Pan-India influenza-like illness (ILI) and Severe acute respiratory infection (SARI) surveillance: epidemiological, clinical and genomic analysis.

Background: Over time, COVID-19 testing has significantly declined across the world. However, it is critical to monitor the virus through surveillance. In late 2020, WHO released interim guidance advising the use of the existing Global Influenza Surveillance and Response System (GISRS) for the integrated surveillance of influenza and SARS-CoV-2. Methods: In July 2021, we initiated a pan-India integrated surveillance for influenza and SARS-CoV-2 through the geographically representative network of Virus Research and Diagnostic Laboratories (VRDLs) across 26 hospital and laboratory sites and 70 community sites. A total of 34,260 cases of influenza-like illness (ILI) and Severe acute respiratory infection (SARI) were enrolled from 4 July 2021 to 31 October 2022. Findings: Influenza A(H3) and B/Victoria dominated during 2021 monsoon season while A(H1N1)pdm09 dominated during 2022 monsoon season. The SARS-CoV-2 "variants of concern" (VoC) Delta and Omicron predominated in 2021 and 2022, respectively. Increased proportion of SARI was seen in extremes of age: 90% cases in < 1 year; 68% in 1 to 5 years and 61% in ≥ 8 years age group. Approximately 40.7% of enrolled cases only partially fulfilled WHO ILI and SARI case definitions. Influenza- and SARS-CoV-2-infected comorbid patients had higher risks of hospitalization, ICU admission, and oxygen requirement. Interpretation: The results depicted the varying strains and transmission dynamics of influenza and SARS-CoV-2 viruses over time, thus emphasizing the need to continue and expand surveillance across countries for improved decision making. The study also describes important information related to clinical outcomes of ILI and SARI patients and highlights the need to review existing WHO ILI and SARI case definitions.

Seroprevalence of Rickettsial disease: A population-based survey from kashmir valley, North India.

Background: Limited studies have been done regarding the prevalence of Rickettsial diseases in India and as far as UT of Jammu and Kashmir is concerned, only a few hospital-based studies are available. Objectives: The present study was therefore planned to find the seroprevalence of Rickettsial diseases in Kashmir Valley. Materials and Methods: A multistage sampling procedure was used for the collection of samples from 10 districts of Kashmir Valley and a total of 1740 samples were collected. In addition, 802 healthy blood donors were included to establish baseline titers for Weil-Felix (WF) Test. Results: Of 1734 subjects, 73 were positive by the WF test. The overall seroprevalence of Rickettsial diseases was 4.1% with the highest prevalence of scrub typhus (2.30%) followed by the spotted fever group (1.5%) and typhus group (0.40%). Maximum seropositive subjects were from district Kulgam (6.97%) followed by Pulwama (5.92%), Shopian (5.79%), Anantnag (5.47%), Ganderbal (5.00%), Kupwara (4.72%), Baramulla (4.62%), Srinagar (2.63%), Bandipora (2.41%), and Budgam (0.54%), respectively. Seropositivity was higher in females and subjects who had contact with ticks and mites like those involved in the collection of firewood and grass or had contact with uncut grass or shrub. The seropositivity was also significantly higher in those working in paddy fields and those living near the forest (P < 0.05). Conclusion: The results of the present study confirm the existence of Rickettsial diseases in this region. This data would promote awareness of rickettsioses among local physicians and will also serve as a baseline to detect changing prevalence in the future.

Rickettsial Infections among the Undifferentiated Febrile Patients Attending a Tertiary Care Teaching Hospital of Northern India: A Longitudinal Study.

