Identification of Missing Probes in rpoB gene in Rifampicin Resistant PTB and EPTB Cases Using Xpert MTB/RIF Assay in Sirmaur, Himachal Pradesh.

INTRODUCTION: India has the highest number of TB (27%) and MDR/RR-TB (24%) cases among the notified TB patients. Xpert MTB/ RIF assay is a fully automated cartridge-based real-time PCR to detect MTB and resistance to rifampicin within two hours using three specific primers and five unique molecular probes to target the rpoB gene. This study was done to detect RR-TB cases and frequency of missing probes, which target mutations in rpoB gene, in the different groups of study population in Sirmaur district of Himachal Pradesh. METHODS: All, pulmonary and extrapulmonary specimens, were processed for AFB microscopy and Xpert MTB/RIF assay to diagnose TB and RR-TB. RESULTS: Xpert detected MTBC in 721 patients. Using AFB microscopy, only 284 samples were positive. Of these MTB positive patients, 671 had pulmonary TB and 50 were EPTB cases. Resistance to RIF was detected in 31 (4.29%) cases of which resistance in presumptive tuberculosis group and presumptive drug resistant tuberculosis was 1.51% and 9.30% respectively. Twentyeight (4.17%) PTB cases and three (6%) EP-TB cases were resistant to RIF. The frequency of probe E was highest (77.41%) and mutation combination of probes C and D and E and D was 3.22%. CONCLUSION: Drug resistance in the MTBC is mainly conferred through point mutations in specific gene targets in the bacterial genome. Molecular assays like Genexpert gives rapid diagnosis and Rifampicin resistance. This study helps to provide baseline data of mutations with in the 81 bp of rpoB gene and stresses the need to further evaluate the mutation patterns in this part of the country.

Predictors of Severity in Scrub Typhus.

AIMS: To study predictors of severity in patients of scrub typhus admitted in a tertiary care hospital. MATERIAL AND METHODS: Total 92 patients of scrub typhus were included in the study. The diagnosis was established by presence of IgM antibodies by Indirect Immunofluorescence Assay (IFA) test which is currently the reference standard for the diagnosis of scrub typhus. The clinical and laboratory profile, course in hospital, and outcome were documented. Factors associated with severe disease were analyzed. OBSERVATIONS: Fever (100%), cough (37%), headache (33%), vomiting (31%), altered sensorium (23%), diarrhea (18%), abdominal pain (16%), myalgia (14%), and seizures (3%) were common clinical features. An eschar was present in 23% of patients. Common laboratory findings included elevated transaminases (61%), thrombocytopenia (39%), and leukocytosis (30%). Severe sepsis was present in 33% patients. Septic shock was present in 4% patients. Presence of one or more organ failure was seen in 34% of patients. The overall case-fatality rate was 4%. Factors significantly associated with organ failure (severe disease) were leucocytosis (p < 0.001), hyperbilirubinemia (p < 0.001), high SGOT levels (p 0.030), hypoalbuminemia (p < 0.001), high urea levels (p < 0.001), and high creatinine levels (p 0.012). Among the criteria used to classify severity of scrub typhus, presence of one or more organ failure was significantly associated with mortality (p 0.004). CONCLUSION: Scrub typhus can manifest with potentially life-threatening complications such as meningoencephalitis, septic shock, ARDS, acute liver failure, acute kidney injury, severe thrombocytopenia. Leukocytosis, hyperbilirubinemia, transaminitis, hypoalbuminemia, and uremia were associated with organ failure and were significantly associated with morbidity and mortality.

Epidemiology, clinical profile and role of rapid tests in the diagnosis of acute bacterial meningitis in children (aged 1-59 months).

