Scrub Typhus as a Cause of Acute Encephalitis Syndrome, Gorakhpur, Uttar Pradesh, India

Evidence on the prevalence of emerging and re-emerging tick- and flea-borne rickettsial agents in acute encephalitis syndrome endemic areas of northeast Uttar Pradesh, India

Outbreaks of acute encephalitis syndrome (AES) with unknown aetiology are reported every year in Gorakhpur district, Uttar Pradesh, India, and Orientia tsutsugamushi, the rickettsial pathogen, responsible for scrub typhus has been attributed as the primary cause of AES problem. However, information on the prevalence of other rickettsial infections is lacking. Hence, this study was carried out to assess any occurrence of tick- and flea-borne rickettsial agents in villages reporting AES cases in this district. In total, 825 peridomestic small mammals were trapped, by setting 9254 Sherman traps in four villages with a trap success rate of 8.9%. The Asian house shrew, Suncus murinus, constituted the predominant animal species (56.2%) and contributed to the maximum number (87.37%) of ectoparasites. In total, 1552 ectoparasites comprising two species of ticks and one species each of flea and louse were retrieved from the trapped rodents/shrews. Rhipicephalus sanguineus, the brown dog tick, was the predominant species retrieved from the trapped rodents/shrews, and the overall infestation rate was 1.75 per animal. In total, 4428 ectoparasites comprising five tick species, three louse species and one flea species were collected from 1798 domestic animals screened. Rhipicephalus microplus was the predominant tick species collected from the domestic animals. The cat flea, Ctenocephalides felis, constituted 1.5% of the total ectoparasites. Of all the ectoparasite samples (5980) from domestic animals and rodents, tested as 1211 pools through real-time PCR assays, 64 pools were positive for 23S rRNA gene of rickettsial agents. The PCR-positive samples were subjected to multi-locus sequence typing (MLST). In BLAST and phylogenetic analysis, the ectoparasites were found to harbour Rickettsia asembonensis (n = 9), Rickettsia conorii (n = 3), Rickettsia massiliae (n = 29) and Candidatus Rickettsia senegalensis (n = 1). A total of 22 pools were detected to have multiple rickettsial agents. The prevalence of fleas and high abundance of tick vectors with natural infections of rickettsial agents indicates the risk of transmission of tick- and flea-borne rickettsial diseases in rural villages of Gorakhpur. Further epidemiological studies are required to confirm the transmission of these agents to humans.

Integration of IgM ELISA and 56 kDa gene PCR in management of pediatric acute encephalitis syndrome associated with scrub typhus

OBJECTIVES

To identify the potential target genes for detection of Orientia tsutsugamushi (OT) in pediatric acute encephalitis syndrome (pAES).

METHODS

DNA was extracted from whole blood of 100 pAES cases having tested positive (n = 41) and negative (n = 59) for scrub typhus (ST) by IgM ELISA. These samples were subjected to standard PCR for 56 kDa, 47 kDa, 16 s rRNA, groEL, traD genes and the newly identified 27 kDa gene.

RESULTS

Among the selected gene targets, 56 kDa demonstrated its superiority for OT detection over the other tested genes. The presence of OT was confirmed via PCR targeting 56 kDa gene in 17 out of the 41 (41.4 %) IgM-positive ST AES cases and 38 out of the 59 (64.4 %) ST IgM negative cases. None of the other gene targets were amplified.

CONCLUSION

Integration of serological diagnosis with molecular diagnostics targeting the 56 kDa gene for routine testing of AES patients would facilitate detection of OT in AES endemic regions.

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.

Molecular detection of spotted fever group of Rickettsiae in acute encephalitis syndrome cases from eastern Uttar Pradesh region of India

The Eastern Uttar Pradesh region of India is known for its endemicity of acute encephalitis syndrome (AES). Decades of research have established that Orientia tsutsugamushi, a causative of scrub typhus, is a substantial contributor (>60%) for the AES cases besides other aetiology, but additional factors in the remaining proportion are still unidentified. Rickettsial infections are challenging to diagnose in clinical settings due to overlapping clinical symptoms, the absence of definitive indicators, a low index of suspicion, and the lack of low-cost, rapid diagnostic tools. Hence, the present study was designed to determine the load of rickettsial infections among AES cases. Furthermore, we aim to find out the prevalent rickettsial species in AES cases as well as in the vector population at this location. The study included the whole blood/cerebrospinal fluid of AES patients and arthropod specimens from rodents. The molecular identification was performed using the 23S-5S intergenic spacer region and ompB gene with genomic DNA obtained from studied specimens. We detected 5.34% (62/1160) of rickettsial infection in AES cases. Among these, phylogenetic analysis confirmed the presence of 54.8% Rickettsia conorii (n = 34) and 16.1% of Rickettsia felis (n = 10), while the rest proportion of the isolates was unidentified at the species level. Furthermore, R. felis was identified in one CSF sample from AES patients and three flea samples from Xenopsylla cheopis. Rickettsia spp. was also confirmed in one Ornithonyssus bacoti mite sample. The results of this investigation concluded the presence of spotted fever group Rickettsia spp. among AES identified cases as well as in the mite and flea vectors that infest rodents.

