Genetic diversity of Orientia tsutsugamushi strains circulating in Northeast India

Scrub typhus in Northeast India: epidemiology, clinical presentations, and diagnostic approaches

Scrub typhus is one of the most neglected tropical diseases, a leading cause of acute undifferentiated febrile illness in areas of the 'tsutsugamushi triangle', diagnosed frequently in South Asian countries. The bacteria Orientia tsutsugamushi is the causative agent of the disease, which enters the human body through the bite of trombiculid mites (also known as chiggers) of the genus Leptotrombidium deliense. Diagnosis of the disease is challenging, as its early symptoms mimic other febrile illnesses like dengue, influenza and corona viruses. Lack of rapid, reliable and cost-effective diagnostic methods further complicates the identification process. Northeast India, a mountainous region with a predominantly rural tribal population, has witnessed a resurgence of scrub typhus cases in recent years. Various ecological factors, including rodent populations, habitat characteristics and climatic conditions, influence its prevalence. Entomological investigations have confirmed the abundance of vector mites, highlighting the importance of understanding their distribution and the probability of transmission of scrub typhus in the region. Proper diagnosis, awareness campaigns and behavioural interventions are essential for controlling scrub typhus outbreaks and reducing its impact on public health in Northeast India. Further research and community-based studies are necessary to accurately assess the disease burden and implement effective prevention strategies.

Scrub Typhus- An Underestimated Infectious Disease Attributable to Community Acquired Acute Kidney Injury

Acute Kidney Injury (AKI) associated with Scrub typhus is an emerging health problem which is more common in the tropics including India. This study intended to find out the occurrence of Scrub typhus among the Community Acquired Acute Kidney Injury patients in a tertiary care hospital in Assam, North East India. AKI patients with acute febrile illness admitted to Gauhati Medical College and Hospital, Guwahati, Assam were included in the study and demographic characteristics along with clinical features were recorded. The detection of Scrub typhus was done by IgM Enzyme Linked Immunosorbent Assay (ELISA) test (Optical Density > 0.5) and polymerase chain reaction (PCR) analysis. Routine haematological and biochemical tests were performed. Molecular characterization of Orientia tsutsugamushi was done followed by phylogenetic analysis. The Graph Pad Prism software 9 was used for statistical analysis. Out of 221 AKI patients admitted to hospital, 45 patients (20.4%) were confirmed to be Scrub typhus positive and among them, 4 cases were co-infected with leptospirosis. Majority of Scrub typhus positive AKI patients were in Stage I (82.2%) under KDIGO guideline. "Karp" was the predominant circulating serotype. The study showed cases of Scrub typhus associated Acute Kidney Injury was high and mortality was 11.1%. Hence, in this region, further studies need to be done with large number of population and more emphasis need to be given on differential diagnosis.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12088-023-01137-x.

Comparative analysis of diagnostic assays for scrub typhus: Unveiling enhanced approaches for accurate detection

The study comparatively evaluated serological assays, namely, Weil Felix assay, and IgM ELISA with the gold-standard immunofluorescence test (IFAT) for the sensitive and specific serodiagnosis of scrub typhus infection in occupationally exposed groups of humans. A total of 78 serum samples collected from persons affected with various ailments and belonging to different risk groups were screened in the study. Out of the 78 serum samples tested, a total of 17, 26, and 47 samples turned out to be positive by IFAT, IgM ELISA, and Weil Felix test, respectively. The Weil Felix assay could not serve as an ideal test for screening scrub typhus infection owing to its poor sensitivity and specificity in comparison with IFAT. IgM-ELISA could be an initial screening test to detect scrub typhus suspected patient in limited resource settings.

