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 Table of Contents  
Year : 2019  |  Volume : 3  |  Issue : 4  |  Page : 67-71

Viral and atypical bacterial infection in young children hospitalized due to acute lower respiratory tract infection in Southern Thailand

1 Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Hat-Yai, Songkhla, Thailand
2 Immunology and Virology Unit, Department of Pathology, Faculty of Medicine, Prince of Songkla University, Hat-Yai, Songkhla, Thailand

Date of Submission13-Apr-2020
Date of Decision08-Jun-2020
Date of Acceptance29-Jun-2020
Date of Web Publication28-Sep-2020

Correspondence Address:
Kanokpan Ruangnapa
Department of Pediatrics, Faculty of Medicine, Prince of Songkla University, Hat-Yai, Songkhla 90110
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Source of Support: None, Conflict of Interest: None

DOI: 10.4103/prcm.prcm_3_20

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Background: The etiology of acute lower respiratory tract infection (ALTI) in Thailand is not well established. Aims: This study aims to determine the prevalence of viral and atypical bacterial infections in young children hospitalized due to ALTI. Settings and Design: This was a retrospective study. Subjects and Methods: Eighty-two leftover nasopharyngeal specimens obtained from children with ALTI admitted from May to October 2017 in Songklanagarind Hospital were analyzed. Multiplex polymerase chain reaction and the bead hybridization method (NxTAG® Respiratory Pathogen Panel) were used to detect 18 instances of respiratory virus and atypical bacteria. The clinical data for the children were retrospectively reviewed and analyzed from the medical records. Results: From a total of 82 ALTI patients, 60% were male. The median (interquartile range) age was 14.8 (8.0–38.1) months. Seventy-six percent of the patients were positive for at least one viral pathogen. The three most identified pathogens were respiratory syncytial virus (RSV) B (39.0%), RSV A (20.7%), and hRV (12.2%), while atypical bacteria were not found. Patients with RSV infection had significantly higher fever on admission (P < 0.01) and a longer duration of fever (log-rank P < 0.001) compared to the non-RSV group. Conclusions: Viral pathogens were detected in 76% of the children hospitalized due to ALTI. Further, 79% were positive for RSV with significantly high-grade fever.

Keywords: Children, etiology, lower respiratory tract infection, virus

How to cite this article:
Ruangnapa K, Kaeotawee P, Surasombatpattana P, Kemapunmanus M, Intusoma U, Saelim K, Anuntaseree W. Viral and atypical bacterial infection in young children hospitalized due to acute lower respiratory tract infection in Southern Thailand. Pediatr Respirol Crit Care Med 2019;3:67-71

How to cite this URL:
Ruangnapa K, Kaeotawee P, Surasombatpattana P, Kemapunmanus M, Intusoma U, Saelim K, Anuntaseree W. Viral and atypical bacterial infection in young children hospitalized due to acute lower respiratory tract infection in Southern Thailand. Pediatr Respirol Crit Care Med [serial online] 2019 [cited 2023 Apr 1];3:67-71. Available from: https://www.prccm.org/text.asp?2019/3/4/67/296483

  Introduction Top

Acute lower respiratory tract infection (ALTI) is a leading cause of hospitalization and death worldwide, especially among children <5 years old.[1],[2] Respiratory viruses are detected in 15%–90% of ALTI episodes depending on the methods of detection and the spectrum of viral studies.[3],[4],[5],[6],[7],[8] The prevalence of each respiratory pathogen varies from study to study due to population, seasonality, and geographic areas as well as detection techniques.

The aim of this study was to determine the prevalence of viral and atypical bacterial infections in young children hospitalized due to ALTI in Southern Thailand using multiplex polymerase chain reaction (PCR) and bead hybridization technique to specify the clinical symptoms for different respiratory pathogens.

  Subjects and Methods Top

This was a retrospective study conducted at Songklanagarind Hospital, Thailand, between May and October 2017 using electronic medical records and leftover nasopharyngeal specimens stored at the microbiological laboratory of Songklanagarind Hospital. Ethics committee approval was obtained [REC-60-388-01-1] before initiation of the study.

The study population included hospitalized children younger than 5 years diagnosed with ALTI with discharge diagnosis of ICD-10 including J09-J18 (influenza and pneumonia) and J20-J22 (other ALTI). During the study period, patients were excluded if they were diagnosed with congenital heart disease, chronic lung disease or bronchopulmonary dysplasia, neuromuscular disease, cerebral palsy, or severe developmental delay with feeding difficulty. Data collection from electronic medical records included demographic data, birth history, past medical history, family history, clinical manifestations and physical examination on admission, medical treatment, oxygen supplementation, and initial laboratory investigation. Total respiratory distress score was estimated daily during hospitalization until discharged using information in the medical records, including vital signs, oxygen saturation (SpO2), and the physician's and nurse's notes of a patient's clinical progression (level of consciousness, nasal flaring, chest retraction, and abdominal breathing). Disease severity was defined according to a respiratory distress score as mild (score < 3), moderate (score 4–6), or severe (score 7–9) respiratory distress.

