Genotyping of Indian Yersinia pestis strains by MLVA and repetitive DNA sequence based PCRs.

India experienced two plague outbreaks in Gujarat and Maharastra during 1994 and then in the Shimla district of Himachal Pradesh during 2002. Yersinia pestis strains recovered from rodents and pneumonic patients during the 1994 outbreaks, pneumonic patients from the 2002 Shimla outbreak and rodents trapped on the Deccan Plateau during a surveillance activity carried out in 1998 were characterized by MLVA, ERIC-PCR and ERIC-BOX-PCR. MLVA genotyping of Indian Y. pestis strains revealed strains of 2 Orientalis, 1 Mediaevalis and 1 Antiqua genotypes distributed in three distinct branches corresponding to their biovar. The Orientalis genotype strains recovered from the 1994 outbreaks and 1998 surveillance activity clustered in one branch while the Antiqua biovar strains from the Shimla outbreak and the Mediaevalis strain recovered from a rodent trapped on the Deccan Plateau region during surveillance formed the other branches. The Orientalis Y. pestis strains recovered from rodents and patients from the 1994 plague outbreaks exhibited similar MLVA, ERIC-PCR and ERIC-BOX-PCR profiles and these were closely related to the Orientalis strains recovered from the rodents trapped on the Deccan Plateau. These data provide evidence for the possible linkage between the Y. pestis strains resident in the endemic region and those that were associated with the 1994 plague outbreaks. Mediaevalis and Antiqua biovars also were recovered from the environmental reservoir on the Deccan Plateau and from the pneumonic patients of 2002 plague outbreak. Therefore, as in Central Asian and African regions, Antiqua and Mediaevalis biovars seem to be well established in the Indian subcontinent as well. ERIC-PCR DNA fingerprinting delineated genotypes similar to those defined by MLVA. Thus ERIC-PCR appears to have the potential to be used as a molecular marker in the molecular epidemiological investigations of plague.