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George E.A.,Sri Sakthi Amma Institute of Biomedical Research | Sankar S.,Sri Sakthi Amma Institute of Biomedical Research | Jesudasan M.V.,Sri Sakthi Amma Institute of Biomedical Research | Sudandiradoss C.,Vellore Institute of Technology | Nandagopal B.,Sri Sakthi Amma Institute of Biomedical Research
Indian Journal of Medical Microbiology | Year: 2015

Purpose: Escherichia coli is a common pathogen causing community-and hospital-acquired infections. The infections caused by the Extended Spectrum Beta Lactamase (ESBL) enzymes-producing E. coli hinder antibiotic treatment. Materials and Methods: Plasmid DNA samples were subjected to PCR specific for TEM, SHV and CTX-M genes obtained from 110 E. coli strains isolated from hospitalized patients, healthy individuals and environment in Vellore, South India. Results: Among the 110 isolates tested, 21.8% were positive for TEM and 2.7% positive for SHV and 91.8% positive for CTX-M. The proportion of CTX-M positive E. coli was not statistically different between the study groups. Nineteen of 20 strains were CTX-M-15 type and the other was CTX-M-14 type. The phylogenetic analysis of 19 strains clustered with the pandemic CTX-M-15-ST131 strain, indicating this as an evolving global problem for antibiotic therapy. The geomapping of samples indicated 'hotspot' areas of healthy individuals, patients and the environmental samples. Conclusion: The spatial presentation of GIS mapping allowed identification of clustering among patients and healthy individuals and contaminated environmental points. Source


Narayanan H.,Sri Sakthi Amma Institute of Biomedical Research | Sankar S.,Sri Sakthi Amma Institute of Biomedical Research | Simoes E.A.F.,Childrens Hospital | Nandagopal B.,Sri Sakthi Amma Institute of Biomedical Research | Sridharan G.,Sri Sakthi Amma Institute of Biomedical Research
Molecular Diagnosis and Therapy | Year: 2013

Background: Human metapneumovirus (hMPV), which has a global distribution, is an important cause of acute respiratory tract infections, especially in children and immunocompromised patients. Methods: We investigated the genetic variability of partial nucleoprotein (N) gene sequences of hMPV strains identified among young children in South India. The sequences of the N gene were compared with previously reported sequences available in the GenBank repository. Results: The results showed that strains are localized in a geographically circumscribed area (topotype). The results also demonstrates that viruses from the same genetic lineage can circulate concurrently within a given location during a given season. The close clustering of the majority of our hMPV isolates indicates that the N gene sequences in the virus population are relatively homogeneous, and suggests temporal rather than geographic variations in the evolutionary pattern. In our study, the majority of the strains belonged to genetic lineage B2 (71.1 %), followed by A2b (18.4 %), A2a (7.9 %), and B1 (2.6 %), demonstrating the presence of 4 of the 5 known genotypes of hMPV. Global alignment of the nucleotide sequences showed that the strains are closely related to sequences from Canada, The Netherlands, and Australasia. Differences at the nucleotide level and the amino acid level were identified. The results provide evidence for the diversity of the N gene of hMPV in samples collected from South India compared with global strains. When investigated for selective pressure, the sequences showed 1 positively selected site and 19 negatively selected sites. Conclusion: These data should prove useful in further investigations of the evolutionary dynamics of hMPV infection. © 2013 Springer International Publishing Switzerland. Source


Narayanan H.,Sri Sakthi Amma Institute of Biomedical Research | Sankar S.,Sri Sakthi Amma Institute of Biomedical Research | Simoes E.A.F.,Childrens Hospital | Nandagopal B.,Sri Sakthi Amma Institute of Biomedical Research | Sridharan G.,Sri Sakthi Amma Institute of Biomedical Research
Molecular Diagnosis and Therapy | Year: 2013