A Case Series of Scrub Meningoencephalitis from a Tertiary Care Center in North India

Scrub typhus infection is reemerging leading cause of acute febrile illnesses in post-rainy or monsoon season in Southeast Asia. It is caused by Orientia tsutsugamushi and spread by the bite of chiggers, larval forms of trombiculid mites. The clinical picture can range from simple acute febrile illness to multiorgan dysfunction. Neurological manifestations also vary from aseptic meningitis, meningoencephalitis, cerebral infarction, acute disseminated encephalomyelitis, transverse myelitis, and psychiatric manifestations. Here, we present a case series of eight cases of scrub meningoencephalitis diagnosed based on clinical, laboratory, and radiological criteria.

Scrub Typhus in Children: A Prospective Observational Study in a Tertiary Care Hospital in Eastern India

Background Scrub typhus is a reemerging, acute, undifferentiating febrile illness and one of the most neglected tropical diseases, calling for an in-depth investigation into its clinical diversity, complications, and mortality, which drives us to carry out this research work. Methods Over a year, prospective observational research was carried out after gaining parental consent and institutional ethical clearance, 206 children of either gender aged between one month and 12 years who had been hospitalized with a fever for at least five days and subsequently tested positive for Orientia​​​​ tsutsugamushi were included in the study. Basic demographic information, clinical characteristics, laboratory findings, complications, related coinfections, and results were gathered and analyzed. A P-value of 0.05 was set as the statistical benchmark. Results The current study found that boys outnumbered girls. The ratio of boys to girls was 1.22:1, and the average age was 5.18 years. All had a fever (100%), and the other most frequently occurring clinical signs and symptoms were abdominal pain (16.99%), vomiting (22.33%), hepatosplenomegaly (49.51%), facial puffiness (39.32%), edema (27.18%), lymphadenopathy (19.90%), eschar (19.90%), macular-erythematous rash (17.96%), cough (21.84%), conjunctival congestion (25.24%), and headache (13.59%). Anemia (81.55%), leucocytosis (20.39%), leucopenia (6.8%), thrombocytopenia (49.51%), thrombocytosis (2.43%), and elevated serum levels of alanine aminotransferase (ALT, 57.28%) and aspartate aminotransferase (AST, 63.59%) were characteristic laboratory results. The coinfections were dengue, enteric fever, urinary tract infections, and malaria. Children who also had dengue were more likely to develop thrombocytopenia, which was statistically significant (P-value = 0.008). With doxycycline medication, early defervescence of fever occurred earlier than with azithromycin, and it was statistically significant (P-value = 0.000). The complications were hepatitis (63.59%), lower respiratory tract infections (LRTIs, 22.82%), scrub typhus meningoencephalitis (STME, 3.88%), acute kidney injury (AKI, 2.91%), myocarditis (1.46%), and acute disseminated encephalomyelitis (ADEM, 0.49%). Except for one who had ADEM, everyone was sent back home after receiving the best care possible. The average duration of hospital stay was 6.89 days. Conclusions Even in the absence of eschar, scrub typhus should be suspected in any febrile child who experiences clinical signs of meningoencephalitis syndrome, capillary leakage, skin rash, conjunctival congestion, LRTI, AKI, lymphadenopathy, hepatosplenomegaly, thrombocytopenia, and liver dysfunction in the post-monsoon season. Strong clinical suspicion and prompt anti-scrub drug administration go a long way in preventing or decreasing the morbidity and mortality of the same.

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.

Scrub typhus seroprevalence from an eastern state of India: findings from the state-wide serosurvey

BACKGROUND

Scrub typhus is a mite-borne infectious disease caused primarily by the obligate intracellular bacteria Orientia tsutsugamushi, which is transmitted by chigger mites. The objective of this study was to determine the prevalence of scrub typhus among adults in Odisha, an eastern state of India.

METHODS

A descriptive cross-sectional study was conducted to analyse 1840 serum samples from five districts (Khordha, Cuttack, Ganjam, Malkangiri and Sundargarh) of Odisha collected during 2020-2021. Both immunoglobulin G (IgG) and IgM antibodies against scrub typhus were tested using commercial enzyme-linked immunosorbent assay kits. Point estimates of the 95% confidence interval and adjusted odds ratio were calculated.

