Forensic Microbiology in India: A missing piece in the puzzle of criminal investigation system.

BACKGROUND: Forensic Microbiology is an emerging branch of science that has great potential to assist criminal investigations. Having said that, microbial analysis is not performed routinely during forensic investigations in India. This could be attributed to lack of specific training and lack of evidence-based standard protocol. OBJECTIVES: The authors attempt to highlight the key areas in forensic microbiology that need to be explored in a developing nation like India. CONTENT: Forensic microbiology could help in linking a person to a crime, determining the cause of death, estimating postmortem interval (PMI), etc. Additionally, applications are being developed by forensic microbiologists across the globe to investigate the coordinated and dynamic changes in microbial activity which occur after the death of a human host. Such evidence from the human postmortem microbiome can aid in criminal investigations and administration of justice. These recent advances and developments have the potential to transform the field of forensic microbiology in a developing country.

Phage-based therapy against biofilm producers in gram-negative ESKAPE pathogens.

Persistent antibiotic use results in the rise of antimicrobial resistance with limited or no choice for multidrug-resistant (MDR) and extensively drug resistant (XDR) bacteria. This necessitates a need for alternative therapy to effectively combat clinical pathogens that are resistant to last resort antibiotics. The study investigates hospital sewage as a potential source of bacteriophages to control resistant bacterial pathogens. Eighty-one samples were screened for phages against selected clinical pathogens. Totally, 10 phages were isolated against A. baumannii, 5 phages against K. pneumoniae, and 16 phages were obtained against P. aeruginosa. The novel phages were observed to be strain-specific with complete bacterial growth inhibition of up to 6 h as monotherapy without antibiotics. Phage plus colistin combinations reduced the minimum-biofilm eradication concentration of colistin up to 16 folds. Notably, a cocktail of phages exhibited maximum efficacy with complete killing at 0.5-1 µg/ml colistin concentrations. Thus, phages specific to clinical strains have a higher edge in treating nosocomial pathogens with their proven anti-biofilm efficacy. In addition, analysis of phage genomes revealed close phylogenetic relations with phages reported from Europe, China, and other neighbouring countries. This study serves as a reference and can be extended to other antibiotics and phage types to assess optimum synergistic combinations to combat various drug resistant pathogens in the ongoing AMR crisis.

Indian microbiology EQAS registered laboratory's capacity building and infection control practices during the COVID-19 pandemic in India: Lessons learnt and gaps identified.

PURPOSE: The COVID-19 pandemic was unique in the history of outbreaks because of the massive scaling up of resources related to diagnostics, treatment modalities, and vaccines. To understand the impact of the pandemic among laboratory professionals, we aimed to conduct a survey to assess the improvement in the lab capacity post-covid in terms of infrastructure and accreditation status across various levels of hospitals and to determine the changes in the practice of infection control precautions during the pandemic. METHODS: This was an anonymous, online-based survey (using 58 item questionnaire) conducted between July 09, 2021, and August 07, 2021. The survey targeted all EQAS registered diagnostic laboratories located in India. RESULTS: The survey reached out to 1182 participants, out of which 721 (61%) laboratories completed the questionnaire. During pre-COVID times, only 39% (282/721) of the laboratories had an RT-PCR facility. Among these 721 labs, 514 used open system RT-PCR assay, 217 labs used Truenat assay, 188 labs used GeneXpert assay, 31 used Abbott ID Now and 350 labs performed rapid antigen tests. During the pandemic, 55.3% got NABL accreditation and 7.4% were in the process of applying for COVID-19 molecular testing. In this, 80.7% of the laboratories participated in the ICMR - COVID quality control assessment. It was estimated that 41.4% of the laboratory professionals were re-using N95 masks. Overall, the infection prevention and control practices varied across each laboratory and hospital. CONCLUSION: These survey findings helped us to understand the strength and efficiency of laboratories in India in setting up new assays during a crisis time. Based on our findings, we propose to connect this network in a sustained manner to efficiently utilize the existing platforms to adapt to future pandemics.

Effectiveness of a monitored home isolation program for COVID-19 infection during the second wave of the pandemic.