Background: Acute respiratory tract infections (ARTIs) are one of the major causes of morbidity and mortality among young children in developing countries. Information on the incidence of human metapneumovirus (hMPV) and human bocavirus (HBoV) infections in developing countries, especially among rural children, is very limited. Objectives: This study was conducted to identify whether these viruses were associated with ARTI among children ≤5 years of age in rural and peri-urban populations in South India. Methods: The study was cross-sectional with prospective sample collection. Oropharyngeal swabs were collected from children ≤5 years of age presenting with ARTI. None of the children in this study were known to have any immunosuppressive conditions. The two viruses, hMPV and HBoV, were identified using semi-nested polymerase chain reaction (PCR) assays and one-step PCR assays, respectively. The lower limits of detection of hMPV and HBoV were 6.69 × 105 plasmid copies and 5.77 × 103 plasmid copies, respectively, per 5 μL PCR reaction input. Results: The frequency of hMPV infection in children was higher than that of HBoV infection. The different frequencies of hMPV in patients in various age groups with upper and lower respiratory tract infections were compared, and the variance was found to be insignificant. In the 38 children who were hMPV positive, the majority (73.7 %) were from rural communities. The overall hMPV-positive rate was higher in the rural population than in the peri-urban population, but the difference was statistically insignificant. The youngest age at which hMPV-positive status was recorded was 5 months. Conclusion: This study demonstrated that hMPV was associated with a significant number (i.e. >10 %) of ARTIs in children in South India, whereas a relatively smaller number of HBoV infections was observed. © 2013 Springer International Publishing Switzerland. Source


Nandagopal B.,Sri Sakthi Amma Institute of Biomedical Research | Sankar S.,Sri Sakthi Amma Institute of Biomedical Research | Sagadevan K.,Sri Sakthi Amma Institute of Biomedical Research | Arumugam H.,Sri Narayani Hospital and Research Center | And 4 more authors.
Indian Journal of Medical Microbiology | Year: 2015

Extended-spectrum beta-lactamase (ESBL) producing strains of Coliform bacilli are on the rise and present a major threat especially in India. We assessed the frequency of ESBL producers among urinary isolates from patients presenting urinary tract infections. ESBL screening was done using Double Disk Synergy Test (DDST) and confirmed using E-test and Polymerase Chain Reaction (PCR). With E-test, 92.2% were positive for ESBL. In PCR, 100% strains were positive for any of the three gene targets tested. CTX-M was positive in majority of the strains followed by TEM and SHV. Two (3.22%) strains were positive for all the three genes; 21% strains were positive for both TEM and CTX-M genes. There was no statistically significant difference in the findings of E-test and PCR testing in the determination of ESBL producers (Fisher exact test P = 0.15). The strength of agreement between them was 'fair' (k = 0.252). Continuous monitoring of ESBL producers among Indian strains is important to rationalize the antibiotic policy to be followed. Source


Sankar S.,Sri Sakthi Amma Institute of Biomedical Research | Vadivel K.,Sri Sakthi Amma Institute of Biomedical Research | Nandagopal B.,Sri Sakthi Amma Institute of Biomedical Research | Jesudason M.V.,Sri Sakthi Amma Institute of Biomedical Research | Sridharan G.,Sri Sakthi Amma Institute of Biomedical Research
Molecular Diagnosis and Therapy | Year: 2014

Background and Objectives: Salmonella typhi, Mycobacterium tuberculosis, and Burkholderia pseudomallei are among the most important monocyte-tropic bacterial agents causing pyrexia of unknown origin (PUO), with a significant number of endemic infections in both South and Southeast Asian regions. These infections pose a major risk to travelers to these regions as well. Methods: We developed and evaluated a multiplex nested polymerase chain reaction (PCR) for the simultaneous detection of the three pathogens in 305 patients' buffy coat samples. Results: The assay for S. typhi and B. pseudomallei was able to detect down to 1 colony forming unit/5 μL PCR input and M. tuberculosis was detected down to 20 genome copies/5 μL PCR input. S. typhi was detected in 10 (3.3 %) individuals, B. pseudomallei in 10 individuals (3.3 %), and M. tuberculosis in 18 individuals (5.9 %). Co-infections of M. tuberculosis and B. pseudomallei were detected in three individuals and S. typhi and B. pseudomallei in two individuals. Conclusion: This protocol is efficient for PUO diagnosis especially in Asian countries. © 2013 Springer International Publishing. Source

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