OBJECTIVES: To study the epidemiology, clinical profile, and the role of rapid tests in the diagnosis of acute bacterial meningitis (ABM) in children (1-59 months). MATERIALS AND METHODS: A total of 250 cerebrospinal fluid (CSF) and 187 blood samples received from clinically suspected cases of ABM were processed based on standard microbiological protocols. CSF samples were also subjected to antigen and nucleic acid detection. Antibiotic susceptibility testing was done according to the Clinical Laboratory Standards Institute guidelines. Children were also evaluated for outcomes and were followed up until 6 months after discharge. RESULTS: Eighty one cases were reported to be having clinically confirmed ABM, out of which group B Streptococcus was the most common pathogen detected in 49.3% (40) patients followed by Streptococcus pneumoniae, Staphylococcus aureus, Hemophilus influenzae type b, Escherichia coli, Klebsiella pneumoniae, and Neisseria meningitidis ACYW135 in 23.4% (19), 7.4% (6), 6.1% (5), 6.1% (5), 6.1% (5), and in 1.2% (1) patients, respectively. Complications were observed in 54.3% of the children. A follow-up of 6 months after discharge was possible in 39.5% (32) patients among whom sequelae were recorded in 93.7% (30) patients. CONCLUSION: ABM remains a major cause of neurological sequelae worldwide. Although culture is the gold standard test for its detection, the investigation takes a longer time and the results are influenced by prior antimicrobial therapy. In such cases, rapid tests aid in the early diagnosis of ABM for instituting appropriate management.

Factors for Severe Outcome in Scrub Typhus: A Hospital Based Study in Sub Himalayan Region.

Background: Scrub typhus is a re-emerging zoonotic rickettsial infection. Mortality is approximately 15% in some areas due to missed or delayed diagnosis. There had been only few studies on the markers for the severity of the disease, so this study has been planned to provide the knowledge regarding various aspects of scrub typhus in adult age group to detect early signs of severity . Methods: All the patients more than 18 years of age admitted with febrile illness with positive IgM ELISA for scrub typhus with or without eschar were included in the study. The clinical profile was observed. The predictors of mortality were explored using univariate and multivariate analysis. Results: On linear regression analysis and logistic regression analysis altered sensorium, low serum albumin, hepatic dysfunction, renal dysfunction, septic shock, MODS, ARDS, duration of fever > 7 days, day of receiving treatment > 7 days at presentation were significantly associated with high in- hospital mortality. Conclusions: Early treatment with doxycycline should be instituted at the clinical suspicion of scrub pending investigation as it is life saving. Close follow up of the patient should be done to indentify subtle signs of organ dysfunction to start early supportive treatment.

Genetic Diversity among Group A Streptococcus Isolated from Throats of Healthy and Symptomatic Children.

BACKGROUND: Group A streptococcus (GAS) is the commonest bacterial cause of pharyngitis. Children in the age group of 5-15 years are most commonly affected. It can also colonize throats of healthy children in this age group. Both cases and carriers can transmit it in the community. METHODS: Throat swab samples were collected from 1849 asymptomatic and 371 symptomatic children. RESULTS: The rate of isolation of GAS was 1.41% among the asymptomatic group and 7.55% among the symptomatic group. Nine different emm types were encountered in the asymptomatic children and 14 among the symptomatic children. CONCLUSION: Throat swab cultures must be used in all cases of pharyngitis. Early and appropriate antibiotic therapy will prevent complications. Asymptomatic throat carriage of GAS in children was low in our study. However, they can still act as reservoirs. Emm typing helps in understanding epidemiology and finding new types.

Clinical Profile and Complications of Scrub Typhus: Hospital-Based Study in Sub-Himalayan Region.

BACKGROUND: Scrub typhus is a documented disease in Himachal Pradesh, but there have been no clinico-epidemiological studies in this area. The present study is done with IgM ELISA as a diagnostic test which has higher sensitivity and specificity as most of previous studies had used Weil Felix test as a diagnostic test. METHODOLOGY: This was a prospective observational study. All the patients more than 18 years of age with positive IgM ELISA for scrub typhus with or without eschar were included. The clinical profile was observed. IgM scrub typhus was done by kit method manufactured by InBios International, Inc. RESULTS: Total 330 patients were observed. Maximum patients were observed in August, September, and October. Fever was the most common presenting complaint. Eschar was present in 40.61% patients. Complications were seen in 71.2 %. CONCLUSIONS: The general physicians should be sensitized for the early diagnosis to reduce mortality.

Pattern of Clinical Presentation, Laboratory Findings and Mortality Risk Among Patients of Scrub Typhus in Western Himalayas.