RESULTS

Of 1840 participants, the prevalence of IgG positivity was 1034 (56.19%) and that of IgM was 523 (28.42%). The majority of participants were in the 18-45 y age group (53.7%). Cuttack had the highest IgG positivity (64.54%) and Malkangiri had the lowest (29.32%). The highest and lowest positivity for IgM were found in Malkangiri (40.84%) and Cuttack (25.30%), respectively.

CONCLUSIONS

With an increasing number of infections detected in the state, scrub typhus is emerging as a public health threat. Increasing awareness among the general public and healthcare professionals through health education campaigns regarding scrub typhus is essential. Early detection of the disease through the establishment of a laboratory surveillance system is required to control the transmission of scrub typhus.

Revisiting scrub typhus: A neglected tropical disease

Scrub typhus is an under diagnosed re-emerging vector borne disease caused by an intracellular gram negative bacteria, Orientia. The disease is commonly prevalent in rural and hilly areas of Tsutsugumashi triangle. The diagnosis of the disease is very challenging due to similarity of its early symptoms with other febrile illnesses, like dengue and COVID 19, as well as non-availability of rapid, reliable and cost-effective methods. Moreover, the diverse clinical presentation in severe cases make it significant health problem. The occupational and behavioral risks responsible for the transmission lead to urgent need of vaccine development against the disease. The complete knowledge about its pathogenesis and the interaction with host's immune cells may help the scientists in developing the appropriate diagnostic methods as well as the vaccines.

Prevalence, clinico-laboratory features, and the functional outcome of children with scrub typhus meningoencephalitis-a cohort study

Scrub typhus is being reported as the most common cause of childhood meningoencephalitis (ME) in India. Hence, we planned to estimate the proportion of scrub typhus infection among children aged 1 month to 12 years with the clinical diagnosis of ME and to evaluate their demographic, clinical and laboratory characteristics. This cohort study was conducted in the Department of Pediatrics of a tertiary care teaching hospital in south India. One hundred and twenty-seven consecutive children aged 1 month to 12 years with the clinical diagnosis of ME were the participants. Their socio-demographic factors, clinical details, laboratory reports and outcomes were analyzed. The etiological agent was identified in 71 (56%) children. Orientia tsutsugamushi (Scrub typhus) was the most common infection (24.4%), of all children with ME. Children aged ≥5 years were frequently affected by scrub typhus ME. Eschar, capillary leak, hepatomegaly and splenomegaly were the predominant clinical features of scrub typhus ME. Thrombocytopenia and deranged liver function tests were common in scrub typhus ME. To conclude, Orientia tsutsugamushi was the most common organism identified in our study. Prompt recognition of some tell-tale clinical signs of scrub typhus (such as eschar, thrombocytopenia and hepatosplenomegaly), and timely initiation of antibiotics would lead to better outcomes as evident from the study.

Genotypic Characterization of Orientia tsutsugamushi Isolated From Acute Encephalitis Syndrome and Acute Febrile Illness Cases in the Gorakhpur Area, Uttar Pradesh, India

Scrub typhus infections caused by Orientiatsutsugamushi (OT), continue to remain underdiagnosed globally, due to the lack of distinctive symptoms. The elusive nature of the Acute Encephalitis Syndrome (AES) outbreak in Gorakhpur, Uttar Pradesh that claimed numerous pediatric lives was the driving force of this study which involved serological diagnosis (IgM-ELISA), isolation of OT in cell culture, confirmation by PCR, and characterization by Sanger sequencing. In total, 12 out of 36 patients were seropositive, of which 4 were positive by PCR. Upon enrichment in cell culture, additional 3 patients (including two seronegative) were detected positive by PCR. In total, three of these 7 patients were found to be infected with two strains of OT. Taken together, this study for the first time reports the occurrence of dual infections in addition to three circulating OT genotypes (Gilliam, Kato, and Karp-like) and highlights the significance of enriching OT in cell culture systems for efficient molecular detection.

