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Campylobacter jejuni and Campylobacter coli represent the leading causes of bacterial gastroenteritis in humans, and infections can produce post-infectious irritable bowel syndrome (PI-IBS). Rhesus macaques ( Macaca mulatta ) (RM) are similarly susceptible to acute campylobacteriosis and represent a potential model of PI-IBS. We characterized the Campylobacter species circulating in an RM breeding colony using culture, qPCR, and whole genome sequencing (WGS). We also compared the C. jejuni and C. coli prevalence in RM as detected with qPCR versus culture and identified risk factors for bacteria presence and intestinal disease. Culture of 275 samples yielded C. coli (103) and C. jejuni (8), of which 21.6% were resistant to quinolones and 3.6% were resistant to macrolides. Multidrug-resistant isolates were obtained exclusively from animals exhibiting diarrhea or with histologically confirmed chronic enterocolitis. WGS revealed a non-clonal population of Campylobacter spp. Genotypic predictions of resistance were excellent except for aminoglycosides. All sequenced isolates contained genes for all subunits of cytolethal distending toxin. qPCR detected a prevalence of 45.9% for C. coli and 29.6% for C. jejuni . The quantity of either bacteria was significantly higher ( P < 0.05) in animals with intestinal disease compared to healthy animals, though only young age was significantly associated with the presence of Campylobacter sp. or intestinal disease. Significantly more C. jejuni positive animals were detected with qPCR than with culture. These results provide a comprehensive characterization of Campylobacter spp. circulating in a breeding colony of RM in the United States and suggest that qPCR is superior for the detection of C. jejuni in RM., Importance: Gastrointestinal disease is one of the most common reasons for hospitalization in non-human primate colonies and accounts for over one-third of non-research related euthanasia. In rhesus macaques, this manifests as both acute diarrhea and chronic enterocolitis (CE), a syndrome of chronic diarrhea resulting in poor weight gain or weight loss which is minimally responsive to treatment. Campylobacter spp. are major causes of acute enterocolitis in rhesus macaques and may predispose individuals to the development of CE, similar to post-infectious irritable bowel syndrome in humans. Despite these concerns, there are few studies characterizing Campylobacter in rhesus macaque colonies, in particular utilizing whole genome sequencing and assessing findings with respect to the health status of the host. Our findings provide insight into Campylobacter strains circulating in rhesus macaque colonies, which can improve clinical monitoring, assist in treatment decisions, and provide new avenues of investigation into campylobacteriosis as a catalyst for CE., Competing Interests: The authors declare no conflict of interest.

Salmonella can persist in the feedlot pen environment, acting as a source of transmission among beef cattle. Concurrently, cattle that are colonized with Salmonella can perpetuate contamination of the pen environment through fecal shedding. To study these cyclical dynamics, pen environment and bovine samples were collected for a 7-month longitudinal comparison of Salmonella prevalence, serovar, and antimicrobial resistance profiles. These samples included composite environment, water, and feed from the feedlot pens ( n  = 30) and cattle ( n  = 282) feces and subiliac lymph nodes. Salmonella prevalence across all sample types was 57.7%, with the highest prevalence in the pen environment (76.0%) and feces (70.9%). Salmonella was identified in 42.3% of the subiliac lymph nodes. Based on a multilevel mixed-effects logistic regression model, Salmonella prevalence varied significantly ( P  < 0.05) by collection month for most sample types. Eight Salmonella serovars were identified, and most isolates were pansusceptible, except for a point mutation in the parC gene, associated with fluoroquinolone resistance. There was a proportional difference in serovars Montevideo, Anatum, and Lubbock comparing the environment (37.2, 15.9, and 11.0%, respectively), fecal (27.5, 22.2, and 14.6%, respectively), and lymph node (15.6, 30.2, and 17.7%, respectively) samples. This suggests that the ability of Salmonella to migrate from the pen environment to the cattle host-or vice versa-is serovar specific. The presence of certain serovars also varied by season. Our results provide evidence that Salmonella serovar dynamics differ when comparing environment and host; therefore, developing serovar-specific preharvest environmental Salmonella mitigation strategies should be considered. IMPORTANCE Salmonella contamination of beef products, specifically from the incorporation of bovine lymph nodes into ground beef, remains a food safety concern. Current postharvest Salmonella mitigation techniques do not address Salmonella bacteria that are harbored in the lymph nodes, nor is it well understood how Salmonella invades the lymph nodes. Alternatively, preharvest mitigation techniques that can be applied to the feedlot environment, such as moisture applications, probiotics, or bacteriophage, may reduce Salmonella before dissemination into cattle lymph nodes. However, previous research conducted in cattle feedlots includes study designs that are cross-sectional, are limited to point-in-time sampling, or are limited to sampling of the cattle host, making it difficult to assess the Salmonella interactions between environment and hosts. This longitudinal analysis of the cattle feedlot explores the Salmonella dynamics between the feedlot environment and beef cattle over time to determine the applicability of preharvest environmental treatments.

The use of antibiotics to treat dairy calves may result in multidrug-resistant extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli . This study investigated fluoroquinolone and macrolide resistance genes among ESBL-producing E. coli isolated from dairy calves. Fresh fecal samples from 147 dairy calves across three age groups were enriched to select for ESBL-producing E. coli. Plasmid-mediated fluoroquinolone ( qnrB ), macrolide ( mph (A)), and beta-lactam ( bla CTX-M groups 1 and 9) resistance genes were identified by PCR and gel electrophoresis in ESBL-producing E. coli . Beta-lactamase variants and antibiotic resistance genes were characterized for eight isolates by whole-genome sequencing. Seventy-one (48.3%) samples were positive for ESBL-producing E. coli , with 159 (70.4%) isolates identified as bla CTX-M variant group 1 and 67 (29.6%) isolates as bla CTX-M variant group 9. Resistance gene mph (A) was more commonly associated with bla CTX-M variant group 1, while resistance gene qnrB was more commonly associated with variant group 9. E. coli growth was quantified on antibiotic media for 30 samples: 10 from each age group. Significantly higher quantities of ceftriaxone-resistant E. coli were present in the youngest calves. Results indicate the dominant bla CTX-M groups present in ESBL-producing E. coli may be associated with additional qnrB or mph (A) resistance genes and ESBL-producing E. coli is found in higher abundance in younger calves.