Determination of bacterial and viral pathogen spectra and identification of multi drugs resistance gene CTX-M1 in Klebsiella pneumoniae isolated from acute respiratory infections children aged under-5 from two hospital settings of Dhaka city

Abstract

This study aimed to determine bacterial and viral pathogen spectra and identify multidrug resistance genes in bacterial isolated from under-5 children with acute respiratory infections from two hospital settings of Dhaka city. Nasal swabs were collected from 150 under-five children hospitalized with clinical signs of ARIs. Screening of viral pathogens targeted ten respiratory viruses using RT-qPCR. Bacterial pathogens were identified by bacteriological culture methods and antimicrobial susceptibility of the isolates was determined following Clinical and Laboratory Standard Institute (CLSI) guidelines. About 78% (n=117) of specimens were positive for pathogens. Of 117 infected cases, 4.27% (n=5) had only single bacterial pathogens, whereas 44% (n=61) cases had only single viral pathogens. The remaining 58% (n=88) cases had coinfections. In viral suspected cases, human rhinovirus was detected as the predominant virus (32%), followed by RSV (17.33%), HMPV (16%), HBoV (13%), HPIV-3 (12%), and adenovirus (9%). Streptococcus pneumoniae was the most frequently isolated bacterial pathogen (8%), where Klebsiella pneumaniae, Streptococcus spp., Enterobacter agglomerans, and Haemophilus influenzae were 6%, 3.3%, 2%, and 2%, respectively. Of 15 multidrug-resistant bacteria, a Klebsiella pneumoniae (KPn) isolate exhibited resistance against more than 10 different antibiotics and extended spectrum beta-lactamase (ESBL) CTX- M1 gene was found in multidrug-resistant KPn using conventional PCR. Sanger sequencing had been used for confirmation of amplified CTX- M1. Both ARI incidence and pathogen detection rates were higher during post-monsoon and winter, peaking in September. Pathogen detection rates and coinfection incidence in less than 1-year group were significantly higher (P=0.04123) than in 1-5 years age group. Human Boca Virus (HBoV) had a significant involvement between single and confections with P value of 0.0152.