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Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents.

ABSTRACT: The effective control of rodent populations on farms is crucial for food safety, as rodents are reservoirs and vectors for several zoonotic pathogens. Clear links have been identified between rodents and farm-level outbreaks of pathogens throughout Europe and Asia; however, comparatively little research has been devoted to studying the rodent-agricultural interface in the USA. Here, we address this knowledge gap by metabarcoding bacterial communities of rodent pests collected from Minnesota and Wisconsin food animal farms. We leveraged the Oxford Nanopore MinION sequencer to provide a rapid real-time survey of putative zoonotic foodborne pathogens, among others. Rodents were live trapped (n = 90) from three dairy and mixed animal farms. DNA extraction was performed on 63 rodent colons along with 2 shrew colons included as outgroups in the study. Full-length 16S amplicon sequencing was performed. Our farm-level rodent-metabarcoding data indicate the presence of multiple foodborne pathogens, including Salmonella spp., Campylobacter spp., Staphylococcus aureus, and Clostridium spp., along with many mastitis pathogens circulating within five rodent species (Microtus pennsylvanicus, Mus musculus, Peromyscus leucopus, Peromyscus maniculatus, and Rattus norvegicus) and a shrew (Blarina brevicauda). Interestingly, we observed a higher abundance of enteric pathogens (e.g., Salmonella) in shrew feces compared to the rodents analyzed in our study. Knowledge gained from our research efforts will directly inform and improve farm-level biosecurity efforts and public health interventions to reduce future outbreaks of foodborne and zoonotic disease.

SUBMITTER: Jahan NA

PROVIDER: S-EPMC8471018 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Background:The 21st century has seen a wide range of diseases resulting from zoonotic infections, of which bacterial infections have led to outbreaks of food-borne diseases. Aim:The study looks at bacterial pathogen carriage by farm rats and their antimicrobial susceptibility, with the view of providing insights for antimicrobial surveillance. Method:Farm rats of Rattus rattus species where randomly collected alive from farms in Al-Ahsa using food baits. They were anaesthetize with urethane within 4?h of collection and were unconscious for the collection of samples. Basic bacteriological culturing methods were used for culturing of bacterial isolates on selective media while the Vitek 2 compact automated system (BioMerieux, Marcy L'Etoile, France) was used for bacteria identification and antimicrobial susceptibility test. Obtained data were analysed using chi-square and paired t-test with significant difference between sensitive and resistance to antimicrobial susceptibility taken at P?<?.05. Results:Isolated Gramme-negative pathogenic bacteria included strains of Escherichia coli, Pseudomonas oryzihabitans, strains of Pseudomonas aeruginosa, and Salmonella. For the Gramme-positive bacteria, 4 strains of Staphylococcus aureus were encountered. Other Gramme-positive bacteria were coagulase-negative Staphylococcal species (CoNS) as well as Staphylococcus lugdunensis. There was a 100% resistance to the penicillins and a high resistance to imipenem (71%) by the Staphylococcal isolates. Resistance was also high against the ?-lactams by the Gramme-positive bacteria isolates. For the Gramme-negative bacteria, there was a higher than 50% resistance by the isolates against the following antibiotics: ampicillin (78%), amoxicillin/clavulanic acid (67%), cefotaxime (77%), ceftazidime (67%), cefepime (78%), norfloxacin (67%), nitrofurantoin (67%), and trimethoprim/sulfamethoxazole (78%). Conclusion:The results showed high antimicrobial resistance that will need monitoring for control of spread from farm rats to humans.

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Nanopore-Based Surveillance of Zoonotic Bacterial Pathogens in Farm-Dwelling Peridomestic Rodents.

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