Background: The rapidity of spread of COVID-19 infection during the second wave of the pandemic placed tremendous stress on healthcare resources. This study evaluated the effectiveness of a monitored home isolation (HI) program. Methods: In this descriptive longitudinal study, symptomatic patients were screened in the HI clinic and eligible patients were followed up at home using tele-consultation, until recovery or hospitalization. HI failure was defined as need for hospitalization. Factors associated with HI failure were assessed using logistic regression analysis and expressed as odds ratio (OR) with 95% confidence interval (CI). Results: During April and May 2021, 1957 RT-PCR confirmed patients (984 male) with mean (SD) age 40 (13.5) years were enrolled; 93.3% (n = 1825) were successfully managed at home. Of the 132 patients (6.7%) who failed HI, 57 (43.2%) required oxygen therapy and 23 needed intensive care admissions. Overall mortality was 0.4% (7/1957). On adjusted analysis, factors associated with HI failure were age ≥60 years (OR 2.24; 95%CI 1.26-3.99), male gender (OR 2.26; 95%CI 1.44-3.57), subjective reporting of breathing difficulty (OR 3.64; 95%CI 2.08-6.37), history of cough (OR 2.08; 95%CI 1.37-3.17), and higher heart rate (OR 1.04; 95%CI 1.02-1.05). Although patient status (non-healthcare workers), no prior vaccination and ≥2 comorbidities were associated with HI failure on unadjusted analysis, these were non-significant on adjusted analysis. Conclusion: Monitored HI program can be used successfully during a pandemic wave to judicially use scare hospital resources. Older male patients presenting with breathlessness or cough may warrant closer monitoring.

Epidemiological investigation of the COVID-19 outbreak in Vellore district in South India using Geographic Information Surveillance (GIS).

OBJECTIVES: Geographical Information Surveillance (GIS) is an advanced digital technology tool that maps location-based data and helps in epidemiological modeling. We applied GIS to analyze patterns of spread and hotspots of COVID-19 cases in the Vellore district in South India. METHODS: Laboratory-confirmed COVID-19 cases from the Vellore district and neighboring taluks from March 2020 to June 2021 were geocoded and spatial maps were generated. Time trends exploring urban-rural burden with an age-sex distribution of cases and other variables were correlated with outcomes. RESULTS: A total of 45,401 cases of COVID-19 were detected, with 20,730 cases during the first wave and 24,671 cases during the second wave. The overall incidence rates of COVID-19 were 462.8 and 588.6 per 100,000 population during the first and second waves, respectively. The spread pattern revealed epicenters in densely populated urban areas with radial spread sparing rural areas in the first wave. The case fatality rate was 1.89% and 1.6% during the first and second waves, which increased with advancing age. CONCLUSIONS: Modern surveillance systems like GIS can accurately predict the trends and spread patterns during future pandemics. In addition, real-time mapping can help design risk mitigation strategies, thereby preventing the spread to rural areas.

Protective effect conferred by prior infection and vaccination on COVID-19 in a healthcare worker cohort in South India.

BACKGROUND: The emergence of newer variants with the immune escape potential raises concerns about breakthroughs and re-infections resulting in future waves of infection. We examined the protective effect of prior COVID-19 disease and vaccination on infection rates among a cohort of healthcare workers (HCW) in South India during the second wave driven mainly by the delta variant. METHODS AND FINDINGS: Symptomatic HCWs were routinely tested by RT-PCR as per institutional policy. Vaccination was offered to all HCWs in late January, and the details were documented. We set up a non-concurrent cohort to document infection rates and estimated protective efficacy of prior infection and vaccination between 16th Apr to 31st May 2021, using a Cox proportional hazards model with time-varying covariates adjusting for daily incidence. Between June 2020 and May 2021, 2735 (23.9%) of 11,405 HCWs were infected, with 1412, including 32 re-infections, reported during the second wave. 6863 HCWs received two doses of vaccine and 1905 one dose. The protective efficacy of prior infection against symptomatic infection was 86.0% (95% CI 76.7%-91.6%). Vaccination combined with prior infection provided 91.1% (95% CI 84.1%-94.9%) efficacy. In the absence of prior infection, vaccine efficacy against symptomatic infection during the second wave was 31.8% (95% CI 23.5%- 39.1%). CONCLUSIONS: Prior infection provided substantial protection against symptomatic re-infection and severe disease during a delta variant driven second wave in a cohort of health care workers.

Campylobacter diarrhea in children in South Asia: A systematic review.

BACKGROUND: Campylobacter spp. are one of the commonest causes of diarrhea in children under five and in resource poor settings also lead to malabsorption and stunting. The purpose of this systematic review was to understand the burden of Campylobacter spp. associated diarrhea among children in the South Asian countries. METHODS: This systematic review followed the PRISMA (Preferred Reporting Items for Systematic reviews and Meta-Analysis) guidelines. Databases were searched with defined keywords for publications from the years 1998-2018. Data on proportion of positive samples was extracted to compare the rates of Campylobacter infection among children (under the age of 19) from different study populations. RESULTS: Of the 359 publications screened, 27 eligible articles were included in this systematic review and categorized based on study design. In 8 case-control studies, Campylobacter spp. was detected more frequently among diarrheal cases (range, 3.2-17.4%) than non-diarrheal cases (0-13%). Although there were variations in the study population, overall, children under the age of two years experienced Campylobacter diarrhea more often than older children. Most studies reported stool culture as the method used to detect Campylobacter spp. however retesting using PCR-based methods significantly increased detection rates. Limited data were available on Campylobacter species. In 4 studies that provided species data, C. jejuni (3.2-11.2%) was shown to be the most common species, followed by C. coli. CONCLUSION: In South Asia, Campylobacter spp. are one of the most common bacterial diarrheal pathogens affecting children but there is a paucity of data on species, risk factors and attributable sources. Although a few studies were available, the epidemiology of campylobacteriosis remains uncertain. To understand the true burden and sources of infection, more detailed studies are needed collecting data from human, animal and environmental sources and using both culture and genomic tools.

