An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

To explore the natural microbial community of any ecosystems by high-resolution molecular approaches including next generation sequencing, it is extremely important to develop a sensitive and reproducible DNA extraction method that facilitate isolation of microbial DNA of sufficient purity and quantity from culturable and uncultured microbial species living in that environment. Proper lysis of heterogeneous community microbial cells without damaging their genomes is a major challenge. In this study, we have developed an improved method for extraction of community DNA from different environmental and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved method has been named as the THSTI method to depict the Institute where the method was developed

Genomic plasticity associated with antimicrobial resistance in Vibrio cholerae.

The Bay of Bengal is known as the epicenter for seeding several devastating cholera outbreaks across the globe. Vibrio cholerae, the etiological agent of cholera, has extraordinary competency to acquire exogenous DNA by horizontal gene transfer (HGT) and adapt them into its genome for structuring metabolic processes, developing drug resistance, and colonizing the human intestine. Antimicrobial resistance (AMR) in V. cholerae has become a global concern. However, little is known about the identity of the resistance traits, source of AMR genes, acquisition process, and stability of the genetic elements linked with resistance genes in V. cholerae Here we present details of AMR profiles of 443 V. cholerae strains isolated from the stool samples of diarrheal patients from two regions of India. We sequenced the whole genome of multidrug-resistant (MDR) and extensively drug-resistant (XDR) V. cholerae to identify AMR genes and genomic elements that harbor the resistance traits. Our genomic findings were further confirmed by proteome analysis. We also engineered the genome of V. cholerae to monitor the importance of the autonomously replicating plasmid and core genome in the resistance profile. Our findings provided insights into the genomes of recent cholera isolates and identified several acquired traits including plasmids, transposons, integrative conjugative elements (ICEs), pathogenicity islands (PIs), prophages, and gene cassettes that confer fitness to the pathogen. The knowledge generated from this study would help in better understanding of V. cholerae evolution and management of cholera disease by providing clinical guidance on preferred treatment regimens.DBT Indi

Ventilator associated pneumonia in a tertiary care hospital in India: Incidence, etiology, risk factors, role of multidrug resistant pathogens

Background: Ventilator associated pneumonia (VAP), a hospital acquired infection (HAI) is seen among critically ill patients on mechanical ventilation (MV) due to various causes, in intensive care units (ICUs). VAP increases morbidity, mortality, as well as the cost of healthcare. Materials and Methods: A prospective study was done over a period of 10 months in a tertiary care hospital in India to determine the incidence, etiological agents, their sensitivity profiles, and risk factors associated with VAP. Combination disc method, ethylenediaminetetraacetic acid (EDTA) disc synergy (EDS) tests, and AmpC disc tests were performed for detection of extended-spectrum beta-lactamases (ESBL), metallo-beta-lactamases (MBL), and AmpC beta-lactamases, respectively. Results: One hundred and forty adult patients, on MV for 48 h and more, were included and 28 (20%) developed VAP. The incidence density rate of VAP was 21.875 per 1,000 ventilator days. Most of the patients had late onset VAP (60.7%) with average number of days for onset around 8 days. Pseudomonas spp. and Acinetobacter spp. were significantly associated with late onset VAP, whereas Enterobacteriaceae, Staphylococcus aureus, Haemophilus influenzae, Streptococcus pneumoniae, Burkholderia cepacia, and Candida species were commonly isolated from early onset VAP. Polymicrobial infections occurred in 14 cases, so overall 43 VAP pathogens were isolated. Thirty (69.7%) of them were multidrug resistant (MDR), among which ESBL contributed 23.25%, MBL 30.23%, AmpC beta-lactamases 9.30%, and to methicillin resistant S. aureus (MRSA) contributed 6.97%. Prior antibiotic therapy (P < 0.0001), hospitalization for 5 days or more (P < 0.0001), MV for 5 days or more (P < 0.0001), supine head position (P < 0.0001), reintubation (P = 0.0012), and impaired consciousness (P = 0.0191) were significant risk factors for VAP. Conclusions: Proper knowledge of risk factors can help identify high risk groups for VAP, among the critically ill patients on MV. MDR pathogens, with production of ESBL, MBL, AmpC beta-lactamases, and MRSA were commonly associated with VAP. So, judicious use of antibiotic is recommended

A case report of nonhealing leg ulcer infected with Stenotrophomonas maltophilia in an immunocompetent patient in a Tertiary Care Hospital of Eastern India

Stenotrophomonas maltophilia is an aerobic, motile Gram-negative, nonfermentative bacillus considered as an opportunistic pathogen causing infection typically in individuals with immunosuppression, organ transplantation and malignancies. Contaminated water or medical devices in the hospital environment are the primary causes of infection. Here, we report a case of nonhealing leg ulcer infected with S. maltophilia in an immunocompetent individual

A case report of white grain eumycetoma caused by Scedosporium apiospermum in a tertiary care hospital of the Eastern India

Scedosporium apiospermum and its asexual state Pseudallecheria boydiiare increasingly recognized as an opportunistic pathogen. Here, we describe a white grain eumycetoma of left foot of a 48-year-old female caused by S. apiospermum. Treatment with oral voriconazole was successful