OBJECTIVE: To study the pattern of the clinical presentation, laboratory findings and mortality risk among patients infected by scrub typhus in Western Himalayan region of India. METHODS: We studied all serologically confirmed cases of scrub typhus admitted to our hospital from July 2010 through December 2011. Presence of IgM antibodies to scrub typhus antigens by ELISA was considered as serological confirmation of the diagnosis. We observed the symptoms, signs, laboratory findings, risk factors for death from the time of admission till discharge/death. We performed bivariate and logistic regression analysis to look for independent risk factors for death. RESULTS: Total 253 patients were studied. All patients came from rural areas. More than 2/3rd were women and below 50 years of age each. High grade fever (90%), chills and rigors (68%), conjunctival suffusion (50%), body aches (43%), headache (41%), myalgias (37%), abdominal pain (21%), lymphadenopathy (17%), splenomegaly (17%), cough (16%), altered sensorium (16%), vomiting (15%), hepatomegaly (13%) were main presenting features. Eschar was present in 112 (44%) patients. Transaminitis (49%); and abnormal renal functions (31%) were predominant biochemical abnormalities. All patients were empirically treated with doxycycline/azithromycin. Thirteen (5%) patients died. CONCLUSIONS: In our region, rural women below 50 years of age presenting with high grade fever with or without eschar should be strongly suspected to be having scrub typhus. Renal dysfunction and altered sensorium are significant mortality risk factors (p < 0.05) and need to be identified at early stage to improve the treatment outcomes.

Schizophillum commune causing sinusitis with nasal polyposis in the sub-Himalayan region: first case report and review.

Schizophillum commune is an environmental fungus rarely causing human infections of diverse nature. Sinusitis occurs in immunocompromised persons and seldom in healthy subjects. Though easily isolated, the lack of awareness of its virulence is a bottleneck in the diagnosis of this infection. We report the first case of S. commune sinusitis with nasal polyps in an immunocompetent male from the sub-Himalayan region. The computerized tomography scan findings established the clinical diagnosis, and causative agent was confirmed as S. commune. A white, woolly mold with septate, hyaline hyphae and characteristic spicules but unclamped connections suggested a monokaryotic isolate. Patient was treated successfully with fiberoptic endoscopic sinus surgery, and no antifungal therapy was instituted. There was no recurrence at review after 1 year.

Hepatitis B in Trans-Himalayan Tribal Population: High Prevalence, High Pediatric Burden, Virologic Patterns, and Implications for Public Health Interventions.

Background/Aims: The prevalence of hepatitis B is higher in tribal populations, compared to non-tribal populations in India. Therefore, this study aimed to investigate the risk factors, virological and biochemical profile of patients with hepatitis B in a tribal population. Methods: This study analyzed data collected from a community-based project conducted in Spiti, Himachal Pradesh, from July 2015 to 2017. The study included adults and children inhabiting 40 cluster villages out of 82 villages in the subdivision. The blood samples were collected for liver panel, hepatitis B surface antigen (HBsAg), hepatitis B e antigen (HBeAg), Anti-HBe antibody (anti-HBe Ab) and Hepatitis B virus DNA (HBV-DNA). Results: HBsAg was positive in 23.08% of the population (968/4201), with a prevalence of 13.51% in children under 5 years of age. HBeAg positivity was seen in 22.4% of the participants, while anti-HBe Ab positivity was seen in 59.03% of the participants. HBeAg positive infection, HBeAg positive hepatitis, HBeAg negative hepatitis and HBeAg negative infection were seen in 18.06%, 1.98%, 6.17% and 74.01% of the participants, respectively. HBeAg positivity was highest in 2nd decade (40.83% vs 22% overall). Patients with HBeAg positivity exhibited higher levels of HBV DNA [1960 (IQR: 0-108) IU/ml vs 97.2 (IQR: 0-2090) IU/ml, P < 0.001] and alanine transaminase (ALT) [22.5 (IQR: 16-33) U/L vs 19 (IQR: 14-26) U/L, P = 0.003] levels compared to HBeAg negative patients. Conclusion: This study shows a high prevalence of hepatitis B in tribal population, particularly among children under 5 years of age.

Scrub typhus associated acute kidney injury--a study from a tertiary care hospital from western Himalayan State of India.