Human rickettsial infections in India - A review

Rickettsial infections are emerging and/or re-emerging disease that poses a serious global threat to humans and animals. Transmission to humans and animals is through the bite of the ectoparasites including ticks, fleas and chigger mites. Most of the rickettsial diseases are endemic in India, but underdiagnosed. This review is aimed at analyzing the prevalence of rickettsiosis in India and the advancement of rickettsial diagnosis. We have conducted a systematic review on the prevalence of rickettsial disease in India ranging from 1.3% to 46.6% for spotted fever, 2.4% to 77.8% for scrub typhus and 1% to 46.4% for Q fever, based on the literature published with the evidence of isolation, serological, and molecular diagnostics. Search engines Medline/PubMed, Science Direct, ProQuest, and EBSCO were used to retrieve the articles from electronic databases by using appropriate keywords to track the emergence of these rickettsial diseases in India for the period of 1865 to till date. We retrieved 153 published rickettsial articles on hospital-based studies from India that were purely made on the basis of prevalence and the laboratory parameters viz., Weil-Felix test (WF) and Rapid Immunochromatographic tests (RICT) with reference to the gold standard IFA and ELISA. More epidemiological studies are required for epidemic typhus to know the exact prevalence status of this louse-borne rickettsiosis in India. Currently, there is no confirmed specific inflammatory marker for rickettsial diseases. Moreover, serological cross-reactivity is an important aspect, and it should be investigated in endemic areas, there is also a need to include molecular diagnostic techniques for further confirmation in healthcare settings.

CRISPR/Cas12a-Based Detection Platform for Early and Rapid Diagnosis of Scrub Typhus

Orientia tsutsugamushi is responsible for causing scrub typhus (ST) and is the leading cause of acute encephalitis syndrome (AES) in AES patients. A rapid and sensitive method to detect scrub typhus on-site is essential for the timely deployment of control measures. In the current study, we developed a rapid, sensitive, and instrument-free lateral flow assay (LFA) detection method based on CRISPR/Cas12a technology for diagnosing ST (named LoCIST). The method is completed in three steps: first, harnessing the ability of recombinase polymerase for isothermal amplification of the target gene; second, CRISPR/Cas12a-based recognition of the target; and third, end-point detection by LFA. The detection limit of LoCIST was found to be one gene copy of ST genomic DNA per reaction, and the process was complete within an hour. In 81 clinical samples, the assay showed no cross-reactivity with other rickettsial DNA and was 100% consistent with PCR detection of ST. LoCIST demonstrated 97.6% sensitivity and 100% specificity. Overall, the LoCIST offers a novel alternative for the portable, simple, sensitive, and specific detection of ST, and it may help prevent and control AES outbreaks due to ST. In conclusion, LoCIST does not require specialized equipment and poses a potential for future applications as a point-of-care diagnostic.

Phylogenetic and immunological investigations of complete TSA56 ORF of Orientia tsutsugamushi present in acute encephalitis syndrome cases from eastern Uttar Pradesh, India

Scrub typhus (ST) caused by Orientia tsutsugamushi (OT), has long been known to cause acute encephalitis syndrome (AES) and acute febrile illness (AFI). The immunodominant 56 kDa protein of OT, which is encoded by the 56 kDa gene (1600 bp encoding 516-541 amino acids) is a commonly studied antigen for genotype and serotype assignment. Previous studies from India have utilized partial type specific antigen (TSA) 56 kDa sequences for OT strain characterisation. On the other hand, understanding the antigenic diversity of current OT strains, is critical for developing specific diagnostic tests and vaccines against ST. As a result, the current study analyses antigenic variants using the entire TSA56 ORF of OT from AES cases. Phylogenetic investigation using complete TSA56 ORF sequences revealed Karp and Gilliam were the circulating predominant strains of OT. Furthermore, Immuno-informatical analysis demonstrated that the majority of high-binding affinity CD4 TCEs against the most prevalent Indian human leukocyte antigen alleles were present in the S-VDIII/IV and S-VDIV spacer regions of TSA56 ORF. TSA56 conserved spacer is crucial for OT immunological response investigations. Further, the pathophysiological effects of spacer domains in ST require further investigation. Furthermore, the characterization of the TSA56 spacer region of the OT from different parts of India is critical for developing region-specific ST diagnostic assays and vaccines.

Evaluation of an in-house PCR for diagnosing scrub typhus along with a preliminary study of genotypic characterization of Orientia tsutshugamushi circulating in Chhattisgarh: A prospective clinico-microbiological study

PURPOSE

Scrub typhus, caused by Orientia tsutsugamushi (O. tsutsugamushi) present nonspecific clinical features during manifestation of acute undifferentiated febrile illness (AUFI) to render its early diagnosis difficult. Accordingly, this study was undertaken to assess an in-house groEL PCR versus IgM ELISA for the diagnosis of scrub typhus and to genotypically characterise the randomly selected scrub typhus positive cases.