Changing spectrum of acute encephalitis syndrome in India and a syndromic approach

Acute encephalitis syndrome (AES) refers to an acute onset of fever and clinical neurological manifestation that includes mental confusion, disorientation, delirium, or coma, which may occur because of infectious or non-infectious causes. Cerebrospinal fluid (CSF) pleocytosis generally favors infectious etiology, and a normal CSF favors an encephalopathy or non-infectious AES. Among the infectious AES, viral, bacterial, rickettsial, fungal, and parasitic causes are the commonest. Geographical and seasonal clustering and other epidemiological characteristics are important in clinical decision making. Clinical markers like eschar, skin rash, myalgia, hepatosplenomegaly, thrombocytopenia, liver and kidney dysfunction, elevated serum CK, fronto-temporal or thalamic involvement on MRI, and anterior horn cell involvement are invaluable clues for the etiological diagnosis. Categorizing the AES cases into neurologic [Herpes simplex encephalitis (HSE), Japanese encephalitis (JE), and West Nile encephalitis (WNE)] and systemic (scrub typhus, malaria, dengue, and Chikungunya) helps in rational utilization of diagnostic and management resources. In neurological AES, cranial CT/MRI revealing frontotemporal lesion is consistent with HSE, and thalamic and basal ganglia lesions are consistent with JE. Cerebrospinal fluid nucleic acid detection test or IgM antibody for JE and HSE are confirmatory. Presence of frontotemporal involvement on MRI indicates acyclovir treatment pending virological confirmation. In systemic AES, CT/MRI, PCR for HSE and JE, and acyclovir therapy may not be useful, rather treatable etiologies such as malaria, scrub typhus, and leptospirosis should be looked for. If smear or antigen for malaria is positive, should receive antimalarial, if negative doxycycline and ceftriaxone should be started pending serological confirmation of scrub typhus, leptospira, or dengue. A syndromic approach of AES based on the prevalent infection in a geographical region may be developed, which may be cost-effective.

Seasonal abundance of Leptotrombidium deliense, the vector of scrub typhus, in areas reporting acute encephalitis syndrome in Gorakhpur district, Uttar Pradesh, India

The rickettsial pathogen Orientia tsutsugamushi, causing scrub typhus, has been implicated as a major cause of acute encephalitis syndrome (AES) in many places in India including Gorakhpur district of Uttar Pradesh. Seasonal abundance of the principal vector mite of the pathogen, Leptotrombidium deliense, its animal hosts, and prevalence of infection on them are important attributes in the assessment of outbreaks of the disease. Hence, these aspects were investigated, seasonally, in rural villages of Gorakhpur district, where peak incidence of AES cases were reported. A total of 903 animals (rodents/shrews) was collected using 6484 Sherman traps in eight study villages (14% overall trap rate). A sum of 5526 trombiculid mites comprising 12 species was collected from 676 live rodents/shrews screened. Suncus murinus, the Asian house shrew was the predominant species (67%). Among trombiculids, the principal vector mite, L. deliense, was predominant (64.7%) and its infestation index (i.e., average number of chiggers per host animal) was 5.3. The L. deliense infestation index was higher during July to November with a peak in October. Out of 401 animal sera samples screened, 68% were positive for antibodies against O. tsutsugamushi. Of 465 blood samples tested by nested PCR, seven were positive for the 56 kDa gene of O. tsutsugamushi. In conventional PCR, 41 out of 265 samples were positive for the 60 kDa groEL gene of O. tsutsugamushi. Among the 5526 mite samples, tested as 352 pools through nested PCR, four pools were positive for 56 kDa gene. Phylogenetic analysis of 56 and 60 kDa genes confirmed circulation of Karp and TA678 (rodents) and TA678 (mite) serotypes of O. tsutsugamushi in Gorakhpur. Peak incidence of AES in Gorakhpur district occurs during the rainy season (July-October), coinciding with the peak abundance of L. deliense. These results indicate involvement of L. deliense as the vector mite transmitting the scrub typhus pathogen O. tsutsugamushi to humans in the rural areas of Gorakhpur district, India.

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.

Emerging infectious encephalitides

PURPOSE OF REVIEW

The COVID-19 pandemic has cast increased attention on emerging infections. Clinicians and public health experts should be aware of emerging infectious causes of encephalitis, mechanisms by which they are transmitted, and clinical manifestations of disease.

RECENT FINDINGS

A number of arthropod-borne viral infections -- transmitted chiefly by mosquitoes and ticks -- have emerged in recent years to cause outbreaks of encephalitis. Examples include Powassan virus in North America, Chikungunya virus in Central and South America, and tick-borne encephalitis virus in Europe. Many of these viruses exhibit complex life cycles and can infect multiple host animals in addition to humans. Factors thought to influence emergence of these diseases, including changes in climate and land use, are also believed to underlie the emergence of the rickettsial bacterium Orientia tsutsugamushi, now recognized as a major causative agent of acute encephalitis syndrome in South Asia. In addition, the COVID-19 pandemic has highlighted the role of bats as carriers of viruses. Recent studies have begun to uncover mechanisms by which the immune systems of bats are poised to allow for viral tolerance. Several bat-borne infections, including Nipah virus and Ebola virus, have resulted in recent outbreaks of encephalitis.

