Genetic typing of isolates of Rickettsia typhi

Abstract

Murine typhus, which is caused by Rickettsia typhi, has a wide range of clinical manifestations. It has a low mortality rate but may result in meningoencephalitis and interstitial pneumonia in severe cases. Comparisons of complete genome sequences of R. typhi isolates from North Carolina, USA (Wilmington), Myanmar (B9991PP), and Thailand (TH1527) identified only 26 single nucleotide polymorphism (SNP) and 7 insertion-deletion (INDEL) sites in these highly syntenic genomes. Assays were developed to further define the distribution of these variant sites among 15 additional isolates of R. typhi with different histories from Asia, the USA, and Africa. Mismatch amplification mutation assays (MAMA) were validated for 22 SNP sites, while the 7 INDEL sites were analyzed directly on agarose gels. Six SNP types, 9 INDEL types, 11 total types were identified among these 18 isolates. Replicate DNA samples as well as comparisons of isolates with different passage and source histories gave consistent genetic typing profiles. Comparison of the SNP and INDEL markers to R. typhi’s nearest neighbor Rickettsia prowazekii demonstrated that the majority of the SNPs represent intra-species variation that arose post divergence of these two species while several INDEL sites also exhibited intraspecies variability among the R. prowazekii genomes that have been completely sequenced. The assays for the presence of these SNP and INDEL sites, particularly the latter, comprise a low technology gel method for consistently distinguishing R. typhi and R. prowazekii as well as for differentiating genetic types of R. typhi.

Murine Typhus: A Review of a Reemerging Flea-Borne Rickettsiosis with Potential for Neurologic Manifestations and Sequalae

“…Through genome reduction, rickettsiae have evolved to develop a niche for obligate intracellular life using the host cell to provide necessary elements for survival-they are unable to produce the enzymes necessary for the synthesis of lipids, nucleotides, and the metabolism of carbohydrates [15]. Rickettsia typhi has a small 1.1 Mb genome [16], and isolates originating from distant geographic regions are genetically conserved [17], likely a result of dispersal of Rattus and rat fleas by trade involving sailing ship. The organism contains and expresses genes for several autotransporters (sca1, sca2, sca3, sca4, and sca5) [18].…”

minSNPs: an R package for the derivation of resolution-optimised SNP sets from microbial genomic data

“…Several research groups have recently developed single nucleotide polymorphisms (SNP)-based genotyping approaches, e.g. , to investigate Mycobacterium species ( Kim et al, 2021 ; Napier et al, 2020 ), attribute hosts for Chlamydia psittaci ( Vorimore et al, 2021 ) and Campylobacter coli ( Jehanne et al, 2020 ), distinguish Rickettsia typhi from different continents ( Kato et al, 2022 ), identify Escherichia coli of specific serotype ( Rahman, Lim & Park, 2022 ), and track the spread of drug resistance in Plasmodium falciparum infections ( Jacob et al, 2021 ).…”

MinSNPs: an R package for derivation of resolution-optimised SNP sets from microbial genomic data

“…While whole genome analysis is now widely applied directly to public health, clinical, and research microbiology, targeted genetic analyses may be complementary to whole genome analysis for purposes such as high-volume, low-cost surveillance, analysis of primary specimens, and/or analyses performed outside the laboratory environment. Several research groups have recently developed SNP-based genotyping approaches, e.g., to investigate Mycobacterium species (1, 2), attribute host for Chlamydia psittaci (3) and Campylobacter coli (4) , distinguish Rickettsia typhi from different continents (5), identify Escherichia coli of specific serotype (6), and track the spread of drug resistance in Plasmodium falciparum infections (7).…”