Transmission Dynamics of COVID-19 and Utility of Contact Tracing in Risk Assessment of Health-Care Worker Exposure during COVID-19 Pandemic.

Background: In the COVID-19 pandemic, the frontline health-care workers (HCWs) are at increased risk of acquiring infection either through household or workplace exposure. Objectives: To assess the risk of acquiring infection after COVID-19 exposure, we evaluated the effectiveness of a contact tracing assessment to identify the high-risk contacts. Materials and Methods: All HCW who tested COVID-19 positive in July 2020 were interviewed to do risk assessment based on their exposure, advised quarantine, and then followed up on day 14 for development of symptoms of COVID-19. Results: Contact tracing identified 2569 HCW contacts for 422 index positive cases, among which 1642 (63.9%) were contactable for follow-up. Among 1642 contacts, 12.97% developed COVID-19 symptoms within 14 days of the exposure. Household contacts comprising (142 out of 956, 14.9%) had a higher risk of becoming symptomatic than workplace contacts (71 out of 686, 10.3%) ([odds ratio 0.66 (confidence interval 0.49-0.89)]. Of these, 76.6% of the household exposure and 55.4% of significant workplace exposure were tested positive for COVID-19. Conclusions: Based on the risk assessment, we found that a HCW is likely to acquire infection at home rather than at the workplace, and hence, an appropriate quarantine policy can help decrease the transmission and mitigate staff shortage.

Factors associated with mortality among moderate and severe patients with COVID-19 in India: a secondary analysis of a randomised controlled trial.

OBJECTIVE: Large data on the clinical characteristics and outcome of COVID-19 in the Indian population are scarce. We analysed the factors associated with mortality in a cohort of moderately and severely ill patients with COVID-19 enrolled in a randomised trial on convalescent plasma. DESIGN: Secondary analysis of data from a Phase II, Open Label, Randomized Controlled Trial to Assess the Safety and Efficacy of Convalescent Plasma to Limit COVID-19 Associated Complications in Moderate Disease. SETTING: 39 public and private hospitals across India during the study period from 22 April to 14 July 2020. PARTICIPANTS: Of the 464 patients recruited, two were lost to follow-up, nine withdrew consent and two patients did not receive the intervention after randomisation. The cohort of 451 participants with known outcome at 28 days was analysed. PRIMARY OUTCOME MEASURE: Factors associated with all-cause mortality at 28 days after enrolment. RESULTS: The mean (SD) age was 51±12.4 years; 76.7% were males. Admission Sequential Organ Failure Assessment score was 2.4±1.1. Non-invasive ventilation, invasive ventilation and vasopressor therapy were required in 98.9%, 8.4% and 4.0%, respectively. The 28-day mortality was 14.4%. Median time from symptom onset to hospital admission was similar in survivors (4 days; IQR 3-7) and non-survivors (4 days; IQR 3-6). Patients with two or more comorbidities had 2.25 (95% CI 1.18 to 4.29, p=0.014) times risk of death. When compared with survivors, admission interleukin-6 levels were higher (p<0.001) in non-survivors and increased further on day 3. On multivariable Fine and Gray model, severity of illness (subdistribution HR 1.22, 95% CI 1.11 to 1.35, p<0.001), PaO2/FiO2 ratio <100 (3.47, 1.64-7.37, p=0.001), neutrophil lymphocyte ratio >10 (9.97, 3.65-27.13, p<0.001), D-dimer >1.0 mg/L (2.50, 1.14-5.48, p=0.022), ferritin ≥500 ng/mL (2.67, 1.44-4.96, p=0.002) and lactate dehydrogenase ≥450 IU/L (2.96, 1.60-5.45, p=0.001) were significantly associated with death. CONCLUSION: In this cohort of moderately and severely ill patients with COVID-19, severity of illness, underlying comorbidities and elevated levels of inflammatory markers were significantly associated with death. TRIAL REGISTRATION NUMBER: CTRI/2020/04/024775.