BACKGROUND: Acute undifferentiated febrile illness (AUFI) is one of the most daunting challenges a physician faces in such settings. Among AUFI, rickettsial infections are most common and related infections (such as anaplasmosis, ehrlichiosis, and Q fever) which are caused by an unusual type of bacteria that can live only inside the cells of another organism. The present study was therefore planned with an objective to estimate the prevalence of rickettsial infection among patients of undifferentiated fever and to determine any association of socio-demographic characteristics with rickettsial disease. MATERIALS AND METHODS: Patients presenting with febrile illness and admitted or attending out-patient department of Sher-i-Kashmir Institute of Medical Sciences, Srinagar was approached and recruited in the study. Weil Felix Assay, enzyme-linked immunosorbent assay and indirect immunofluorescence assay were done to detect the anti-rickettsial antibodies. Serological evidence of a fourfold increase in IgG-specific antibody titer reactive with spotted fever group rickettsial antigen by indirect immunofluorescence antibody assays between paired serum specimens was considered a confirmatory diagnosis for the rickettsial disease. RESULTS: Most of the patients were males 61.6%, and most 46.2% were in the age group of 20 -39 years. Most of the patients, 80.8% belonged to rural areas, and 48% belonged to the upper middle (II) class of the socio-economic class according to modified Kuppuswamy scale. Of the studied participants, a majority, 47.0%, were determined undiagnosed, while 15.4% studied participants were diagnosed to have a rickettsial disease. In patients positive for typhus group, 67.8% were IgM positive, 28.5% were IgG positive, and only 3% were positive for IgM and IgG. In patients positive for Scrub Typhus Group, 32.7% were positive for IgM, and 62.0% were positive for IgG, and only 5.0% were positive for both IgM and IgG. In patients positive for spotted fever group, 36.1% were positive for IgM, and 58.5% were positive for IgG, and only 5.5% were positive for both IgM and IgG. The prevalence of rickettsial disease was found to be 11.3%. CONCLUSION: Rickettsial diseases, typhoid and brucellosis, were the most prevalent diseased diagnosed among patients reporting to hospitals with undifferentiated febrile illness. Clinicians must consider rickettsial diseases as one of the differential diagnosis while treating patients with fever.

Airway Microbiology in Children with Cystic Fibrosis: A Prospective Cohort Study from Northern India.

OBJECTIVE: The objective of this study is to find the organism profile and antimicrobial susceptibility patterns in children with cystic fibrosis (CF). DESIGN: Prospective cohort study. SETTING: Hospital-based study. INTERVENTION: Sputum cultures/throat swabs were collected from the study population. Relevant details like anthropometry, systemic examination findings and investigations were entered in a pre-designed format. Sputum culture was subjected to microbiological analysis at the hospital microbiology laboratory. MAIN OUTCOME MEASURE: Prevalence of positive sputum/cough swab culture in CF patients, their organism profile and antibiotic sensitivity. RESULTS: A total of 63 patients were enrolled in the study. A total of 136 organisms were grown in our study population. Thirteen different organisms were isolated, which included five gram-positive bacteria, six gram-negative bacteria, eight Candida spp. and one filamentous. Antibiotic sensitivity profile of the Pseudomonas aeruginosa showed excellent sensitivity to all the aminoglycosides, piperacillin-tazobacteum and polymixin, similarly methicillin-sensitive Staphylococcus aureus, methicillin-resistant S. aureus and Enterococcus spp. were uniformly sensitive to vancomycin, linezolid and teicoplanin. Fungal isolates showed 100% sensitivity to all the antifungals tested including azoles and amphotericin B. CONCLUSION: We observed 61% of culture positivity for different organisms in our study. Staphylococcus aureus and P. aeruginosa were the most frequently isolated organisms. Pseudomonas aeruginosa isolates were largely sensitive to aminoglycosides, carbapenems and polymixin. We found an unusually higher incidence of enterococcal infection in our study cohort with few vancomycin-resistant isolates.

Healthcare-Associated Pneumonia and Hospital-Acquired Pneumonia: Bacterial Aetiology, Antibiotic Resistance and Treatment Outcomes: A Study From North India.

