. Forty (63%) of 64 patients noted cattle contact before illness. Thirteen (33%) of 40 patients with exposure to calves reported that calves were sick or had died. Seven individuals purchased calves from a single Wisconsin livestock market. One hundred forty cattle from 14 states were infected with the outbreak strain. WGS indicated that human, cattle, and environmental isolates from the livestock market were genetically closely related. Most isolates (88%) had resistance or reduced susceptibility to antibiotics of ≥5 antibiotic classes. This resistance profile included first-line antibiotic treatments for patients with severe salmonellosis, including ampicillin, ceftriaxone, and ciprofloxacin. In this outbreak, MDR Salmonella Heidelberg likely spread from sick calves to humans, emphasizing the importance of illness surveillance in animal populations to prevent future spillover of this zoonotic disease.

Apparent prevalence of Mycoplasma wenyonii, Candidatus Mycoplasma haemobos, and bovine leukemia virus in Wisconsin and Michigan dairy cattle herds

Mycoplasma wenyonii (formerly Eperythrozoon wenyonii) is a hemotrophic, epicellular bacterial parasite of cattle that has been associated with clinical disorders, including hemolytic anemia, decreased milk yield, and peripheral edema. Mycoplasma wenyonii and a related organism, Candidatus Mycoplasma haemobos, have been detected in both ill and apparently healthy cattle, but little is known about their prevalence in US dairy cattle. The objective of this prospective, cross-sectional study was to determine herd-level apparent prevalence of M. wenyonii and C. M. haemobos in dairy cattle located in Wisconsin and Michigan compared with seroprevalence of bovine leukemia virus (BLV) in the same herds. In summer 2018, researchers collected blood samples from 30 lactating cows per herd from randomly recruited farms in selected dairy-intensive counties in each state. During the farm visit, a brief survey was used to collect herd management information. Detection of M. wenyonii and C. M. haemobos were based on PCR testing, and ELISA was used to test for antibodies to BLV. Blood samples were collected from lactating cows located in 64 Wisconsin herds (n = 1,930 samples) and 18 Michigan herds (n = 591 samples). Herd-level apparent prevalence was 100% for both M. wenyonii and C. M. haemobos. Herd-level seroprevalence for BLV was 83 and 100% for Wisconsin and Michigan herds, respectively. Estimated within-herd apparent prevalence of M. wenyonii was 71.7% ± 1.0% (ranging from 23.3 to 93.5%) and for C. M. haemobos was 77.3% ± 1.0% (ranging from 16.7 to 100%). Within-herd prevalence of BLV positive samples was 39.8% ± 1.0% and ranged from 0 to 86.7%. About 22% of cows were concurrently positive for all 3 organisms. Parity and stage of lactation were recorded for 2,317 cows. Prevalence of positive cows for parity groups 1, 2, and ≥3 were 72.0, 73.8, and 67.7% for M. wenyonii; 80.9, 76.8, and 74.9% for C. M. haemobos; and 25.3, 39.7, and 55.5% for BLV, respectively. None or only minor differences in apparent prevalence were observed based on stage of lactation. This is the first report of the prevalence of hemotrophic mycoplasmas in Wisconsin and Michigan dairy herds and indicates that infection with these organisms is endemic. The impact of infection on cattle health and productivity remains unknown, and risk factors associated with infection warrant further study.

Genome divergence and increased virulence of outbreak associated Salmonella enterica subspecies enterica serovar Heidelberg

Salmonella enterica serotype Heidelberg is primarily a poultry adapted serotype of Salmonella that can also colonize other hosts and cause human disease. In this study, we compared the genomes of outbreak associated non-outbreak causing Salmonella ser. Heidelberg strains from diverse hosts and geographical regions. Human outbreak associated strains in this study were from a 2015 multistate outbreak of Salmonella ser. Heidelberg involving 15 states in the United States which originated from bull calves. Our clinicopathologic examination revealed that cases involving Salmonella ser. Heidelberg strains were predominantly young, less than weeks-old, dairy calves. Pre-existing or concurrent disease was found in the majority of the calves. Detection of Salmonella ser. Heidelberg correlated with markedly increased death losses clinically comparable to those seen in herds infected with S. Dublin, a known serious pathogen of cattle. Whole genome based single nucleotide polymorphism based analysis revealed that these calf isolates formed a distinct cluster along with outbreak associated human isolates. The defining feature of the outbreak associated strains, when compared to older isolates of S. Heidelberg, is that all isolates in this cluster contained Saf fimbrial genes which are generally absent in S. Heidelberg. The acquisition of several single nucleotide polymorphisms and the gain of Saf fimbrial genes may have contributed to the increased disease severity of these Salmonella ser. Heidelberg strains.

Molecular characterization of noroviruses detected in diarrheic stools of Michigan and Wisconsin dairy calves: circulation of two distinct subgroups

Noroviruses have emerged as the leading worldwide cause of acute non-bacterial gastroenteritis in humans. The presence of noroviruses in diarrheic stool samples from calves on Michigan and Wisconsin dairy farms was investigated by RT-PCR. Norovirus-positive samples were found on all eight farms studied in Michigan and on 2 out of 14 farms in Wisconsin. Phylogenetic analyses of partial polymerase and capsid sequences, derived for a subset of these bovine noroviruses, showed that these strains formed a group which is genetically distinct from the human noroviruses, but more closely related to genogroup I than to genogroup II human noroviruses. Examination of 2 full and 10 additional partial capsid (ORF2) sequences of these bovine strains revealed the presence of two genetic subgroups or clusters of bovine noroviruses circulating on Michigan and Wisconsin farms. One subgroup is "Jena-like", the other "Newbury agent-2-like".