Azithromycin for Bacterial Watery Diarrhea: A Reanalysis of the AntiBiotics for Children With Severe Diarrhea (ABCD) Trial Incorporating Molecular Diagnostics.

BACKGROUND: Bacterial pathogens cause substantial diarrhea morbidity and mortality among children living in endemic settings, yet antimicrobial treatment is only recommended for dysentery or suspected cholera. METHODS: AntiBiotics for Children with severe Diarrhea was a 7-country, placebo-controlled, double-blind efficacy trial of azithromycin in children 2-23 months of age with watery diarrhea accompanied by dehydration or malnutrition. We tested fecal samples for enteric pathogens utilizing quantitative polymerase chain reaction to identify likely and possible bacterial etiologies and employed pathogen-specific cutoffs based on genomic target quantity in previous case-control diarrhea etiology studies to identify likely and possible bacterial etiologies. RESULTS: Among 6692 children, the leading likely etiologies were rotavirus (21.1%), enterotoxigenic Escherichia coli encoding heat-stable toxin (13.3%), Shigella (12.6%), and Cryptosporidium (9.6%). More than one-quarter (1894 [28.3%]) had a likely and 1153 (17.3%) a possible bacterial etiology. Day 3 diarrhea was less common in those randomized to azithromycin versus placebo among children with a likely bacterial etiology (risk difference [RD]likely, -11.6 [95% confidence interval {CI}, -15.6 to -7.6]) and possible bacterial etiology (RDpossible, -8.7 [95% CI, -13.0 to -4.4]) but not in other children (RDunlikely, -0.3% [95% CI, -2.9% to 2.3%]). A similar association was observed for 90-day hospitalization or death (RDlikely, -3.1 [95% CI, -5.3 to -1.0]; RDpossible, -2.3 [95% CI, -4.5 to -.01]; RDunlikely, -0.6 [95% CI, -1.9 to .6]). The magnitude of risk differences was similar among specific likely bacterial etiologies, including Shigella. CONCLUSIONS: Acute watery diarrhea confirmed or presumed to be of bacterial etiology may benefit from azithromycin treatment. CLINICAL TRIALS REGISTRATION: NCT03130114.

Colistin resistance in carbapenem non-susceptible Acinetobacter baumanii in a tertiary care hospital in India: clinical characteristics, antibiotic susceptibility and molecular characterization.

INTRODUCTION: Acinetobacter baumanii (AB) is a bacterium of concern in the hospital setup due to its ability to thrive in unfavorable conditions and the rapid emergence of antibiotic resistance. Carbapenem resistance in this organism is disheartening, further clouded by the emergence of colistin resistance. AIM: The present prospective study aims to note the epidemiology, molecular profile, and clinical outcome of patients with colistin resistance AB infections in a multispecialty tertiary care setup in Odisha, Eastern India. METHODS: All AB strains received from March 2021 to February 2022, identified by Vitek2 (Biomerieux) and confirmed by oxa-51 genes, were included. Carbapenem and colistin resistance were identified as per CLSI guidelines. Known mutations for blaOXA-23-like, blaIMP, blaVIM, blaKP, lpxA, lpxC, pmrA, pmrB, and plasmid mediated mcr (mcr1-5) were screened by conventional PCR techniques. The clinical outcome was noted retrospectively from case sheets. Data was entered in MS Excel and tabulated using SPSS software. RESULTS: In the study period, 350 AB were obtained, of which 317(90.5%) were carbapenem resistant (CRAB). Among the CRAB isolates, 19 (5.9%) were colistin resistant (ABCoR). The most valuable antibiotics in the study were tigecycline (65.4% in ABCoI; 31.6% in ABCoR) and minocycline (44.3% in CI; 36.8% in CR). There was a significant difference in mortality among ABCoI and ABCoR infections. bla OXA was the predominant carbapenem resistance genotype, while pmrA was the predominant colistin resistant genotype. There were no plasmid mediated mcr genes detected in the present study.

Intussusception after Rotavirus Vaccine Introduction in India.