BACKGROUND: Data regarding the comparative profiling of HCAP and HAP from developing countries like India are scant. We set out to address the microbial aetiology, antibiotic resistance and treatment outcomes in patients with HCAP and HAP. METHODS: 318 consenting patients with HCAP (n = 165, aged 16-90 years; median 60 years; 97 males) or HAP (n = 153; aged 16-85 years; median 45 years; 92 males) presenting to a tertiary care hospital in North India from 2013 to 2015 were prospectively recruited for the study. Data on patient characteristics, microbial aetiology, APACHE II scores, treatment outcomes and mortality were studied. Clinical outcomes were compared with various possible predictors employing logistic regression analysis. RESULTS: Patients in HCAP had more comorbidity. Escherichia coli (30, 18%) and Acinetobacter baumannii (62, 41%) were the most commonly isolated bacteria in HCAP and HAP, respectively. Multidrug-resistant bacteria were isolated more frequently in HCAP, only because the incidence of extensively drug-resistant bacteria was markedly high in HAP (p = 0.00). The mean APACHE II score was lower in HCAP (17.55 ± 6.406, range 30) compared to HAP (19.74 ± 8.843, range 37; p = 0.013). The length of stay ≥ 5 days (p = 0.036) and in-hospital mortality was higher in HAP group (p = 0.002). The most reliable predictors of in-hospital mortality in HCAP and HAP were APACHE II score ≥ 17 (OR = 14, p = 0.00; HAP: OR = 10.8, p = 0.00), and septic shock (OR = 4.5, p = 0.00; HAP: OR = 6.9, p = 0.00). CONCLUSION: The patient characteristics in HCAP, treatment outcomes, bacterial aetiology, and a higher incidence of antibiotic-resistant bacteria, suggest that HCAP although not as severe as HAP, can be grouped as a separate third entity.

Hypertonic xylose agar medium: A novel medium for differentiation of Candida dubliniensis from Candida albicans.

BACKGROUND: Candida dubliniensis is a pathogenic Candida species which shares many phenotypic features with Candida albicans. These similarities have caused significant problems in the identification of C. dubliniensis in an average clinical mycology laboratory. Several phenotypic-based tests have been developed to distinguish C. albicans from C. dubliniensis but none has been demonstrated being sufficient alone for accurate differentiation of the two species. AIM: To facilitate the differentiation of these species, we evaluated the utility of a novel medium 'Hypertonic Xylose Agar Medium' (HXAM). MATERIALS AND METHODS: A total of 200 Candida spp. were tested in this study which included 186 stock strains of C. albicans and 14 strains of C. dubliniensis. Identification of all these strains was confirmed by polymerase chain reaction-restriction fragment length polymorphism using Bln I (Avr II) enzyme. All isolates were inoculated on HXAM, incubated at 28°C and examined for visible growth every day up to 7 days. RESULTS: On this medium at 28°C, all 186 C. albicans isolates showed visible growth at 48 h of incubation whereas none of the 14 C. dubliniensis isolates did so even on extending the incubation period up to 7 days. CONCLUSION: Hence, we propose HXAM as a sole phenotypic method for identifying C. dubliniensis from germ-tube-positive isolates or from stock collections of known C. albicans.

Sero-epidemiological survey of human cystic echinococcosis in Kashmir, North India.