OBJECTIVE: To report the clinical profile of acute kidney injury (AKI) associated with scrub typhus. METHODS: Retrospective study of hospitalized patients of acute febrile illness who were diagnosed scrub typhus and had AKI. RESULTS: 174 (35%) patients (75.9% female), mean age (41.4 ± 15.9 years) were studied. The laboratory abnormalities were: anemia (63.2%), leukocytosis (44.3%), thrombocytopenia (61.5%), hyponatremia (35.6%), hypernatremia (2.9%), and hypokalemia (12.1%), hyperkalemia (11.5%), hypoalbuminemia (56.9%), hepatic dysfunction (70%) and metabolic acidosis (28.7%). The complications of hypotension (5.7%), septic shock (3.4%), pneumonia (10.9%), acute respiratory distress syndrome (ARDS) (11.5%), meningoencephalitis (6.9%), encephalopathy (5.2%), gastrointestinal bleed (1.3%), myocarditis (3.4%), disseminated intravascular coagulation (2.9%) and multi organ failure (MOF) (10.3%) developed during course of hospitalization in these patients. Twenty-five (14.4%) patients required intensive care support (ICU) support and seven (4%) patients were dialyzed. 146 (83.9%) patients survived. Twenty-eight (16.1%) patients died. There was a significant difference in the age, various hematological & biochemical abnormalities, complications and need for ICU support in the non-survival group as compared the survival group. CONCLUSION: This study shows that AKI in scrub typhus is common and a severe disease. Age, a shorter hospital stay, severities of leukocytosis, thrombocytopenia, azotemia, hypoalbuminemia, hepatic dysfunction and the complications of ARDS, encephalopathy, MOF and need for ICU support are the factors associated with mortality.

Facial chromoblastomycosis in sub-Himalayan region misdiagnosed as cutaneous leishmaniasis: brief report and review of Indian literature.

Cases of chromoblastomycosis, although not uncommon, have rarely been reported in the literature from our region. These are usually misdiagnosed as cases of cutaneous leishmaniasis because we reside in an endemic region for this disease. We present herein patients with facial chromoblastomycosis. They were treated with long-term sodium stibogluconate, but showed no response to therapy. A biopsy revealed these to be cases of chromoblastomycosis, after which the patients were started on antifungal agents. There was marked improvement after the correct treatment was initiated.

Hospital-based sentinel surveillance for bacterial meningitis in under-five children prior to the introduction of the PCV13 in India.

INTRODUCTION: A hospital-based sentinel surveillance network for bacterial meningitis was established in India to estimate the burden of bacterial meningitis, and the proportion of major vaccine-preventable causative organisms. This report summarises the findings of the surveillance conducted between March 2012, and September 2016 in eleven hospitals. METHODS: We enrolled eligible children with bacterial meningitis in the age group of one to 59 months. CSF samples were collected and processed for biochemistry, culture, latex agglutination, and real-time PCR. Pneumococcal isolates were serotyped and tested for antimicrobial susceptibility. RESULTS: Among 12 941 enrolled suspected meningitis cases, 586 (4.5%) were laboratory confirmed. S. pneumoniae (74.2%) was the most commonly detected pathogen, followed by H. influenzae (22.2%), and N. meningitidis (3.6%). Overall 58.1% of confirmed bacterial meningitis cases were children aged between one, and 11 months. H. influenzae meningitis cases had a high (12.3%) case fatality rate. The serotypes covered in PCV13 caused 72% pneumococcal infections, and the most common serotypes were 14 (18.3%), 6B (12.7%) and 19F (9.9%). Non-susceptibility to penicillin was 57%. Forty-five (43.7%) isolates exhibited multidrug resistance, of which 37 were PCV13 serotype isolates. CONCLUSIONS: The results are representative of the burden of bacterial meningitis among under-five children in India. The findings were useful in rolling out PCV in the National Immunization Program. The non-susceptibility to penicillin and multidrug resistance was an important observation. Timely expansion of PCV across India will significantly reduce the burden of antimicrobial resistance. Continued surveillance is needed to understand the trend after PCV expansion in India.

Catheter-related candidemia caused by Candida lipolytica in a child with tubercular meningitis.