SUMMARY

Infectious causes of encephalitis continue to emerge worldwide, in part because of climate change and human impacts on the environment. Expansion of surveillance measures will be critical in rapid diagnosis and limiting of outbreaks in the future.

Investigations of seasonal outbreaks of acute encephalitis syndrome due to Orientia tsutsugamushi in Gorakhpur region, India: A One Health case study

Gorakhpur division consisting of Gorakhpur and neighboring districts Deoria, Kushinagar and Maharajganj in Uttar Pradesh, India, have been witnessing seasonal outbreaks of acute encephalitis syndrome (AES) among children for the last three decades. Investigations conducted during 2005 identified Japanese encephalitis (JE) virus as an aetiology of AES. With the introduction of JE vaccination and other control strategies, the incidence of JE in the region declined, however, outbreaks of acute febrile illness with neurological manifestations continued to occur. Subsequent investigations identified Orientia tsutsugamushi, as the major aetiology of AES outbreaks in the region. This review details clinical, epidemiological, animal and entomological investigations conducted for AES due to O. tsutsugamushi during 2015 and 2017 in Gorakhpur region. Surveillance of acute febrile illness among children attending peripheral health facilities identified scrub typhus as an important aetiology of febrile illness during monsoon and post-monsoon months. Population-based serosurveys indicated high endemicity of scrub typhus. Entomological studies demonstrated natural infection of O. tsutsugamushi in small animal hosts and vector mites. Children acquired this infection through recent exposure to outdoor environment, while playing, or visiting fields or defecating in open fields. A few of the children with scrub typhus progress to develop CNS manifestations. Hence, early administration of appropriate antibiotics is crucial in preventing progression of AFI due to scrub typhus to AES. The investigations conducted by the multi-disciplinary team helped understand the transmission dynamics of scrub typhus in Gorakhpur division and recommend strategies for its control.

An outbreak investigation of scrub typhus in Nepal: confirmation of local transmission

Background

Scrub typhus is a largely ignored tropical disease and a leading cause of undifferentiated febrile illness in the areas of tsutsugamushi triangle caused by Orientia tsutsugamushi. It is frequently diagnosed in South Asian countries, although clear epidemiological information is not available from Nepal. After the 2015 earthquake in Nepal, a sudden upsurge in scrub typhus cases was reported. The objective of this study was to investigate epidemiology of scrub typhus and its causative agents in humans, animals, and chigger mites to understand the ongoing transmission ecology.

Methods

Scrub typhus cases with confirmed diagnosis throughout the country were included in the analysis. Studies were concentrated in the Chitwan district, the site of a major outbreak in 2016. Additional nation-wide data from 2015 to 2017 available from the government database included to analyse the disease distribution by geographical mapping.

Results

From 2015 to 2017, 1239 scrub typhus cases were confirmed with the largest outbreak occurring in 2016 with 831 (67.1%) cases. The case fatality rate was 5.7% in 2015 which declined to 1.1% in 2017. A nationwide outbreak of scrub typhus was declared as the cases were detected in 52 out of the 75 districts of Nepal. Seasonal trend was observed with a peak during August and September. In addition to the human cases, the presence of O. tsutsugamushi was also confirmed in animals (rodents) and chigger mites (Leptotrombidium imphalum) from the outbreak areas of southern Nepal.

Conclusion

The detection of O. tsutsugamushi in humans, animals, and chigger mites from outbreak locations and wide-spread reports of scrub typhus throughout the country consecutively for 3 years confirms the ongoing transmission of O. tsutsugamushi with a firmly established ecology in Nepal. The country’s health system needs to be strengthened for systematic surveillance, early outbreak detection, and immediate actions including treatment and preventive measures.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-05866-6.

Scrub typhus in patients with acute febrile illness: a 5-year study from India

BACKGROUND

Scrub typhus was once thought to be a disease of rural origin and was confined to specific pockets in South Asia. Early diagnosis and treatment is extremely important as it is associated with high mortality if left untreated.

AIM

To delineate the clinical and molecular epidemiology of scrub typhus in patients presenting with acute febrile illness from various parts of India.

METHODS

During the study period of 5 years (October 2013 to October 2018), a total of 1742 patients with acute febrile illness <15 days were enrolled after taking informed consent. Patients were diagnosed using IgM Enzyme-linked immunosorbent assay (ELISA) based on the pre-determined region specific cut offs. Patients with positive IgM ELISA were also subjected to IgM Immunofluorescence assay and nested polymerase chain reaction (PCR) assay. The demographic and relevant clinical details of the patients were documented and analyzed.