BACKGROUND: A three-dose, oral rotavirus vaccine (Rotavac) was introduced in the universal immunization program in India in 2016. A prelicensure trial involving 6799 infants was not large enough to detect a small increased risk of intussusception. Postmarketing surveillance data would be useful in assessing whether the risk of intussusception would be similar to the risk seen with different rotavirus vaccines used in other countries. METHODS: We conducted a multicenter, hospital-based, active surveillance study at 27 hospitals in India. Infants meeting the Brighton level 1 criteria of radiologic or surgical confirmation of intussusception were enrolled, and rotavirus vaccination was ascertained by means of vaccination records. The relative incidence (incidence during the risk window vs. all other times) of intussusception among infants 28 to 365 days of age within risk windows of 1 to 7 days, 8 to 21 days, and 1 to 21 days after vaccination was evaluated by means of a self-controlled case-series analysis. For a subgroup of patients, a matched case-control analysis was performed, with matching for age, sex, and location. RESULTS: From April 2016 through June 2019, a total of 970 infants with intussusception were enrolled, and 589 infants who were 28 to 365 days of age were included in the self-controlled case-series analysis. The relative incidence of intussusception after the first dose was 0.83 (95% confidence interval [CI], 0.00 to 3.00) in the 1-to-7-day risk window and 0.35 (95% CI, 0.00 to 1.09) in the 8-to-21-day risk window. Similar results were observed after the second dose (relative incidence, 0.86 [95% CI, 0.20 to 2.15] and 1.23 [95% CI, 0.60 to 2.10] in the respective risk windows) and after the third dose (relative incidence, 1.65 [95% CI, 0.82 to 2.64] and 1.08 [95% CI, 0.69 to 1.73], respectively). No increase in intussusception risk was found in the case-control analysis. CONCLUSIONS: The rotavirus vaccine produced in India that we evaluated was not associated with intussusception in Indian infants. (Funded by the Bill and Melinda Gates Foundation and others.).

Characterizing Environmental Surveillance Sites in Nigeria and Their Sensitivity to Detect Poliovirus and Other Enteroviruses.

BACKGROUND: Environmental surveillance (ES) for poliovirus is increasingly important for polio eradication, often detecting circulating virus before paralytic cases are reported. The sensitivity of ES depends on appropriate selection of sampling sites, which is difficult in low-income countries with informal sewage networks. METHODS: We measured ES site and sample characteristics in Nigeria during June 2018-May 2019, including sewage physicochemical properties, using a water-quality probe, flow volume, catchment population, and local facilities such as hospitals, schools, and transit hubs. We used mixed-effects logistic regression and machine learning (random forests) to investigate their association with enterovirus isolation (poliovirus and nonpolio enteroviruses) as an indicator of surveillance sensitivity. RESULTS: Four quarterly visits were made to 78 ES sites in 21 states of Nigeria, and ES site characteristic data were matched to 1345 samples with an average enterovirus prevalence among sites of 68% (range, 9%-100%). A larger estimated catchment population, high total dissolved solids, and higher pH were associated with enterovirus detection. A random forests model predicted "good" sites (enterovirus prevalence >70%) from measured site characteristics with out-of-sample sensitivity and specificity of 75%. CONCLUSIONS: Simple measurement of sewage properties and catchment population estimation could improve ES site selection and increase surveillance sensitivity.

An overview of colistin resistance: A breach in last line defense.

Rising prevalence of antibiotic resistance and the unavailability of newer drugs to tackle this menace is one of the major hindrances to the goal of health and well-being set up by the General Assembly of the United Nations. The genes responsible for this resistance are often disseminated from hospitals to different environmental sources. In 2015, for the first time, resistance to Colistin was detected caused by chromosomal genetic mutations. Later, plasmid-mediated colistin resistance (MCR-1 to MCR-10) was detected, first from China and then from various other countries. As per Clinical and Laboratory Standards Institute (CLSI), commonly available diffusion techniques cannot detect colistin resistance appropriately. Even commercial susceptibility systems fail in this regard. Keeping in mind the importance of surveillance of colistin-resistant bugs, we present an update on the prevalence, mechanism of resistance, and detection.

Seroprevalence of SARS-CoV-2 in Bhubaneswar, India: findings from three rounds of community surveys.