METHODS

Blood samples, collected from two hundred twenty one (221) AUFI cases were subjected to groEL PCR and IgM ELISA for diagnosis of scrub typhus. Eleven randomly selected PCR positive cases were processed for DNA sequencing to determine the genetic diversity of O. tsutsugamushi in Chhattisgarh.

RESULTS

Scrub typhus prevalence of 35.2% were detected among AUFI cases using both in-house groEL PCR and IgM ELISA. PCR alone showed sensitivity, specificity, positive and negative predictive values of 66.6% (CI: 55.08-76.94), 100% (CI: 90 to 100),100% (CI: 93.15 to 100) and 57.37% (CI: 44.05 to 69.96) while for IgM ELISA, these parameters were 62.8% (CI: 51.13-73.50), 100% (CI: 90 to 100), 100% (CI: 92.75 to 100) and 54.68% (CI: 41.75 to 67.18) respectively. PCR and ELISA could detect scrub typhus in 37.2% and 33.3% cases, when tested alone. groEL PCR detected the O. tsutsugamushi throughout the course of infection. Phylogenetic analysis depicted 5 of 11 positive cases belonged to Kuroki, Japan strain of O. tsutsugamushi, followed by Gilliam and Karp strain in 4 and 2 cases respectively.

CONCLUSION

Scrub typhus should be considered in differential diagnosis of AUFI. groEL PCR may aid on to IgM ELISA test for optimum laboratory diagnosis of scrub typhus by its implementation especially in seronegative cases. Predominance of Kuroki-like strain followed by Gillian and Karp strains of O. tsutsugamushi in Chhattisgarh confirm variable geographical distribution of O. tsutsugamushi and provide the baseline epidemiological data which will eventually be used to help the researchers for developing better diagnostic tests and vaccine covering the predominant genotypes.

Detection of Orientia tsutsugamushi in Novel Trombiculid Mite Species in Northern Tamil Nadu, India: Use of Targeting the Multicopy traD Gene

Detection of Orientia tsutsugamushi DNA in a trombiculid mite chigger species suggests that it might be a potential vector of scrub typhus in an endemic area. Over a period of 20 mo, 85 rats were trapped, 57 had chiggers that were identified by standard morphometric techniques. The chigger pools were assessed by performing PCR assays targeting fragments of the single-copy genes 56 kDa type-specific antigen gene (TSA56) by nested PCR and the 47 kDa (htrA) quantitative real-time PCR (qPCR). The novel traD SYBR green assay that detects a multicopy gene was also performed. In total, 27 chigger pools were positive by traD qPCR, of which only 7 were positive by 47 kDa qPCR and in 3 of these, 56 kDa gene was amplified by nested PCR. Orientia tsutsugamushi-specific DNA was detected in Ascoschoengastia spp., Schoengastiella ligula, Leptotrombidium rajasthanense, Leptotrombidium deliense, and Leptotrombidium jayawickremei chigger pools. Therefore, they could be potential vectors of scrub typhus in Southern India. The three 56 kDa sequences belonged to TA716 genotype and Kato genogroup. Further studies are needed to confirm these chigger species as scrub typhus vectors in Northern Tamil Nadu.

Molecular Detection and Genetic Characterization of Orientia tsutsugamushi from Hospitalized Acute Encephalitis Syndrome Cases During Two Consecutive Outbreaks in Eastern Uttar Pradesh, India

Background: Seasonal outbreaks of acute encephalitis syndrome (AES) have been reported especially in the pediatric population with a high case fatality rate in Eastern Uttar Pradesh, India. Orientia tsutsugamushi (OT) is a causative agent of scrub typhus that has been recently identified as a major cause of AES. However, the specific genotypes of OT responsible for AES cases of this region are not known. Therefore, the present study was undertaken to understand the molecular epidemiology of OT prevailing in the AES endemic Eastern Uttar Pradesh region of India. Methods: The study was conducted on 2529 hospitalized AES cases from August 2016 to December 2017. The presence of antibodies against OT from cerebrospinal fluid (CSF) and serum samples were tested using OT IgM enzyme-linked immunosorbent assay (ELISA), whereas OT DNA was tested from whole blood and CSF specimens targeting the partial gene of 56 kDa using nested PCR. Phylogenetic analysis was conducted with sequences (n = 241) generated in this study. Findings: Among the studied AES cases, 50% were found positive for antibodies against OT, whereas 37% of cases were positive for OT DNA. The genetic analysis study revealed that Gilliam (93.8%) is the prevailing genotype of OT followed by Karp (6.16%) genotype in AES cases. Furthermore, the Gilliam strains of this study showed they were >99% identical to earlier reported Gilliam strains from AES cases. Conclusion: We observed the presence of two main OT genotypes in AES cases, among which the majority of OT genotypes fall under the Gilliam clade. The understanding of predominant genotype will be beneficial for its future implications in vaccine development strategies and the development of rapid diagnostic tests.

