Bacterial and viral pathogen spectra of acute respiratory infections in under-5 children in hospital settings in Dhaka city

Abstract

The study aimed to examine for the first time the spectra of viral and bacterial pathogens along with the antibiotic susceptibility of the isolated bacteria in under-5 children with acute respiratory infections (ARIs) in hospital settings of Dhaka, Bangladesh. Nasal swabs were collected from 200 under-five children hospitalized with clinical signs of ARIs. Nasal swabs from 30 asymptomatic children were also collected. 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 CLSI guidelines. About 82.5% (n = 165) of specimens were positive for pathogens. Of 165 infected cases, 3% (n = 6) had only single bacterial pathogens, whereas 43.5% (n = 87) cases had only single viral pathogens. The remaining 36% (n = 72) cases had coinfections. In symptomatic cases, human rhinovirus was detected as the predominant virus (31.5%), followed by RSV (31%), HMPV (13%), HBoV (11%), HPIV-3 (10.5%), and adenovirus (7%). Streptococcus pneumoniae was the most frequently isolated bacterial pathogen (9%), whereas Klebsiella pneumaniae, Streptococcus spp., Enterobacter agglomerans, and Haemophilus influenzae were 5.5%, 5%, 2%, and 1.5%, respectively. Of 15 multidrug-resistant bacteria, a Klebsiella pneumoniae isolate and an Enterobacter agglomerans isolate exhibited resistance against more than 10 different antibiotics. Both ARI incidence and predominant 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 = 0.0034 and 0.049, respectively) than in 1-5 years age group. Pathogen detection rate (43%) in asymptomatic cases was significantly lower compared to symptomatic group (P<0.0001). Human rhinovirus, HPIV-3, adenovirus, Streptococcus pneumonia, and Klebsiella pneumaniae had significant involvement in coinfections with P values of 0.0001, 0.009 and 0.0001, 0.0001 and 0.001 respectively. Further investigations are required to better understand the clinical roles of the isolated pathogens and their seasonality.

Fig 1. The frequency of specimen collection during the study period.

Y-axis indicates the number of specimens, whereas X-axis indicates months of the year.

Fig 2. Detection and identification of bacterial pathogens isolated from 200 under-five children hospitalized with ARIs.

Fig 2A shows the rates of culture positive and culture negative specimens. Fig 2B shows the proportion of different bacterial strains among culture positive specimens. In the Figure, CP = Culture Positive, CN = Culture Negative, Spn = Streptococcus pneumoniae, Kpn = Klebsiella pneumaniae, Hin = Haemophilus influenzae, Eag = Enterobacter agglomerans, Ssp = Streptococcus spp.

Fig 3. Comparison of frequencies of each pathogen identified in single infections and coinfections.

Fig 3A compares the frequencies of viruses and Fig 3B compares the bacterial pathogen frequencies in single infections and coinfections. Fisher's exact test was performed for each group. P< 0.05 was considered significant. SPn = S. pneumoniae, KPn = K. pneumoniae, SSp = Streptococcus species.

Fig 4. Monthly distribution of respiratory pathogens detected in this study.

Fig 4A shows the distribution of the detected viruses and Fig 4B displays the distribution of the isolated bacteria, in nasal swab specimens collected in different months during the study period. In 4A, Inf A = influenza A, Inf B = influenza B and in 4B, Spn = S. pneumoniae, Kpn = K. pneumaniae, HI = H. influenzae, Eag = E. agglomerans, Ssp = Streptococcus spp.