The study aims to estimate and compare the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seroprevalence, the fraction of asymptomatic or subclinical infections in the population, determine the demographic risk factors and analyse the antibody development at different time points among adults in Bhubaneswar city, India. This was a serial three-round cross-sectional, community-based study where participants were selected from the residents of Bhubaneswar city using multi-stage random sampling. Blood samples were collected during household visits along with demographic and clinical data from every participant. Total anti-SARS-CoV-2 antibody present in serum was assessed using the electro-chemiluminescence immunoassay platform. Temporal comparisons of the community seroprevalence were performed against the detected number of cumulative cases, active cases, recoveries and deaths. A total of 3693 participants were enrolled in this study with a cumulative non-response rate of 18.33% in all the three rounds. The gender-weighted seroprevalence for the city in the first round was 1.55% (95% confidence interval (CI) 0.84-2.58), second round was 5.27% (95% CI 4.13-6.59) and in the third round was 49.04% (95% CI 46.39-51.68). In the first round, the seroprevalence was found to be highest in the elderly population, whereas the seroprevalence for the second and third phases was highest in the age group of 30-39 years. Seroprevalence showed an increasing trend over the three time periods, with the highest seropositivity rates among individuals sampled between 16 and 18 September 2020. By the third round, 93.93% of those who had previously been tested positive by real-time reverse transcription polymerase chain reaction had seroconversion and 46.57% of those who had been tested negative also showed seroconversion. Infection to case ratio during first round was 27.05, for second round and third round it was 5.62 and 17.91, respectively.

Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing.

Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR, and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived, and wild-type polioviruses and to ensure an appropriate response. This cell culture algorithm takes 2 to 3 weeks on average between sample receipt and sequencing. Direct detection of viral RNA using PCR allows faster detection but has traditionally faced challenges related to poor sensitivity and difficulties in sequencing common samples containing poliovirus and enterovirus mixtures. We present a nested PCR and nanopore sequencing protocol that allows rapid (<3 days) and sensitive direct detection and sequencing of polioviruses in stool and environmental samples. We developed barcoded primers and a real-time analysis platform that generate accurate VP1 consensus sequences from multiplexed samples. The sensitivity and specificity of our protocol compared with those of cell culture were 90.9% (95% confidence interval, 75.7% to 98.1%) and 99.2% (95.5% to 100.0%) for wild-type 1 poliovirus, 92.5% (79.6% to 98.4%) and 98.7% (95.4% to 99.8%) for vaccine and vaccine-derived serotype 2 poliovirus, and 88.3% (81.2% to 93.5%) and 93.2% (88.6% to 96.3%) for Sabin 1 and 3 poliovirus alone or in mixtures when tested on 155 stool samples in Pakistan. Variant analysis of sequencing reads also allowed the identification of polioviruses and enteroviruses in artificial mixtures and was able to distinguish complex mixtures of polioviruses in environmental samples. The median identity of consensus nanopore sequences with Sanger or Illumina sequences from the same samples was >99.9%. This novel method shows promise as a faster and safer alternative to cell culture for the detection and real-time sequencing of polioviruses in stool and environmental samples.

Severe acute respiratory illness surveillance for coronavirus disease 2019, India, 2020.

Background & objectives: Sentinel surveillance among severe acute respiratory illness (SARI) patients can help identify the spread and extent of transmission of coronavirus disease 2019 (COVID-19). SARI surveillance was initiated in the early phase of the COVID-19 outbreak in India. We describe here the positivity for COVID-19 among SARI patients and their characteristics. Methods: SARI patients admitted at 41 sentinel sites from February 15, 2020 onwards were tested for COVID-19 by real-time reverse transcription-polymerase chain reaction, targeting E and RdRp genes of SARS-CoV-2. Data were extracted from Virus Research and Diagnostic Laboratory Network for analysis. Results: A total of 104 (1.8%) of the 5,911 SARI patients tested were positive for COVID-19. These cases were reported from 52 districts in 20 States/Union Territories. The COVID-19 positivity was higher among males and patients aged above 50 years. In all, 40 (39.2%) COVID-19 cases did not report any history of contact with a known case or international travel. Interpretation & conclusions: COVID-19 containment activities need to be targeted in districts reporting COVID-19 cases among SARI patients. Intensifying sentinel surveillance for COVID-19 among SARI patients may be an efficient tool to effectively use resources towards containment and mitigation efforts.

Healthcare workers & SARS-CoV-2 infection in India: A case-control investigation in the time of COVID-19.

