Detection of Zoonotic Pathogens and Characterization of Novel Viruses Carried by Commensal Rattus norvegicus in New York City

Abstract

Norway rats (Rattus norvegicus) are globally distributed and concentrate in urban environments, where they live and feed in closer proximity to human populations than most other mammals. Despite the potential role of rats as reservoirs of zoonotic diseases, the microbial diversity present in urban rat populations remains unexplored. In this study, we used targeted molecular assays to detect known bacterial, viral, and protozoan human pathogens and unbiased high-throughput sequencing to identify novel viruses related to agents of human disease in commensal Norway rats in New York City. We found that these rats are infected with bacterial pathogens known to cause acute or mild gastroenteritis in people, including atypical enteropathogenic Escherichia coli, Clostridium difficile, and Salmonella enterica, as well as infectious agents that have been associated with undifferentiated febrile illnesses, including Bartonella spp., Streptobacillus moniliformis, Leptospira interrogans, and Seoul hantavirus. We also identified a wide range of known and novel viruses from groups that contain important human pathogens, including sapoviruses, cardioviruses, kobuviruses, parechoviruses, rotaviruses, and hepaciviruses. The two novel hepaciviruses discovered in this study replicate in the liver of Norway rats and may have utility in establishing a small animal model of human hepatitis C virus infection. The results of this study demonstrate the diversity of microbes carried by commensal rodent species and highlight the need for improved pathogen surveillance and disease monitoring in urban environments.

High prevalence of Seoul hantavirus in a breeding colony of pet rats

“…1) shows them clustering with the previously published UK SEOV strains; laboratory rat SEOV strain IR461 and wild rat Humber SEOV strain, located within the SEOV Phylogroup A lineage 9 [7,19]. The UK SEOV strains clustered in lineage 9 with the Baxter SEOV strain (95% sequence identity), originating from a wild brown rat trapped in New York City in 2013 [5]. The SEOV/Sweden/RN1466/2013 sequence (Accession KY688131) obtained from the pet rat imported from the UK into Sweden in 2011 [14] clusters with SEOV lineage 7 rather than the lineage 9.…”

Gut microflora may facilitate adaptation to anthropic habitat: A comparative study in Rattus

“…In this study, human pathogens such as Brucella , Chlamydia , Clostridium , Staphylococcus , and Rickettsia were observed in the commensal host gut microflora. Rodents are well known as reservoirs for zoonotic pathogens (Firth et al., 2014), and studies which assess the presence of potential pathogens in commensal species may be designed especially in small towns such as those found in this study area.…”

“…While very few studies have documented the intestinal microflora of wild rats (Firth et al., 2014), none have examined the gut microflora of mammals in the context of commensalism. In this study, we used a comparative approach to characterize and describe the gut microflora of commensal R. rattus and noncommensal R. satarae .…”

Immune protection against reinfection with nonprimate hepacivirus

“…Recently, multiple novel animal hepaciviruses naturally infecting various species have been identified (9,10). Viruses classified within the genus Hepacivirus have been discovered in dogs (11) and subsequently in horses (12), rodents (13)(14)(15), bats (16), Old World primates (17), cattle (18), and recently catsharks (19). These viruses display different homologies to HCV and offer new insights into the origin and evolution of Hepaciviruses.…”