Candida lipolytica is weakly pathogenic yeast, which is rarely isolated from the blood. We recovered this species from repeated blood samples and in the central venous catheter in a debilitated pediatric patient of tubercular meningitis. Identity was established on the basis of colony morphology and sugar assimilation tests (ID 32C assimilation profile). The fungemia and associated fever subsided after the removal of catheter and amphotericin B therapy. The data suggest that though of low virulence and usually a contaminant, C. lipolytica is emerging yeast pathogen in cases of catheter-related candidemia. Pathogenicity is indicated by isolation from repeated samples as in our case. Intensive therapy is recommended in cases not resolving spontaneously or responding to removal of catheter alone.

Are We Neglecting Nontuberculous Mycobacteria Just as Laboratory Contaminants? Time to Reevaluate Things.

OBJECTIVES: Nontuberculous mycobacteria (NTM) incidences are on the rise worldwide, including the tuberculosis endemic areas. They should be identified rapidly to the species level and should be carefully differentiated as contamination, colonization, or disease. This study was aimed at determining the prevalence and clinicoepidemiological profile of mycobacteriosis cases. MATERIALS AND METHODS: Cultures were made on liquid and solid media. NTM were identified by polymerase chain reaction (PCR) restriction analysis (PRA) and gene sequencing. Data was analyzed using Epi-info 7. RESULTS: Out of the 1042 processed specimens, 16% were positive for M. tuberculosis complex and 1.2% for clinically significant NTM. M. intracellulare was the commonest species isolated. NTM were treated mainly on outdoor basis (92%), involving more extrapulmonary system (62%) and higher age-group of 41-60 years (69%). No significant factor was seen to be associated clinically, radiologically, and biochemically with the NTM infections. CONCLUSIONS: Our study highlights the importance of early diagnosis and differentiation among Mycobacterium tuberculosis and NTM so that these NTM are not underestimated in routine diagnostic procedures merely as environmental or laboratory contaminants.

Immunochromatography in CSF improves data on surveillance of S. pneumoniae meningitis in India.

INTRODUCTION: Streptococcus pneumoniae is a significant cause of childhood bacterial meningitis in India. The United States Food and Drug Administration has licensed an immunochromatographic (ICT) test, Binax®NOW™, to detect the C polysaccharide antigen of S. pneumoniae in cerebrospinal fluids (CSF). Accurate etiological diagnosis of bacterial meningitis in India is essential for effective treatment strategies and preventive interventions. MATERIALS AND METHODS: CSF samples from 2081 children admitted, with clinically suspected bacterial meningitis at 11 sentinel sites of hospital based sentinel surveillance network for bacterial meningitis in India between September 2009 and December 2016 were tested with ICT. Concurrent CSF cultures were processed using standard procedures. RESULTS AND DISCUSSION: S. pneumoniae was detected thrice the number of times by ICT than by CSF culture, with a sensitivity and specificity of 100% and 95.3% respectively. This rapid ICT test proves to be of immense use as a diagnostic test for meningitis patients with/without prior antibiotic treatment, especially in facilities with limited laboratory infrastructure in resource limited settings.

Influenza A(H1N1)pdm09 cases in sub-Himalayan region, 2014-2015 India.

Current influenza A(H1N1)pdm09 strain severely involved many parts of the country. The study was conducted to analyze the clinicoepidemiological trend of influenza A(H1N1)pdm09 cases from October 2014 to March 2015. Samples processing was done as per the Center for Disease Control guidelines. A total of 333 specimens were processed out of which influenza A(H1N1)pdm09 constituted 24% (81) of total, 5% (18) cases were seasonal influenza A virus strains. Mean age group involved was 49 years with case fatality rate of 20%. Patients died were 63% males and 44% had comorbidities, and among them, 38% patients died within 24 h of hospitalization. The mean age of comorbid patients who died was 59 years; whereas the mean age of patients died having no co-morbidities was 41 years (P < 0.005). Mortality was seen among 81% (13) of patients who were on ventilator support. Added mortality in specific human group demands continuous surveillance monitoring followed by the detection of mutation, even in susceptible animal population.

Clinical Profile of Scrub Typhus in Pregnancy in Sub-Himalayan Region.