BACKGROUND & OBJECTIVES: Healthcare workers (HCWs) are at an elevated risk of contracting COVID-19. While intense occupational exposure associated with aerosol-generating procedures underlines the necessity of using personal protective equipment (PPE) by HCWs, high-transmission efficiency of the causative agent [severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)] could also lead to infections beyond such settings. Hydroxychloroquine (HCQ), a repurposed antimalarial drug, was empirically recommended as prophylaxis by the National COVID-19 Task Force in India to cover such added risk. Against this background, the current investigation was carried out to identify the factors associated with SARS-CoV-2 infection among HCWs in the country. METHODS: A case-control design was adopted and participants were randomly drawn from the countrywide COVID-19 testing data portal maintained by the ICMR. The test results and contact details of HCWs, diagnosed as positive (cases) or negative (controls) for SARS-CoV-2 using real-time reverse transcription-polymerase chain reaction (qRT-PCR), were available from this database. A 20-item brief-questionnaire elicited information on place of work, procedures conducted and use of PPE. RESULTS: Compared to controls, cases were slightly older (34.7 vs. 33.5 yr) and had more males (58 vs. 50%). In multivariate analyses, HCWs performing endotracheal intubation had higher odds of being SARS-CoV-2 infected [adjusted odds ratio (AOR): 4.33, 95% confidence interval (CI): 1.16-16.07]. Consumption of four or more maintenance doses of HCQ was associated with a significant decline in the odds of getting infected (AOR: 0.44; 95% CI: 0.22-0.88); a dose-response relationship existed between frequency of exposure to HCQ and such reductions (χ[2] for trend=48.88; P <0.001). In addition, the use of PPE was independently associated with the reduction in odds of getting infected with SARS-CoV-2. INTERPRETATIONS & CONCLUSIONS: Until results of clinical trials for HCQ prophylaxis become available, this study provides actionable information for policymakers to protect HCWs at the forefront of COVID-19 response. The public health message of sustained intake of HCQ prophylaxis as well as appropriate PPE use need to be considered in conjunction with risk homoeostasis operating at individual levels.

Pooled testing for COVID-19 diagnosis by real-time RT-PCR: A multi-site comparative evaluation of 5- & 10-sample pooling.

BACKGROUND & OBJECTIVES: Public health and diagnostic laboratories are facing huge sample loads for COVID-19 diagnosis by real-time reverse transcription-polymerase chain reaction (RT-PCR). High sensitivity of optimized real-time RT-PCR assays makes pooled testing a potentially efficient strategy for resource utilization when positivity rates for particular regions or groups of individuals are low. We report here a comparative analysis of pooled testing for 5- and 10-sample pools by real-time RT-PCR across 10 COVID-19 testing laboratories in India. METHODS: Ten virus research and diagnostic laboratories (VRDLs) testing for COVID-19 by real-time RT-PCR participated in this evaluation. At each laboratory, 100 nasopharyngeal swab samples including 10 positive samples were used to create 5- and 10-sample pools with one positive sample in each pool. RNA extraction and real-time RT-PCR for SARS-CoV-2-specific E gene target were performed for individual positive samples as well as pooled samples. Concordance between individual sample testing and testing in the 5- or 10-sample pools was calculated, and the variation across sites and by sample cycle threshold (Ct) values was analyzed. RESULTS: A total of 110 each of 5- and 10-sample pools were evaluated. Concordance between the 5-sample pool and individual sample testing was 100 per cent in the Ct value ≤30 cycles and 95.5 per cent for Ctvalues ≤33 cycles. Overall concordance between the 5-sample pooled and individual sample testing was 88 per cent while that between 10-sample pool and individual sample testing was 66 per cent. Although the concordance rates for both the 5- and 10-sample pooled testing varied across laboratories, yet for samples with Ct values ≤33 cycles, the concordance was ≥90 per cent across all laboratories for the 5-sample pools. INTERPRETATION & CONCLUSIONS: Results from this multi-site assessment suggest that pooling five samples for SARS-CoV-2 detection by real-time RT-PCR may be an acceptable strategy without much loss of sensitivity even for low viral loads, while with 10-sample pools, there may be considerably higher numbers of false negatives. However, testing laboratories should perform validations with the specific RNA extraction and RT-PCR kits in use at their centres before initiating pooled testing.