Dataset Information

Epidemiology and phylogenetic analysis of respiratory viruses from 2012 to 2015 - A sentinel surveillance report from union territory of Puducherry, India.

ABSTRACT: Background:Acute respiratory infections (ARI) are the most common illnesses affecting people of all ages worldwide. Viruses contribute to 30-70% of acute respiratory infections. Identification of these respiratory viruses is not given high priority except influenza; however, the knowledge about prevalence of non-influenza viruses, their seasonal pattern and genetic evolution have significant epidemiological value. Methods:As a part of National Influenza-like illness surveillance programme, respiratory specimens were collected children and adults with symptoms of ILI or ARI, between January 2012 and March 2015 (including SARI cases). Real-time PCR was done to identify 13 respiratory viruses. Sequencing was done for representative isolates of each virus using ABI 3730 Genetic Analyzer. Results:During the study period between January 2012 and March 2015, a total of 648 patients with symptoms of ARI were included in this study. The mean age of the patients was 20.2 years (SD = 19.13, median = 18); 292 (45.1%) were children (?13 years) and 356 (54.9%) were adults. Respiratory viruses were identified in 44% (287/648) of all patients. Influenza accounted for the maximum number of cases- 179/648 (27.6%). Among the non-influenza viruses, RSV predominated with 34 cases (5.2%), followed by HMPV 24 (3.7%) and PIV-3 20 (3%). Four patients died due to INF A/H1N1 (2012-2, 2015-2) as a result of acute respiratory distress syndrome (ARDS) (CFR 3.7%). Among the non-influenza viruses, no particular seasonality pattern was observed over the different months of the study period. Conclusion:Antibiotic usage in treating acute respiratory infections empirically is not justified as nearly half of ARI are due to viruses; nearly 28% of them were due to influenza viruses. Among the non-influenza viruses, RSV predominated, followed by HMPV. This study is based on an active influenza surveillance initiated after 2009 pandemic influenza outbreak, in the Union territory of Puducherry which has contributed significantly to the knowledge of the burden of influenza and non-influenza viruses among children and adults. Such surveillance network has paved the way for better diagnosis and timely therapeutic interventions.

SUBMITTER: Palani N

PROVIDER: S-EPMC7187823 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Epidemiology and phylogenetic analysis of respiratory viruses from 2012 to 2015 - A sentinel surveillance report from union territory of Puducherry, India.

Palani Nandhini N Sistla Sujatha S

Clinical epidemiology and global health 20200428 4

<h4>Background</h4>Acute respiratory infections (ARI) are the most common illnesses affecting people of all ages worldwide. Viruses contribute to 30-70% of acute respiratory infections. Identification of these respiratory viruses is not given high priority except influenza; however, the knowledge about prevalence of non-influenza viruses, their seasonal pattern and genetic evolution have significant epidemiological value.<h4>Methods</h4>As a part of National Influenza-like illness surveillance p ...[more]

PMID: 32346655

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Project description:Background In 2015, antimicrobial resistance was identified as a public health priority for the South-Western Indian Ocean (SWIO) (i.e. Comoros, Madagascar, Mauritius, Mayotte (France), Reunion Island (France), and Seychelles). However, in 2020, colonization rates of antimicrobial-resistant bacteria (ARB) in human populations on most islands in SWIO were still not known and neither hospital nor community colonization rates had been estimated. The aim of this study was to estimate the prevalence of colonization of six ARB groups in hospitalized patients residing in the SWIO territories. The six groups comprise extended-spectrum betalactamase producing Enterobacteriaceae (ESBL-E), carbapenem-resistant Enterobacteriaceae (CRE), methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and both ceftazidime and/or imipenem-resistant Acinetobacter spp. (ACB), and ceftazidime and/or imipenem-resistant Pseudomonas spp. (PSA)). Methods Based on comprehensive hospital laboratory ARB screening data, we provide the first estimation of ARB colonization rates in hospitalized patients residing in SWIO (2015–2017). Using ARB colonization rates in Reunion Island (France) as the reference for estimating odds ratio, we identified at risk patients based on their territory of residence. Results The survey pointed to significantly higher overall ARB colonization rates in patients from Comoros, Madagascar, Mayotte, and Seychelles compared to Reunion Island as the reference. Extended-spectrum betalactamase producing Enterobacteriaceae was found to be the most common ARB group colonizing patients from SWIO territories. The highest MRSA colonization rates were observed in patients from Mayotte and Seychelles. Colonization by carbapenem-resistant Enterobacteriaceae (CRE) was highest in patients from Mauritius. Conclusion These results identify high ARB colonization rates in hospitalized patients from SWIO territories that require further investigation, particularly CRE in Mauritius and MRSA in Seychelles and Mayotte. This study is the first step toward the implementation of a broader regional ARB surveillance system.

Project description:Salmonella Typhi (S. Typhi) is the causative agent of typhoid fever; a systemic disease affecting ~20 million people per year globally. There are little data regarding the contemporary epidemiology of typhoid in Latin America. Consequently, we aimed to describe some recent epidemiological aspects of typhoid in Colombia using cases reported to the National Public Health Surveillance System (Sivigila) between 2012 and 2015. Over the four-year reporting period there were 836 culture confirmed cases of typhoid in Colombia, with the majority (676/836; 80.1%) of reported cases originated from only seven departments. We further characterized 402 S. Typhi isolates with available corresponding data recovered from various departments of Colombia through antimicrobial susceptibility testing and molecular subtyping. The majority (235/402; 58.5%) of these typhoid cases occurred in males and were most commonly reported in those aged between 10 and 29 years (218/402; 54.2%); there were three (0.74%) reported fatalities. The overwhelming preponderance (339/402; 84.3%) of S. Typhi were susceptible to all tested antimicrobials. The most common antimicrobial to which the organisms exhibited non-susceptibility was ampicillin (30/402;7.5%), followed by nalidixic acid (23/402, 5.7%). Molecular subtyping identified substantial genetic diversity, which was well distributed across the country. Despite the diffuse pattern of S. Typhi genotypes, we identified various geographical hotspots of disease associated with local dominant genotypes. Notably, we found limited overlap of Colombian genotypes with organisms reported in other Latin American countries. Our work highlights a substantial burden of typhoid in Colombia, characterized by sustained transmission in some regions and limited epidemics in other departments. The disease is widely distributed across the country and associated with multiple antimicrobial susceptible genotypes that appear to be restricted to Colombia. This study provides a current perspective for typhoid in Latin America and highlights the importance of pathogen-specific surveillance to add insight into the limited epidemiology of typhoid in this region.

Dataset Information

Epidemiology and phylogenetic analysis of respiratory viruses from 2012 to 2015 - A sentinel surveillance report from union territory of Puducherry, India.

Publications

Epidemiology and phylogenetic analysis of respiratory viruses from 2012 to 2015 - A sentinel surveillance report from union territory of Puducherry, India.

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