RESULTS

A total of 210 (12.1%) patients were diagnosed with scrub typhus. Of these, nested PCR was positive in only 85 patients. Sequencing and phylogenetic analysis showed that the predominant circulating genotypes were Gilliam and Karp. On multivariate analysis, acute respiratory distress syndrome, myocarditis, encephalitis/encephalopathy, jaundice and splenomegaly were significantly more common in those patients who were diagnosed with scrub typhus. A total of 14 patients diagnosed with scrub typhus succumbed to the illness.

CONCLUSION

Patients with fever, headache, pulmonary manifestations, CNS manifestations, myocarditis, transaminitis or thrombocytopenia presenting in the monsoon and post-monsoon season should be evaluated for scrub typhus irrespective of the geographical location in India.

Understanding and managing acute encephalitis

Encephalitis is an important cause of morbidity, mortality, and permanent neurologic sequelae  globally. Causes are diverse and include viral and non-viral infections of the brain as well as autoimmune processes. In the West, the autoimmune encephalitides are now more common than any single infectious cause, but, in Asia, infectious causes are still more common. In 2006, the World Health Organization coined the term "acute encephalitis syndrome", which simply means acute onset of fever with convulsions or altered consciousness or both. In 2013, the International Encephalitis Consortium set criteria for diagnosis of encephalitis on basis of clinical and laboratory features. The most important infectious cause in the West is herpes simplex virus, but globally Japanese encephalitis (JE) remains the single largest cause. Etiologic diagnosis is difficult because of the large number of agents that can cause encephalitis. Also, the responsible virus may be detectable only in the brain and is either absent or transiently found in blood or cerebrospinal fluid (CSF). Virological diagnosis is complex, expensive, and time-consuming. Different centres could make their own algorithms for investigation in accordance with the local etiologic scenarios. Magnetic resonance imaging (MRI) and electroencephalography are specific for few agents. Clinically, severity may vary widely. A severe case may manifest with fever, convulsions, coma, neurologic deficits, and death. Autoimmune encephalitis (AIE)  includes two major categories: (i) classic paraneoplastic limbic encephalitis (LE) with autoantibodies against intracellular neuronal antigens (Eg: Hu and Ma2) and (ii) new-type AIE with autoantibodies to neuronal surface or synaptic antigens (Eg: anti-N-methyl-D-aspartate receptor). AIE has prominent psychiatric manifestations: psychosis, aggression, mutism, memory loss, euphoria, or fear. Seizures, cognitive decline, coma, and abnormal movements are common. Symptoms may fluctuate rapidly. Treatment is largely supportive. Specific treatment is available for herpesvirus group and non-viral infections. Various forms of immunotherapy are used for AIE.

Rickettsial infections of the central nervous system

As a result of migrations and globalization, people may face a possible increase in the incidence of central nervous system rickettsial infections (CNS R). These diseases, caused by Rickettsia species and transmitted to humans by arthropod bites, are putatively lethal. However, the diagnosis of CNS R is challenging and often delayed due to their nonspecific clinical presentation and the strict intracellular nature of rickettsiae. Furthermore, transfer of rickettsiae to the brain parenchyma is not yet understood. The aim of this review is to analyze and summarize the features and correlated findings of CNS R in order to focus attention on these intriguing but frequently neglected illnesses. We also incorporated data on CNS infections caused by Rickettsia-related microorganisms.

Risk factors for acquisition of scrub typhus in children admitted to a tertiary centre and its surrounding districts in South India: a case control study

BACKGROUND

Scrub typhus is a mite borne zoonosis common in the tropics with no good preventive strategy. Children are also affected leading to considerable morbidity and mortality. We conducted a case control study and a vector survey to determine the risk factors for acquisition of scrub typhus.

METHODS

A case control study with a 1:2 case control ratio was conducted over a 2 year period at a tertiary care centre and its surrounding districts in South India. Cases were children < 15 years with confirmed scrub typhus. Controls were age and locality matched community controls without fever. Demographic, environmental and behavioural risk factors were obtained in cases and controls by an interview and an environmental survey. A vector survey was also undertaken in the immediate vicinity of the cases.

RESULTS

Case Control study: 101 cases and 167 controls were analysed. On multivariate analysis, significant association was observed with environmental factors such as the presence of a water body within 100 m of the house (OR 3.56(1.36,9.75); p 0.011), cooking outside the house (OR 5.61 (1.51,23.01); p 0.011), owning pets (OR 3.33(1.16,9.09); p 0.031), and the presence of bushes within 5 m of the house (OR 2.78 (1.11,7.69); p 0.033). Of the behavioural factors, the child going to school by a vehicle (OR 3.12 (2.29,8.37); p 0.006) was associated with an increased risk. Drying clothes on a clothesline showed a trend towards protection from acquiring scrub typhus (OR 0.31 (0.08, 1.08); p 0.077). Vector survey:26 rodents were trapped in as many houses. Trombiculid mites were isolated in 24 houses with 9(34.6%) being able to transmit scrub typhus. 254 trombiculid mites belonging to four species and two genera were collected. Leptotrombidium deliense, (33.5%). Schoengastiella ligula, (11.0%) of the total mite specimens collected. S. ligula always co-existed with L. deliense. The estimated Chigger index for Leptotrombidium deliense and Schoengastiella ligula was 3.27and 1.08 per animal respectively.

