Redefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics

Abstract

Yersinia pestis, the causative agent of plague, is best known for historical pandemics, but still actively causes disease in many parts of the world. Y. pestis is a recently derived clone of the pathogenic species Yersinia pseudotuberculosis, but is more associated with human infection. Numerous studies have documented genomic changes since the two species differentiated, although all of these studies used a relatively small sample set for defining these differences. In this study, we compared the complete genomic content between a diverse set of Y. pestis and Y. pseudotuberculosis genomes, and identified unique loci that could serve as diagnostic markers or for better understanding the evolution and pathogenesis of each group. Comparative genomics analyses also identified subtle variations in gene content between individual monophyletic clades within these species, based on a core genome single nucleotide polymorphism phylogeny that would have been undetected in a less comprehensive genome dataset. We also screened loci that were identified in other published studies as unique to either species and generally found a non-uniform distribution, suggesting that the assignment of these unique genes to either species should be re-evaluated in the context of current sequencing efforts. Overall, this study provides a high-resolution view into the genomic differences between Y. pestis and Y. pseudotuberculosis, demonstrating fine-scale differentiation and unique gene composition in both species.

Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in Silico Peptide Mass Libraries

“…pestis is known to be highly similar to the enteric pathogen Y. pseudotuberculosis (44,45). In fact, Y. pestis can be considered a clone of Y. pseudotuberculosis which has evolved only recently (45,46).…”

Crohn’s Disease: Is the Cold Chain Hypothesis Still Hot?

“…As an example, such a mechanism has been proposed for a mutation in the haemoglobin gene that confers protection against malaria in heterozygotes but causes sickle cell anaemia in homozygotes 90 . Since Y. pseudotuberculosis is genetically very similar to Y. pestis 34 , we hypothesised that NOD2 mutations may have provided a survival advantage to mutation carriers in the past during plague epidemics 35 . As supposed, the current frequencies of CD-associated NOD2 mutations [ie, in the offspring of plague survivors] are correlated with the intensity of past Y. pestis epidemics in European and Mediterranean countries.…”

Identification of Microorganisms by Liquid Chromatography-Mass Spectrometry (LC-MS1) and in silico Peptide Mass Data

“…On a genomic level Y. pestis is known to be highly similar to the enteric pathogen Y. pseudotuberculosis (Achtman et al, 1999;Demeure et al, 2019). In fact, Y. pestis can be considered a clone of Y. pseudotuberculosis which has evolved only recently (Achtman et al, 1999;Califf et al, 2015). Moreover, the top scored strain of Y. pestis is a member of the subspecies Y. pestis ssp.…”