Molecular characterization and evolutionary analysis of Orientia tsutsugamushi in eastern Indian population

Abstract

Scrub typhus is a bacterial zoonotic acute febrile illness (AFI) caused by the obligate intracellular bacterium Orientia tsutsugamushi , which is an antigenically diverse strain frequently observed in the tropical region of Southeast Asian countries. The recent investigation was conducted to delineate the genotype identification of Orientia tsutsugamushi predominating in the eastern zone of India such as Odisha to decipher its strain type, and evaluate its diversity as well as evolutionary pattern based on the nucleotide analysis of the immune dominant 56 KDa gene. During this study, we have investigated 100 clinical samples (2014–2018), out of which 28 were positive for scrub typhus followed by its molecular characterization and phylogenetic analysis utilizing 56 KDa partial genes. Population genetic parameters showed the presence of 287 polymorphic sites within the analyzed 56 KDa gene. The gene diversity (Hd) and sequence diversity ( π ) was estimated 0.638 and 0.280, respectively. Selection pressure analysis ( θ = dN/dS) having the value 0.222 suggests that the gene lied under purifying selection. The present study suggested a high rate of genetic diversity within the isolates. This research study sheds light on the hereditary and evolutionary relationships of Orientia strains found in the eastern Indian population. Understanding regional genetic variation is critical for vaccine development and sero-diagnostics methods. A significant level of genetic variability was observed during this study. This information has a way to understand more about antigen diversity that leads to develop an effective vaccine candidate for this pathogen.

Seroprevalence and Genotypic Characterization of Orientia tsutsugamushi in Febrile Pediatric Patients Admitted in Tertiary Care Hospital of Chennai, South India

“…7,[23][24][25] A study from eastern region of India reported the occurrence of Kato as the single most prevalent strain. 19 In a study from North India, Gilliam has been identified to be the most common genotype, followed by Karp-like strains. 26 Kato-like strains have been observed to be widespread throughout the country.…”

“…40 The possible reason for increase in ST prevalence in urban area may be due to globalization, climate change, larger influx of population into urban region, and deforestation of adjacent rural region for city expansion led to displacement of vectors as well as rodents from one place to other 41 ; that may widen the endemic area further. 19 Scrub typhus is largely under-diagnosed in India as the clinical symptoms of ST are nonspecific and mostly indistinguishable from other tropical febrile illness like malaria, dengue fever, typhoid fever and leptospirosis. The presence of eschar is an important clue for the initial diagnosis of ST. 42,43 However, their presence varies widely in the endemic region, ranging from 7-97%, 44 and this difference may be influenced by the factors like skin color, physical examination done by the investigator and strain variation.…”

“…Nested PCR was used to amplify a 483bp hypervariable region of the O.tsutsugamushi 56kDa type specific antigen gene using previously published nucleotide primers and conditions with little modification. 18,19 The PCR condition for both the rounds were same as follows: Initial denaturation at 95°C for 5 min, followed by 35 cycles of denaturation at 95°C for 50s, annealing at 55°C for 60s, extension at 72°C for 90s and a final extension at 72°C for 7 min. After the second round, the final PCR amplicon was resolved on 2% agarose gel and visualized using a UV transilluminator.…”

Gene expression and involvement of signaling pathways during host–pathogen interplay in Orientia tsutsugamushi infection

“…Previously, it was endemic to the Asia–pacific region known as the “tsutsugamushi triangle”, but many reports suggest that it is spreading all over the world including Dubai, United Arab Emirates, Chile, Peru, and Africa and cause a severe public health problem throughout the globe (Xu et al 2017 ). Though scrub typhus is becoming a common life-threatening and re-emerging disease that accounts for one million cases every year with a high mortality rate, still, it is neglected and underdiagnosed (Luce-Fedrowet al 2018 ; Swain et al 2022 ).…”

Epidemiological analysis and risk prediction of scrub typhus from 2006 to 2021 in Sichuan, China

“…Generally, chiggers are only active within a certain area of their breeding site. However, alterations in human behavior and social environment lead to migration of vectors and hosts from one location to another, which may spread pathogens to more distant areas and cause disease transmission (9)(10)(11). ST is widespread in the "tsutsugamushi triangle" area ranging from Afghanistan in the west to the east coast of Russia in the north to northern Australia in the south (12).…”