CONCLUSIONS

Our study highlights risk factors for scrub typhus, some of which may be modifiable. A clean peri-domestic environment free of vegetation, drying clothes on a clothesline and cooking indoors may decrease the risk of scrub typhus.

Detection of human parvovirus 4 DNA in the patients with acute encephalitis syndrome during seasonal outbreaks of the disease in Gorakhpur, India

Seasonal outbreaks of acute encephalitis syndrome (AES) at Gorakhpur, India have been recognized since 2006. So far, the causative agent has not been identified. Use of next generation sequencing identified human parvovirus 4 (HPARV4) sequences in a CSF/plasma pool. These sequences showed highest identity with sequences earlier identified in similar patients from south India. Real-time PCR detected HPARV4 DNA in 20/78 (25.6%) CSF and 6/31 (19.3%) plasma of AES patients. Phylogenetic analysis classified three almost complete genomes and 24 partial NS1 sequences as genotype 2A. The observed association of HPARV4 with AES needs further evaluation. ELISAs for the detection of IgM and IgG antibodies against scrub typhus (Orientia tsutsugamushi, OT) showed ∼70% IgM/IgG positivity suggestive of etiologic association. Prospective, comprehensive studies are needed to confirm association of these agents, singly or in combination with AES in Gorakhpur region.

Risk Factors for Acquiring Scrub Typhus among Children in Deoria and Gorakhpur Districts, Uttar Pradesh, India, 2017

Scrub typhus is associated with outbreaks of acute encephalitis syndrome in Uttar Pradesh, India. A case-control study indicated that children residing, playing, or visiting fields; living with firewood stored indoors; handling cattle fodder; and practicing open defecation were at increased risk for scrub typhus. Communication messages should focus on changing these behaviors.

Diagnosis and Management of Acute Encephalitis in Children

Acute encephalitis is a common cause of death and neurodevelopmental problems in children. The causative agents are numerous including infectious agents such as viruses, bacteria, mycobacteria and protozoa; para-infectious and immune mediated disorders such as acute disseminated encephalomyelitis (ADEM) and autoimmune encephalitis, especially the recently described anti-NMDA receptor encephalitis. Also, many viral associated encephalopathies such as acute necrotizing encephalopathy can mimic the presentation of acute encephalitis. In this article, authors describe the approach to the diagnosis and management of acute encephalitis in children.

Seroprevalence of spotted fever group and typhus group rickettsiae in individuals with acute febrile illness from Gorakhpur, India

BACKGROUND

The aim of this study was to estimate the seroprevalence of spotted fever group (SFG) and typhus group (TG) rickettsiae among individuals with acute febrile illness (AFI) in the scrub typhus endemic district of Gorakhpur in India. This district is one of the worst affected by annual seasonal acute encephalitis syndrome (AES) outbreaks.

METHODS

Antibodies against SFG and TG rickettsiae and the associated risk factors were determined in 294 individuals presenting with an AFI, encountered during a community-based survey conducted during the AES outbreak period October-November 2016.

RESULTS

Respective IgM and IgG seropositivity was 13.6% and 36.7% for SFG, and 7.1% and 15.3% for TG. SFG IgM positivity was significantly higher among females, while IgG positivity was significantly higher among individuals ≥45 years of age. IgM and IgG seropositivity for TG rickettsiae were significantly higher in individuals involved in outdoor activities and housewives, but did not differ according to age group, sex, or educational status.

CONCLUSION

The study results present serological evidence of SFG and TG rickettsiosis, in addition to scrub typhus, among individuals with AFI in Gorakhpur region and indicate the need to explore their roles as potential causes of AES in the region.

Acute Encephalitis Syndrome in Gorakhpur, Uttar Pradesh, 2016: Clinical and Laboratory Findings

BACKGROUND

Seasonal outbreaks of acute encephalitis syndrome (AES) with high fatality have been occurring in Gorakhpur, Uttar Pradesh, India, for several years. We conducted investigations during the 2016 outbreak to identify the etiology.