Evaluation of the Diagnostic Accuracy of Antibody Assays for Patients with Scrub Typhus

This study was carried out to evaluate the accuracy of various antibody tests for scrub typhus, namely, the indirect immunofluorescence assay (IFA) from the Korea Centers for Disease Control and Prevention (KCDC) and four commercial kits (companies A to D). The test accuracy was based on the diagnosis of scrub typhus, as defined by a positive PCR or culture. In total, serum samples from 97 patients with scrub typhus and 200 non-scrub typhus patients were tested. The respective sensitivity and specificity of each test were as follows. For the KCDC IFA, sensitivity and specificity were 55.7% (95% confidence interval [CI], 45.2 to 65.8%) and 94.8% (95% CI, 90.4 to 97.3%) for IgM and 42.3% (95% CI, 32.3 to 52.7%) and 96.3% (95% CI, 92.6 to 98.5%) for IgG, with diagnostic cutoffs of ≥1:16 for IgM and ≥1:256 for IgG. For kit A, the sensitivity and specificity were 70.1% (95% CI, 59.8 to 78.8%) and 74.6% (95% CI, 67.6 to 80.6%) for total immunoglobulins, with a cutoff of ≥1:40. For kit B, the sensitivity and specificity were 64.3% (95% CI, 51.9 to 75.1%) and 94.9% (95% CI, 81.4 to 99.1%) for IgM and 67.1% (95% CI, 54.8 to 77.6%) and 74.4% (95% CI, 57.6 to 86.4%) for IgG. For kit C, the sensitivity and specificity were 53.6% (95% CI, 43.2 to 63.7%) and 99.5% (95% CI, 96.8 to 100%) for IgM and 36.1% (95% CI, 26.8 to 46.5%) and 100% (95% CI, 97.6 to 100%) for IgG. For kit D, the sensitivity and specificity were 73.2% (95% CI, 63.1 to 81.4%) and 89.5% (95% CI, 84.2 to 93.2%) for total immunoglobulins. These results are all unsatisfactory, highlighting an urgent need for the development of more highly sensitive and specific tests.

International Rickettsia Disease Surveillance: An Example of Cooperative Research to Increase Laboratory Capability and Capacity for Risk Assessment of Rickettsial Outbreaks Worldwide

Cooperative research that addresses infectious disease surveillance and outbreak investigations relies heavily on availability and effective use of appropriate diagnostic tools, including serological and molecular assays, as exemplified by the current COVID-19 pandemic. In this paper, we stress the importance of using these assays to support collaborative epidemiological studies to assess risk of rickettsial disease outbreaks among international partner countries. Workforce development, mentorship, and training are important components in building laboratory capability and capacity to assess risk of and mitigate emerging disease outbreaks. International partnerships that fund cooperative research through mentoring and on-the-job training are successful examples for enhancing infectious disease surveillance. Cooperative research studies between the Naval Medical Research Center's Rickettsial Diseases Research Program (RDRP) and 17 institutes from nine countries among five continents were conducted to address the presence of and the risk for endemic rickettsial diseases. To establish serological and molecular assays in the collaborative institutes, initial training and continued material, and technical support were provided by RDRP. The laboratory methods used in the research studies to detect and identify the rickettsial infections included (1) group-specific IgM and IgG serological assays and (2) molecular assays. Twenty-six cooperative research projects performed between 2008 and 2020 enhanced the capability and capacity of 17 research institutes to estimate risk of rickettsial diseases. These international collaborative studies have led to the recognition and/or confirmation of rickettsial diseases within each of the partner countries. In addition, with the identification of specific pathogen and non-pathogen Rickettsia species, a more accurate risk assessment could be made in surveillance studies using environmental samples. The discoveries from these projects reinforced international cooperation benefiting not only the partner countries but also the scientific community at large through presentations (n = 40) at international scientific meetings and peer-reviewed publications (n = 18). The cooperative research studies conducted in multiple international institutes led to the incorporation of new SOPs and trainings for laboratory procedures; biosafety, biosurety, and biosecurity methods; performance of rickettsia-specific assays; and the identification of known and unknown rickettsial agents through the introduction of new serologic and molecular assays that complemented traditional microbiology methods.

