Genetic diversity of Francisella tularensis subsp. holarctica in Kazakhstan

Abstract

Tularemia is a highly dangerous zoonotic infection due to the bacteria Francisella tularensis. Low genetic diversity promoted the use of polymorphic tandem repeats (MLVA) as first-line assay for genetic description. Whole genome sequencing (WGS) is becoming increasingly accessible, opening the perspective of a time when WGS might become the universal genotyping assay. The main goal of this study was to describe F. tularensis strains circulating in Kazakhstan based on WGS data and develop a MLVA assay compatible with in vitro and in silico analysis. In vitro MLVA genotyping and WGS were performed for the vaccine strain and for 38 strains isolated in Kazakhstan from natural water bodies, ticks, rodents, carnivores, and from one migratory bird, an Isabellina wheatear captured in a rodent burrow. The two genotyping approaches were congruent and allowed to attribute all strains to two F. tularensis holarctica lineages, B.4 and B.12. The seven tandem repeats polymorphic in the investigated strain collection could be typed in a single multiplex PCR assay. Identical MLVA genotypes were produced by in vitro and in silico analysis, demonstrating full compatibility between the two approaches. The strains from Kazakhstan were compared to all publicly available WGS data of worldwide origin by whole genome SNP (wgSNP) analysis. Genotypes differing at a single SNP position were collected within a time interval of more than fifty years, from locations separated from each other by more than one thousand kilometers, supporting a role for migratory birds in the worldwide spread of the bacteria.

The First Finding of <em>Francisella Tularensis</em> Subsp. <em>Mediasiatica</em> in Krasnoyarsk Territory, Siberia and an Update of the Subspecies Genetic Diversity

“…The WGS data produced in the course of this work confirms the low level of genetic diversity within subspecies mediasiatica of strains collected across a wide geographic area. This is in sharp contrast with the diversity observed for instance in subspecies holarctica over similar geographic distances [6].…”

“…The distance between the Altai focus and the place of isolation of the almost identical K-334 strain exceeds 500 km over very rough terrain. A previous investigation pointed to migratory birds as potential long-distance carriers for the spreading of F. tularensis [6]. Almost all strains of subsp.…”

“…Core whole genome SNP analyses were performed essentially as previously described [6]. Assemblies and sequence reads archives (SRA) were downloaded from EBI ENA.…”

The First Finding of Francisella tularensis subsp. mediasiatica in Krasnoyarsk Territory, Siberia, and an Update of the Subspecies Genetic Diversity

“…The distance between the Altai focus and the place of isolation of the almost identical K-334 strain exceeds 500 km over very rough terrain. A previous investigation pointed to migratory birds as potential long-distance carriers for the spreading of F. tularensis [7]. Almost all strains of subsp.…”

Francisella and tularemia in western Asia, Iran: a systematic review

“…For instance, the outbreak of 2007–2018 and a lesser one in 2014 coincided with irruptions of common voles, Microtus arvalis in Castilla y León [ 39 , 40 ]. In addition, F. tularensis is present in East Kazakhstan by periodic epizootics in rodents or Spain large pneumonic outbreak was associated with direct contact with common voles, Microtus arvalis [ 41 , 42 ]. According to different reports in Iran, the epidemiological situation of the F. tularensis was introduced by the role of different rodents and hares that known as a vector and interepizootic reservoir.…”