BACKGROUND: Scrub typhus is rare in pregnancy, but it has now become an important cause of febrile illness in pregnancy in sub-Himalayan region of India. Only a few case reports have been published so far, and they show adverse maternal and fetal outcomes. No consensus has been reached till now regarding treatment. METHODOLOGY: All the pregnant patients irrespective of period of gestation admitted with febrile illness with positive IgM ELISA for scrub typhus with or without eschar were included. The clinical profile was observed using a detailed history of symptoms, travel, recreation, agricultural activities, treatment record prior to admission, and a detailed examination, and the treatment outcome was noted. Fever workup including cultures, CXR, CSF analysis, serology for scrub was done. IgM scrub typhus was done by kit method manufactured by InBios Intertational, Inc. RESULTS: We observed in total 14 pregnant patients out of which eight were in the the second trimester and six were in the third trimester. The clinical features of the disease observed for pregnant females were the same as for nonpregnant females. There was no difference in the severity of scrub typhus between pregnant and nonpregnant women. No mortality was found in these patients. On follow-up, they had normal peripartum and postpartum periods. All were treated with azithromycin 500 mg once a day for 5 days. CONCLUSION: Although rare, scrub typhus should be considered in differential diagnosis of fever in pregnant patients especially in scrub season. Azithromycin should be the drug of choice in pregnancy as it has no adverse effect on fetus and pregnancy outcome.

Clinico-Epidemiological Profile, Pandemic Influenza A H1N1/2009 and Seasonal Influenza, August 2009-March 2013, Himachal Pradesh, India.

BACKGROUND: Novel influenza A (H1N1) virus emerged in April, 2009, spread rapidly to become pandemic by June, 2009. OBJECTIVE: To study the clinco-epidemiological profile of pH1N1and seasonal influenza (SI) from 2009 to 2013. MATERIALS AND METHODS: Retrospective, hospital-based study was done by reviewing medical records for collecting demographic and clinical profile of the study samples. RESULT: Out of 969 samples, positivity and case fatality for pH1N1 and SI was 9.39 and 20.87% vs 11.76 and 7.89%, respectively. Among pH1N1and SI, sex distribution, mean age, and age group involved were 54.95% females, 37.10 years, and 20-29 years (23.08%) vs 43.86% females, 40.32 years, and 20-29 years (22.81%), respectively. Mortality shift was observed from younger to older and healthier, 75% to comorbid, 100% from 2009-2010 to 2012-13 for pH1N1. CONCLUSION: We observed seasonal variation, cocirculation, similar clinical features, decreased virulence, and community spread with respect to pH1N1 and SI from 2009-2013.

Typhoidal Salmonellae: Use of Multi-Locus Sequence Typing to Determine Population Structure.

Enteric fever is an invasive infection predominantly caused by Salmonella enterica serovars Typhi and Paratyphi A. The pathogens have evolved from other nontyphoidal salmonellaeto become invasive and host restricted. Emergence of antimicrobial resistance in typhoidal salmonellae in some countries is a major therapeutic concern as the travelers returning from endemic countries carry resistant strains to non endemic areas. In order to understand the epidemiology and to design disease control strategies molecular typing of the pathogen is very important. We performed Multilocus Sequence Typing (MLST) of 251 S. Typhi and 18 S. Paratyphi strains isolated from enteric fever patients from seven centers across India during 2010-2013to determine the population structure and prevalence of MLST sequence types in India. MLST analysis revealed the presence of five sequence types (STs) of typhoidal salmonellae in India namely ST1, ST2 and ST3 for S. Typhi and ST85 and ST129 for S. Paratyphi A.S. Typhi strains showed monophyletic lineage and clustered in to 3 Sequence Types-ST1, ST2 and ST3 and S. Paratyphi A isolates segregated in two sequence types ST85 and ST129 respectively. No association was found between antimicrobial susceptibility and sequence types. This study found ST1 as the most prevalent sequence type of S. Typhi in India followed by ST2, which is in concordance with previous studies and MLST database. In addition a rare sequence type ST3 has been found which is reported for the first time from the Indian subcontinent. Amongst S. Paratyphi A, the most common sequence type is ST129 as also reported from other parts of world. This distribution and prevalence suggest the common spread of the sequence types across the globe and these findings can help in understanding the disease distribution.