BACKGROUND: Echinococcosis is a human and animal health problem in many endemic areas worldwide. There are numerous reports and hospital-based studies from Kashmir, North India, yet there has been no epidemiological study conducted in Kashmir, the apparently endemic area for human hydatidosis. This study was designed to determine the seroprevalence of hydatid infection in Kashmir Valley and to find out association of risk factors for acquisition of this infection. METHODOLOGY: Fourteen hundred and twenty-nine samples were collected from different districts in the Kashmir region (North India) using systematic random sampling. The 130 control samples included were from apparently healthy blood donors (100), patients with other parasitic infections (20), surgically confirmed hydatidosis patients (5), and apparently healthy subjects excluded for hydatidosis and intestinal parasitic infections (5). Hydatid-specific IgG antibody was detected by enzyme-linked immunosorbent assay, and seropositive samples were analysed further by Western blotting. RESULTS: Out of 1,429 samples, 72 (5.03%) were IgG positive by ELISA. The percentage occurrence of the highly immunoreactive antigenic fractions in IgG ELISA positive samples was 57 kDa (72.2%) followed by 70 kDa (66.7%) and 39 kDa (58.3%) by immunoblotting. Samples with other parasitic infections were reactive with the cluster of 54-59 kDa antigenic fractions. Age <15 years, male gender, contact with dog, and rural residence were the most significant factors associated with the seropositivity. CONCLUSION: The study revealed that 72 (5.03%) out of 1,429 subjects asymptomatic for hydatidosis were seropositve to E.granulosus antigen by ELISA. Western blot analysis of 72 ELISA seropositive samples showed that 66.7% and 58.3% of samples were immunoreactive with 70 and 39 kDa specific antigenic fractions, respectively. The seropositivity was significantly higher (5.79%) in the younger age group (<15 years) as compared to the 16-55 years (4.07%) and > 55 years (3.05%) age groups, suggesting ongoing transmission of this infection in the younger age group. The number of seropositive males was significantly higher as compared to females. The risk factors identified were rural residence and contact with dogs. The study suggests the presence of asymptomatic infection in subjects in Kashmir, North India, and efforts need to be made for implementation of effective prevention measures to reduce the infection burden, which may otherwise lead to symptomatology and complications in the infected subjects.

NDM-1 (New Delhi metallo beta lactamase-1) producing Gram-negative bacilli: emergence & clinical implications.

UNLABELLED: BACKGOUND & OBJECTIVES: Resistance to carbapenems in Gram-negative bacteria conferred by NDM-1 is a global health problem. We investigated the occurrence of NDM-1 in clinical isolates of Gram-negative bacilli in a tertiary care hospital in Kashmir valley, India. METHODS: Gram-negative bacilli from different clinical isolates were included in the study. Antimicrobial susceptibility was performed by Kirby Bauer disk diffusion method and interpreted using Clinical Laboratory Standards Institute (CLSI) guidelines. Isolates resistant to carbapenems were subjected to different phenotypic test such as modified Hodge test (MHT), boronic acid and oxacillin based MHT ( BA-MHT and OXA-MHT), combined disk test and minimum inhibitory concentration (MIC) with imipenem and imipenem -EDTA for determination of class B metallo enzymes. Presence of blaNDM-1 gene was established by PCR and confirmed by sequencing. RESULTS: Of the total 1625 Gram-negative isolates received, 100 were resistant to imipenem. Of the 100 isolates, 55 (55%) were positive by modified Hodge test indicating carbapenemase production. Of the 100 isolates tested by MHT, BA-MHT and OXA-MHT, 29 (29%) isolates belonged to Class A and 15 (15%) to Class B, while 56 (56%) isolates were negative. Of the 15 class B metallo beta lactamase producers, nine carried the bla(NDM-1) gene. NDM-1 was found among Escherichia coli (2 isolates), Klebsiella pneumoniae (2 isolates), Citrobacter freundii (3 isolates), Acinetobacter spp (1 isolate), and one isolate of Pseudomonas aeruginosa. Isolates were resistant to all antibiotic tested except polymyxin B and tigecycline. INTERPRETATION & CONCLUSIONS: Our study showed the presence of clinical isolates expressing NDM-1 in Srinagar, Jammu & Kashmir, India. These isolates harbour plasmid mediated multiple drug resistant determinants and can disseminate easily across several unrelated genera. To halt their spread, early identification of these isolates is mandatory.

Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature.

The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA). Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi) gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes). Further the nucleotide sequences (retrieved from GenBank) for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima's D test and Fu's FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia), indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.

Molecular characterization of Echinococcus granulosus cysts in north Indian patients: identification of G1, G3, G5 and G6 genotypes.