Diagnosis of scrub typhus: recent advancements and challenges

Scrub typhus is a mite-borne, acute febrile illness caused by the bacterium Orientia tsutsugamushi. It is a re-emerging infectious disease of the tsutsugamushi triangle. Scrub typhus is transmitted through bites of contaminated chiggers (larval stage). Diagnosis of scrub typhus is challenging as its symptoms mimic with other acute febrile illnesses. Several methods are effectual for diagnosis of scrub typhus that includes enzyme-linked immunosorbent assay (ELISA), immunofluorescence assay (IFA), immunochromatographic test (ICT), Weil-Felix, polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP). Weil-Felix test was initially used for the diagnosis of scrub typhus in underdeveloped countries but not preferred due to a lack of both specificity and sensitivity. Other immuno-based methods like IFA and ELISA are most outrank for detection of scrub typhus due to their higher sensitivity and specificity, but not vigorous to lay bare the infection at early stages and need the convalescent sampling for verification of positive samples. On another deed, PCR based methods becoming acceptable over era due to its dexterity of early-stage diagnosis with higher specificity and sensitivity but lack its applicability in circumstances of scrub typhus due to the variegated genetic makeup of Orientia tsutsugamushi among its serotypes. The present review focused on various detection methods along with their advantages and disadvantages used in the diagnosis of scrub typhus. A comparison between available methods of diagnosis with challenges in the detection of scrub typhus is also summarized.

Molecular characterization of Orientia tsutsugamushi causing scrub typhus among febrile patients in north-central Bangladesh

Scrub typhus is a mite-borne rickettsial disease caused by Orientia tsutsugamushi, which is endemic in Asia Pacific region. In this study, infection rate and molecular epidemiologic traits of O. tsutsugamushi was investigated in Mymensingh, located in north-central Bangladesh. Among the blood samples from 453 febrile patients who visited Mymensingh medical college hospital in 2018, the 47 kDa protein gene of O. tsutsugamushi was detected in 78 samples (17.2%) by nested PCR. Phylogenetic analysis of the O. tsutsugamushi 56 kDa protein gene (18 samples) revealed a predominance of Karp-related genotype (89%), while the remaining belonged to Gilliam genotype. Samples of the Karp-related genotype mostly clustered with those of China, Taiwan, Thailand and India, etc., in emergent subgroups clades 2 and 4, which were distinct from clade 1, including prototype Karp strains. Among the 18 samples, three variable domains (VD) of 56 kDa type-specific antigen had different types of sequence diversity; VDI contained two or three repeats of eight amino acid units, while VDII and VDIII had amino acid substitution, deletion or insertion. The present study documented a potentially high prevalence of genetically diverse O. tsutsugamushi in north-central Bangladesh.

Evaluation of Th1 and Th2 immune response in clinical and sub-clinical scrub typhus infection

Scrub typhus (ST), caused by a gram negative intracellular bacteria- Orientia tsutsugamushi, is one among the leading causes of febrile illness across Southeast Asia, including India. Clinical presentation can vary from asymptomatic to severely fatal. Th1-cell mediated immunity has been suggested to play an important role against ST infection in animal models. However, human data on protective immunity are limited. The present study was undertaken to identify host immune correlates that could confer protection in individuals that remain clinically asymptomatic/sub-clinical. Serum cytokine profiling and mRNA expression levels of Th1 (TNF-α, IFN-γ, IL-2) and Th2 (IL-10, IL-6, IL-4) cytokines was studied amongst the clinical and sub-clinical infections. It was observed that a Th1/Th2 pattern is not involved in human ST infection irrespective of being a symptomatic or asymptomatic presentation. However, significant difference was observed in IL-10 serum and gene expression levels. This study suggests a possible role of IL-10 in disease phenotypic presentation. Over-production of IL-10 was found to be a significant factor contributing to the severity of the disease whereas a protective immune mechanism might exist with a low level of IL-10 in ST infection.