Correlation of severity & clinical outcomes of COVID-19 with virus variants: A prospective, multicentre hospital network study.

BACKGROUND OBJECTIVES: The clinical course of COVID-19 and its prognosis are influenced by both viral and host factors. The objectives of this study were to develop a nationwide platform to investigate the molecular epidemiology of SARS-CoV-2 (Severe acute respiratory syndrome Corona virus 2) and correlate the severity and clinical outcomes of COVID-19 with virus variants. METHODS: A nationwide, longitudinal, prospective cohort study was conducted from September 2021 to December 2022 at 14 hospitals across the country that were linked to a viral sequencing laboratory under the Indian SARS-CoV-2 Genomics Consortium. All participants (18 yr and above) who attended the hospital with a suspicion of SARS-CoV-2 infection and tested positive by the reverse transcription-PCR method were included. The participant population consisted of both hospitalized as well as outpatients. Their clinical course and outcomes were studied prospectively. Nasopharyngeal samples collected were subjected to whole genome sequencing to detect SARS-CoV-2 variants. RESULTS: Of the 4972 participants enrolled, 3397 provided samples for viral sequencing and 2723 samples were successfully sequenced. From this, the evolution of virus variants of concern including Omicron subvariants which emerged over time was observed and the same reported here. The mean age of the study participants was 41 yr and overall 49.3 per cent were female. The common symptoms were fever and cough and 32.5 per cent had comorbidities. Infection with the Delta variant evidently increased the risk of severe COVID-19 (adjusted odds ratio: 2.53, 95% confidence interval: 1.52, 4.2), while Omicron was milder independent of vaccination status. The independent risk factors for mortality were age >65 yr, presence of comorbidities and no vaccination. INTERPRETATION CONCLUSIONS: The authors believe that this is a first-of-its-kind study in the country that provides real-time data of virus evolution from a pan-India network of hospitals closely linked to the genome sequencing laboratories. The severity of COVID-19 could be correlated with virus variants with Omicron being the milder variant.

Diagnostic utility and performance of rapid antigen test in SARS CoV- 2 in symptomatic and asymptomatic patients during the second pandemic wave in Kashmir, North India.

PURPOSE: Real time reverse transcriptase PCR (rRT PCR) although gold standard test for the diagnosis of SARS CoV-2, carries disadvantages of a sophisticated set up, long time to results and centralized services. The rapid antigen tests (RAT) can be used as a primary screening tool with the advantages of rapid turnaround time and ease of use. The study was conducted to determine the performance of rapid antigen test (standard Q COVID 19 Ag) in comparison to rRT PCR in symptomatic patients and asymptomatic contacts and asymptomatic patients with no apparent contact history. METHODS: Nasopharyngeal swabs taken in duplicate from 1034 patients were collected over a 5 months period. These included 248 (23.98%) symptomatic, 386 (37.34%) asymptomatic contacts and 400 (38.68%) asymptomatic subjects who were routinely screened in pre-operative period, as a prerequisite for travel, or pregnant females. Both rRT PCR and RAT were performed as per manufacturers' instructions. Performance of test in different subgroups of patients was evaluated. Performance of RAT test on basis of duration of illness and Ct values was also analyzed. RESULTS: In this study, 445 (43.04%) were rRT PCR positive, out of which 374 samples were RAT positive as well. 31 samples were RAT positive but PCR negative. The sensitivity, specificity, PPV and NPV of the rapid antigen test was 84.04%, 94.74%, 92.35% and 88.71% respectively. The negative predictive value of the test in asymptomatic patients without any significant contact history was 97.07%. CONCLUSIONS: This study recommends the use of the antigen test as a method of diagnosis for SARS CoV-2. However a negative result with RAT in suspected patients and their contacts should be viewed with caution. This study also finds the utility of using RAT test in the community settings as a screening test in schools, colleges and mass gatherings.

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.

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.