BACKGROUND: Cystic echinococcosis (CE) caused by the Echinococcus granulosus, is a major public health problem worldwide, including India. The different genotypes of E. granulosus responsible for human hydatidosis have been reported from endemic areas throughout the world. However, the genetic characterization of E. granulosus infecting the human population in India is lacking. The aim of study was to ascertain the genotype(s) of the parasite responsible for human hydatidosis in North India. METHODOLOGY/PRINCIPAL FINDINGS: To study the transmission patterns of E. granulosus, genotypic analysis was performed on hydatid cysts obtained from 32 cystic echinococcosis (CE) patients residing in 7 different states of North India. Mitochondrial cytochrome c oxidase subunit1 (cox1) sequencing was done for molecular identification of the isolates. Most of the CE patients (30/32) were found to be infected with hydatid cyst of either G3 (53.1%) or G1 (40.62%) genotype and one each of G5 (cattle strain) and G6 (camel strain) genotype. CONCLUSIONS/SIGNIFICANCE: These findings demonstrate the zoonotic potential of G1 (sheep strain) and G3 (buffalo strain) genotypes of E. granulosus as these emerged as predominant genotypes infecting the humans in India. In addition to this, the present study reports the first human CE case infected with G5 genotype (cattle strain) in an Asian country and presence of G6 genotype (camel strain) in India. The results may have important implications in the planning of control strategies for human hydatidosis.

Effect of second dose of measles vaccine on measles antibody status: a randomized controlled trial.

OBJECTIVE: To evaluate the effect of the second dose of measles vaccine on measles antibody status during childhood. SETTING: Immunization centre of Under-five Clinic of the Department of Community Medicine at a tertiary-hospital. STUDY DESIGN: Randomized Controlled trial. SUBJECTS: Children from 6 years to 17 year old. 188 with simple obesity, and 431 with obesity and metabolic abnormalities. 274 age and gender-matched healthy children as controls. METHODS: Blood samples were collected from all subjects for baseline measles serology by heel puncture at 9-12 months of age. All subjects were given the first dose of measels vaccine. At second visit (3-5 months later), after collecting the blood sample from all, half the children were randomized to receive the second dose of measles vaccine (study group), followed by collection of the third sample six weeks later in all the subjects. RESULTS: A total of 78 children were enrolled and 30 children in each group could be analyzed. 11(36.6%) children in the study group and 13 (43.3%) children in the control group had protective levels of measles IgG at baseline. Around 93.3% of children in the study group had protective measles antibody titers as against 50% in the control group at the end of the trial. The Geometric Mean Titre (GMT) of measles IgG increased from 14.8 NTU/mL to 18.2 NTU/mL from baseline to six weeks following receipt of the second dose of the vaccine in the study group, as compared to a decrease from 16.8 NTU/mL to 12.8 NTU/mL in the control group. CONCLUSION: A second dose of measles vaccine boosts the measles antibody status in the study population as compared to those who receive only a single dose.

Phenotypic detection of constitutive and inducible clindamycin resistance in clinical isolates of Staphylococcus aureus and coagulase negative Staphylococcus on routine susceptibility plate.

Increasing frequency of methicillin resistant Staphylococcus aureus infections and changing patterns in antimicrobial resistance have led to renewed interest in the use of macrolidelincosamide-streptogramin antibiotics. However therapy may fail either due to constitutive or inducible resistance. This study was undertaken to detect different phenotypes including inducible clindamycin resistance in clinical isolates of Staphylococcus aureus and coagulase negative Staphylococcus. Four hundred sixty five Staphylococcus aureus and 84 coagulase negative Staphylococci isolated from different clinical specimens were included in the study. On routine susceptibility testing plate clindamycin (2 microg) disk was placed at a distance of 15mm towards the centre from a peripherally placed erythromycin (15 microg) disk. Fisher exact test was used for statistical analysis. Out of 465 Staphylococcus aureus isolates, 237 (50.96%) were methicillin sensitive (MSSA) and 228 (49.03%) methicillin resistant (MLS(B)c).Over all 118 (25.37%) isolates showed constitutive resistance (MLS(B)c), 70 (15.05%) inducible clindamycin resistance, 143 (30.75%) MS(B) phenotype and 134 (28.81%) were susceptible to both erythromycin as well as clindamycin. Constitutive and inducible resistance to clindamycin were significantly higher in MRSA than MSSA (P=0.0000 and 0.0001 respectively). Out of 84 isolates of coagulase negative Staphylococci, 43 (51.19%) were methicillin sensitive (MSCNS) and 41(48.80%) methicillin resistant (MRCNS). Constitutive MLS(B) resistance was detected in 32 (38.09%), inducible clindamycin resistance 10 (11.90%), MS(B) phenotype 27 (32.14%) and 15 (17.85%) were susceptible to both erythromycin and clindamycin. Performing D test on a routine susceptibility plate saves material, manpower and time as inducible resistance can be reported simultaneously along with other susceptibility results.

