New Genotype of Yersinia pestis Found in Live Rodents in Yunnan Province, China

Abstract

Yunnan Province, China is thought to be the original source of biovar Orientalis of Yersinia pestis, the causative agent of the third plague pandemic that has spread globally since the end of the 19th century. Although encompassing a large area of natural plague foci, Y. pestis strains have rarely been found in live rodents during surveillance in Yunnan, and most isolates are from rodent corpses and their fleas. In 2017, 10 Y. pestis strains were isolated from seven live rodents and three fleas in Heqing County of Yunnan. These strains were supposed to have low virulence to local rodents Eothenomys miletus and Apodemus chevrieri because the rodents were healthy and no dead animals were found in surrounding areas, as had occurred in previous epizootic disease. We performed microscopic and biochemical examinations of the isolates, and compared their whole-genome sequences and transcriptome with those of 10 high virulence Y. pestis strains that were isolated from nine rodents and one parasitic flea in adjacent city (Lijiang). We analyzed the phenotypic, genomic, and transcriptomic characteristics of live rodent isolates. The isolates formed a previously undefined monophyletic branch of Y. pestis that was named 1.IN5. Six SNPs, two indels, and one copy number variation were detected between live rodent isolates and the high virulence neighbors. No obvious functional consequence of these variations was found according to the known annotation information. Among genes which expression differential in the live rodent isolates compared to their high virulent neighbors, we found five iron transfer related ones that were significant up-regulated (| log2 (FC) | > 1, p.adjust < 0.05), indicating these genes may be related to the low-virulence phenotype. The novel genotype of Y. pestis reported here provides further insights into the evolution and spread of plague as well as clues that may help to decipher the virulence mechanism of this notorious pathogen.

Genomic epidemiological analysis of county-scale Yersinia pestis spread pattern over 50 years in a Southwest Chinese prefecture

“…Samples, including lymph fluid from patients, liver and spleen from captured live rodents, gastric contents of fleas on captured rodents, heart, gland, lung, spleen, liver, bone marrow from dead rodents, and soil samples, were cultured on plates [ 23 ]. Y .…”

“…69506). Gel electrophoresis was conducted for quality control prior to next-generation sequencing [ 23 ].…”

“…Samples, including lymph fluid from patients, liver and spleen from captured live rodents, gastric contents of fleas on captured rodents, heart, gland, lung, spleen, liver, bone marrow from dead rodents, and soil samples, were cultured on plates [23]. Y. pestis strains were isolated and identified from these samples in accordance with Appendix B of the Diagnostic criteria of plague, WS279-2008, within the Health of the People's Republic of China industry standards.…”

Genomic diversity of Yersinia pestis from Yunnan Province, China, implies a potential common ancestor as the source of two plague epidemics

“…Although Y. pestis can shape the natural plague foci under suitable ecological conditions, sylvatic plagues in these foci exhibit recurrent cycles of epidemic and silent periods with intervals ranging from several years to decades, rather than a single continuous epidemic 9 , 10 . During the epidemic period, animal plague usually occurs prior to human plague, whereas in the silent period, human plague disappears and animal plague fades out with occasional rodents detected carrying the F1 antibody or antigen around the corresponding foci 11 , 12 . However, there is a lack of knowledge regarding the genomic diversity of Y. pestis during these epidemic-silent intervals.…”