Laboratory Diagnosis of SARS Corona Virus-2 Infection: Single Centre Experience of First 12,000 Samples

Introduction: First spotted in Wuhan, China, World Health Organisation declared the deadly outbreak caused by novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2) as global pandemic on March 11, 2020. With over 72 million cases globally till December 2020, countries need to gear up to detect, isolate and treat Corona Virus Disease-2019 (COVID-19) cases. Laboratories play a crucial role in diagnosis thereby instituting early contact tracing and quarantine measures. The laboratory based COVID-19 diagnostic testing data may help in formulating strategies to contain the spread of infection. Aim: To describe key patient variables of the respiratory samples processed for SARS-CoV-2 by Real Time Polymerase Chain Reaction (RT-PCR) at a diagnostic laboratory. Materials and Methods: In this descriptive, single centre study carried out at ICMR approved COVID-19 diagnostic laboratory, nasopharyngeal swabs received in Viral Transport Medium (VTM) were tested for SARS-CoV-2 infection by RT-PCR. Key patient variables, like age, gender, symptoms and sample positivity rate were tabulated. The demographic and clinical data of samples tested were summarised by medians and Interquartile Range (IQR) for continuous variables and by proportions for categorical variables. Results: A total of 12,187 samples were received between 21st March to 8th July 2020. The data from 11,196 individuals were complete and were included in the analysis. Overall, 2,053 samples were tested positive for SARS-CoV-2 indicating positivity rate of 18.33%. Sample positivity was highest (63.91%) among high-risk contacts of a laboratory confirmed case. The maximum number of samples tested belonged to age group of 21-40 years and male predominance was observed. Conclusion: Although social distancing, mask usage, hand hygiene and respiratory etiquettes are important measures for containment of COVID-19, strengthening and capacity building of laboratory network is crucial for mitigating the pandemic.

Whole genome sequence of colistin-resistant Escherichia coli from western India

Background

With virtually dried out new antibiotic discovery pipeline, emergence and spread of antimicrobial resistance is a cause for global concern. Colistin, a cyclic polypeptide antibiotic, often regarded as last resort for multi drug resistance gram-negative bacteria, is also rendered ineffective by horizontal transfer of resistance genes. Surveillance of colistin resistance in GNB is essential to ascertain molecular epidemiology.

Methods

Whole genome sequencing (WGS) of an unusual colistin resistant urinary isolate of Escherichia coli was performed using Illumina MiSeq platform using 2x250bp V2 chemistry by following the manufactures protocol (Illumina Inc. USA). Multiple web-based bio-informatic tools were utilized to ascertain antibiotic resistant genes.

Results

An approximate 5.4 Mb of genome of the urinary isolate AFMC_UC19 was sequenced successfully. Mobile colistin resistance gene (mcr) on the plasmid responsible for horizontal spread was absent in the isolate.

Conclusion

Colistin resistance has been reported previously in Klebsiella pneumoniae and it is a rare occurrence in Escherichia coli in Indian setting. Although the isolate lack mcr mediated colistin resistance, emergence and spread of colistin resistant in gram-negative bacteria pose a threat.

Molecular characterization and phylogenetic analysis of Chikungunya virus from Delhi, India

Background

Chikungunya virus is an alpha virus with high similarity to Dengue and Zika viruses, both in transmission cycle and in clinical presentation. Chikungunya is a re-emerging mosquito-borne infection known to cause small to very large outbreaks/epidemics at frequent intervals. In 2016, India witnessed a large outbreak of Chikungunya infection affecting more than 58,000 people. This study was undertaken to look at the genotypic phylogeny to know the relatedness with previously reported strains.

Methods

During the 2016 outbreak, samples from all patients clinically suspected to have Chikungunya were collected and subjected to testing for IgM antibody by ELISA and viral RNA detection by RT-PCR. Sequencing of the E1 gene segment was done to create a phylogenetic tree comparison with other strains.

Results

Serum samples were collected from 142 patients of clinically suspected Chikungunya infection. Majority of the patients were in the age group of 31-50 years accounting for more than 35% of the total cases. Twenty eight samples were positive for IgM antibody. Thirty seven samples were positive for viral RNA by RT-PCR. Only 06 cases were positive by both tests. Mutations in the amino acids K211E, M269V and D284E in the E1 gene segment of the Chikungunya virus were observed in the seven strains that were sequenced. On phylogeny tree, all the strains were found to belong to the ECSA genotype.

Conclusion

Actively searching for the potential epidemic causing mutations and reporting of novel mutations may help in better understanding and probably forecasting of future CHIKV outbreaks and its nature.

Molecular detection of blaNDM-1 (New Delhi metallobetalactamase-1) in nosocomial Enterobacteriaceae isolates by nested, multiplex polymerase chain reaction

BACKGROUND

Carbapenems are considered "drugs of last resort" in many life-threatening infections. Advent of carbapenemases like KPC, OXA-48, VIM, IMP, and NDM have greatly affected the efficacy of these drugs, posing serious threat to global health and infection control. NDM bears special significance to the India subcontinent, labeled as place of origin and reservoir. NDM tends to escape detection by routine phenotypic methods, requiring molecular confirmation. This study utilizes nested, multiplex polymerase chain reaction (PCR) for reliable detection of bla_NDM-1 in nosocomial Enterobacteriaceae isolates.

METHODS

This study was conducted to detect prevalence of bla_NDM-1, bla_IMP, bla_VIMand bla_KPC genes by multiplex PCR among multidrug/carbapenem-resistant nosocomial Enterobacteriaceae isolates. From March 2013 to April 2014, 100 consecutive non-repeat isolates of Enterobacteriaceae from various inpatient clinical samples were analyzed. Imipenem-resistant isolates identified by Kirby Bauer disk diffusion method with Clinical and Laboratory Standards Institute guidelines were further subjected to nested, multiplex PCR to simultaneously detect bla_NDM-1, bla_IMP, bla_VIMand bla_KPC genes.

RESULTS

Out of 100 isolates, 17 (17%) were found to be imipenem-resistant. bla_NDM-1 was detected in all 17 isolates by nested, multiplex PCR. bla_VIM was co-carried in 4 isolates while one isolate co-harbored bla_IMP with bla_NDM-1. Imipenem resistance and NDM-1 carriage was predominant amongst Klebsiella isolates. Maximum NDM-1 producers were isolated from the intensive care unit (70.6%).

CONCLUSION

NDM-1 prevalence in nosocomial Enterobacteriaceae isolates in our hospital was found to be 17%. A nested, multiplex PCR was used for rapid detection of various carbapenemase genes with high sensitivity and specificity which is essential not only for favorable patient outcome but also for timely implementation of appropriate infection control practices to prevent further spread of such organisms.