Integrated genomic view of SARS-CoV-2 in India.

Background: India first detected SARS-CoV-2, causal agent of COVID-19 in late January 2020, imported from Wuhan, China. From March 2020 onwards, the importation of cases from countries in the rest of the world followed by seeding of local transmission triggered further outbreaks in India. Methods: We used ARTIC protocol-based tiling amplicon sequencing of SARS-CoV-2 (n=104) from different states of India using a combination of MinION and MinIT sequencing from Oxford Nanopore Technology to understand how introduction and local transmission occurred. Results: The analyses revealed multiple introductions of SARS-CoV-2 genomes, including the A2a cluster from Europe and the USA, A3 cluster from Middle East and A4 cluster (haplotype redefined) from Southeast Asia (Indonesia, Thailand and Malaysia) and Central Asia (Kyrgyzstan). The local transmission and persistence of genomes A4, A2a and A3 was also observed in the studied locations. The most prevalent genomes with patterns of variance (confined in a cluster) remain unclassified, and are here proposed as A4-clade based on its divergence within the A cluster. Conclusions: The viral haplotypes may link their persistence to geo-climatic conditions and host response. Multipronged strategies including molecular surveillance based on real-time viral genomic data is of paramount importance for a timely management of the pandemic.

Epidemiological and microbiological profile of infective keratitis in Ahmedabad.

CONTEXT: Study of patients attending tertiary care ophthalmology institute at Ahmedabad. AIMS: To study the microbiological etiology and epidemiological factors associated with suppurative keratitis. SETTINGS AND DESIGN: A total of 150 corneal scrapings were evaluated from patients presenting with corneal ulcers at a tertiary ophthalmology center, Ahmedabad from July 2007 to June 2008. MATERIALS AND METHODS: Scrapings were subjected to Gram stain, potassium hydroxide preparation and culture for bacterial and fungal pathogens. Socio-demographic data and risk factors were recorded. RESULTS: Ninety percent (135/150) people with corneal ulcers had trauma as predisposing factor for keratitis. Trauma due to wooden objects was the leading cause (46/135) followed by vegetable matter and stone injury (23/135). Microbial etiology was established in 59.3% (89/150) of scrapings. Out of 89 positive isolates, 65.1% (58/89) were bacterial while 34.9% (31/89) were fungal. Among the bacterial isolates, 60.3% (35/58) were Gram-positive cocci while 39.7% (23/58) were Gram-negative bacilli. The most common bacterial isolate was Staphylococus aureus (32.7%, 19/58) followed by coagulase-negative Staphylococci (25.8%, 15/58) and Pseudomonas (18.9%, 11/58). Among the 31 fungal pathogens, Aspergillus species was the most common (35.4%11/31), followed by Fusarium species (22.5%, 7/31). CONCLUSION: Trauma with wooden material is the most common predisposing factor for suppurative keratitis. Males were more affected than females. Bacterial ulcers were more common than fungal in areas in and around Ahmedabad. Staphylococcus aureus and Aspergillus were the commonest bacterial and fungal isolates respectively. Geographical variation persists in microbial etiology of suppurative keratitis.

Comparative analysis of the Vitek 2 antifungal susceptibility system and E-test with the CLSI M27-A3 broth microdilution method for susceptibility testing of Indian clinical isolates of Cryptococcus neoformans.

The emergence of antifungal resistance among Cryptococcus neoformans isolates is a matter of great concern. The Clinical and Laboratory Standards Institute (CLSI) broth microdilution reference method (BMD) for antifungal susceptibility testing of C. neoformans is tedious and time-consuming. Consequently, there is a greater need for a reproducible in vitro susceptibility testing method for use in clinical microbiology laboratories. By random amplified polymorphic DNA analysis, the 62 Indian clinical isolates were characterized as Cryptococcus neoformans var. grubii. We evaluated the susceptibilities of these isolates for amphotericin B (AMB) and fluconazole (FLC) by two commercial techniques, i.e., Vitek 2 and E-test against the CLSI M27-A3 BMD. The essential agreement (EA) between the Vitek 2 and E-test with the reference procedure for FLC was similar (82.2%). For AMB, EA of 92 and 76% was obtained with E-test and Vitek 2. Excellent categorical agreement (CA) (98.3% and 100% by Vitek 2 and E-test, respectively) was obtained for AMB. The CA for FLC was 81 and 77.4% by Vitek 2 and E-test. We conclude that both E-test and Vitek 2 system have acceptable levels of accuracy for susceptibility testing of both the drugs. Both of them could identify fluconazole-resistant strains. Vitek 2 could be used for testing susceptibility of voriconazole and 5-flucytosine also at the same time.