METHODS

We included 407 hospitalized AES patients with cerebrospinal fluid pleocytosis (>5 cells/mm) in our study. These patients were clinically examined; their blood and cerebrospinal fluid samples were collected and investigated for scrub typhus (ST), Japanese encephalitis virus (JEV), dengue virus and spotted fever group of Rickettsia by serology and/or polymerase chain reaction.

RESULTS

Of the 407 AES patients, 266 (65.4%), 42 (10.3%) and 29 (7.1%) were diagnosed to have ST, JEV and dengue infection, respectively. Four patients were diagnosed to have spotted fever group of Rickettsia infection. A significantly higher proportion of ST patients with AES had hepatomegaly, splenomegaly and facial edema. The common hematologic and biochemical abnormalities among ST-positive patients include thrombocytopenia, raised liver enzymes and bilirubin levels. The case fatality ratio was significantly higher among ST-negative AES patients (36.2% vs. 15.2%; P < 0.05).

CONCLUSIONS

ST accounted for approximately two third of the AES case-patients. Efforts are required to identify the etiology of AES case-patients who are negative for ST, JEV and dengue fever.

Acute Encephalitis Syndrome in Eastern Uttar Pradesh, India: Changing Etiological Understanding

Seasonal outbreaks of acute encephalitis syndrome (AES) with high case fatality have been occurring in Gorakhpur division in Eastern Uttar Pradesh, India, for more than three decades. Japanese encephalitis virus (JEV) accounted for <10% of AES cases, while the etiology of the remaining cases remained largely unknown. Investigations conducted during the 2014 and 2015 outbreaks indicated Orientia tsutsugamushi (Haruo Hayashi 1920) (Norio Ogata 1929) Tamura et al. 1995 (Rickettsiales: Rickettsiaceae) as the etiology in about 60% of AES cases. Hospital-based surveillance studies indicated that about one-fifth of the patients with acute febrile illness were due to scrub typhus. Further studies are required to identify the etiology of about a third of AES cases that test negative for scrub typhus, JEV, or dengue.

Meningitis due to scrub typhus: the importance of a differential diagnosis in an endemic area

A patient with fever and neck stiffness was treated as partially treated bacterial meningitis based on history, examination and cerebrospinal fluid analysis. After initial improvement with ceftriaxone, vancomycin and dexamethasone, symptoms recurred. Fever resolved promptly after treatment was started with doxycycline, when scrub typhus immunoglobulin M test came positive. Meningitis is a well-known complication of scrub typhus. However, scrub typhus is seldom considered in the differential diagnosis of meningitis in the Indian subcontinent. Early diagnosis and prompt institution of doxycycline therapy may lead to early cure of scrub typhus even when features of meningitis supervene. However, ceftriaxone which is commonly used to treat bacterial meningitis is suboptimal in the treatmenwgt36t of scrub typhus.

Febrile illness in Asia: gaps in epidemiology, diagnosis and management for informing health policy

BACKGROUND

Increasing evidence is becoming available on the aetiology and management of fevers in Asia; the importance of these fevers has increased with the decline in the incidence of malaria.

AIMS

To conduct a narrative review of the epidemiology and management of fevers in South and South-East Asia and to highlight gaps in our knowledge that impair evidence-based health policy decisions.

SOURCES

A narrative review of papers published since 2012 on developments in fever epidemiology, diagnosis and treatment in South and South-East Asia. The papers that the authors felt were pivotal, from their personal perspectives, are discussed.

CONTENT

We identified 100 studies. Among the 30 studies (30%)-including both children and adults-that investigated three or more pathogens, the most frequently reported fever aetiology was dengue (reported by 15, 50%), followed by leptospirosis (eight, 27%), scrub typhus (seven, 23%) and Salmonella serovar Typhi (six, 20%). Among four studies investigating three or more pathogens in children, dengue and Staphylococcus aureus were the most frequent, followed by non-typhoidal Salmonella spp, Streptococcus pneumoniae, Salmonella serovar Typhi, and Orientia tsutsugamushi. Increased awareness is needed that rickettsial pathogens are common but do not respond to cephalosporins, and that alternative therapies, such as tetracyclines, are required.

IMPLICATIONS

Many key gaps remain, and consensus guidelines for study design are needed to aid comparative understanding of the epidemiology of fevers. More investment in developing accurate and affordable diagnostic tests for rural Asia and independent evaluation of those already on the market are needed. Treatment algorithms, including simple biomarker assays, appropriate for empirical therapy of fevers in different areas of rural Asia should be a major aim of fever research. Enhanced antimicrobial resistance (AMR) surveillance and openly accessible databases of geography-specific AMR data would inform policy on empirical and specific therapy. More investment in innovative strategies facilitating infectious disease surveillance in remote rural communities would be an important component of poverty reduction and improving public health.