Soil-transmitted helminths in relation to hemoglobin status among school children of the Kashmir Valley.

Soil-transmitted helminths (STHs) remain a major threat to the health of children throughout the world, mostly in developing nations. The aim of the present study was to determine any relationship between STHs and hemoglobin status in school children of Kashmir Valley (India). Stool and blood samples were collected from 382 male and female school children in the age group of 5-15 yr from all 6 school districts of the Kashmir Valley. Finger-prick blood samples were used to collect the hemoglobin, which was then measured on-site by Sahli's acid hematin method; stool samples were processed using both simple smear and zinc sulphate concentration methods. Of the 382 children surveyed, 299 (78.27%) were infected with Ascaris lumbricoides, Trichuris trichiura, or both. Children infected by STHs were found to have lower mean values of hemoglobin than uninfected children. The present study reveals that STHs are abundant among school children of Kashmir Valley, creating a negative effect on the hemoglobin values and indicating the necessity of implementing control measures.

Serum cytokine levels in human ascariasis and toxocariasis.

Cytokine-mediated regulation of chronic intestinal helminth infections is well documented. The present study reports the serum cytokine responses in 38 ascariasis (stool samples positive for Ascaris lumbricoides ova) and toxocariasis (seropositive) patients, 8 ascariasis-positive and toxocariasis-seronegative patients, 22 endemic, normal, healthy subjects residing in areas hyperendemic for ascariasis and 16 normal healthy subjects residing in a low-endemic area in India. The results indicated T-helper type-2-type cytokine responses in ascariasis and toxocariasis (seropositive) and ascariasis-positive and toxocariasis-seronegative patients. The important observation was that both patients and healthy individuals in ascariasis-hyperendemic areas had significantly higher interleukin-5 (IL-5) responses than non-endemic control subjects. The altered immune responses of patients in areas hyperendemic of ascariasis may have further implications. Earlier reports suggest that the geohelminth parasites in endemic areas may modulate the immune response to oral vaccines. A critical role for IL-5 in the immune response against challenge infection consistent with the association of type-2 cytokines with vaccine-mediated protection has been reported. Furthermore, co-infection by pathogens that elicit opposing immune responses, particularly helminths vs HIV and tuberculosis, could influence the infection dynamics, progression and immunoprophylaxis of the diseases they cause. Further studies are warranted to ascertain these findings.

Seroprevalence of rubella in pregnant women in Kashmir.

The present study was conducted to determine the seroprevalence of rubella in pregnant women in Kashmir. One thousand nine hundred and eighteen pregnant women in age group of 20-35 were divided into two groups. Group I (n=892) consisted of women with previous history of repeated abortion (507), single abortion (220), intrauterine death (149), stillbirth (14) and premature delivery (2). Group II (n=1028) pregnant women with previous normal delivery. A total of 1918 pregnant women were screened for rubella IgM antibodies out of which 16.74% were positive. In women with bad obstetric history (Group I) 26.12% were positive as compared to 8.96% in women with no significant obstetric history (Group II). The IgM antibody positivity was higher in women with previous history of intrauterine death (IUD) 58.38% followed by stillbirth 57.14%, premature delivery 50%, abortion 21.8% and recurrent abortion 17.55%. The high prevalence of disease in this region demands urgent needs for prevention. Moreover antenatal cases should be screened as early diagnosis and time intervention will help in proper management of these cases.