Nasopharyngeal specimens were routinely collected for RSV and influenza antigen detection from every hospitalized child with ALTI during the study period. Further, leftover nasopharyngeal specimens were used for the potential detection of respiratory pathogens by multiplex PCR methods. Nucleic acid was extracted from specimens using the silica absorption spin column technique and tested for twenty viral and atypical bacterial respiratory pathogens using a NxTAG ® respiratory pathogen panel kit. Multiplexing PCR and bead hybridization was performed for the detection of influenza (type A, AH1, AH3, and B), parainfluenza virus (PIV type 1–4), respiratory syncytial virus (RSV type A and B), rhinovirus/enterovirus (HRV/HEV), human metapneumovirus (hMPV), human bocavirus (HBoV), adenovirus (AdV), coronavirus (CoV HKU1, CoV NL63, and CoV 229E), and atypical bacteria including Chlamydia pneumoniae and Mycoplasma pneumoniae.

Statistical analysis

Data were analyzed using R program (open source) with R studio. Descriptive data were presented as percentile, mean (standard deviation), and median (interquartile range). The comparison of continuous data and categorical data was carried out using Mann–Whitney U-test and Chi-square/a Fisher's exact test, respectively. Survival analysis was carried out using Kaplan–Meier analysis and log-rank test to explain and compare the probability of fever and respiratory distress score between different respiratory pathogens during hospitalization. P < 0.05 was considered statistically significant.

  Results Top

A total of 87 hospitalized children with ALTI were enrolled from May to October 2017. Five were excluded due to incomplete medical records or inadequate leftover specimens. From the total of 82 children enrolled, 49 were male (59.8%) and the median (range) age was 15 (4–39) months. The median respiratory distress score on admission was 3 (2–4), considered to be mild respiratory distress, while the median length of hospital stay was 3 (2–5) days. The routine rapid antigen test for RSV and influenza detected RSV in 40 from 82 children (48.7%) but did not positive for influenza virus.

Using multiplex PCR method, the viral or atypical bacterial pathogens were detected in 62/82 (75.6%) children [Table 1]. The three most identified pathogens were RSV B (39.0%), RSV A (20.7%), and hRV (12.2%). Co-infection of RSV with other viral pathogens was detected in 6 patients (7.3%), with the most frequent combination being RSV B/hRV in 2 patients (2.4%). No atypical bacterium was detected in this study.
Table 1: Prevalence of respiratory pathogens detected in 82 acute lower respiratory tract infection patients*

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As RSV infection was the major pathogen detected in this study, we identified the clinical characteristics of the RSV-detected patients (PCR positive for RSV A or B) as “RSV group” (n = 43) and RSV nondetected patients (negative study or PCR positive for other pathogens) as “non-RSV group” (n = 39). There were no significant differences in median age, sex ratio, or clinical diagnosis between the RSV and non-RSV groups [Table 2]. Previous history of recurrent wheezing was significantly higher in the non-RSV group than in the RSV group (41% vs. 9%; P = 0.02).
Table 2: Comparison of demographic data, symptoms and signs between respiratory syncytial virus (RSV) and non- RSV patients

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The appearance of respiratory symptoms was not significantly different between the RSV and non-RSV groups, including cough (97.7% vs. 97.4%), dyspnea (86% vs. 97.4%), and rhinorrhea (83.7% vs. 84.6%) [Table 2]. Gastrointestinal symptoms reported in terms of diarrhea and vomiting, for 10.9% and 13.4% of the children, respectively, were not significantly different between the RSV and non-RSV groups. Peak body temperature on admission was significantly higher in the RSV group (38.6°C in RSV vs. 38°C in non-RSV; P = 0.01).

Overall, 86.5% (n = 71) of the children were treated with oxygen supplementation, including low-flow oxygen support (n = 61) and high-flow nasal cannula (n = 10), but no patients required intubation or support with positive pressure ventilation. Antibiotics were prescribed for 10% of the children, which was not significantly different between the RSV and non-RSV groups (P = 0.86 and 1.00, respectively).

The Kaplan–Meier survival curve [Figure 1]a showed a nonsignificant difference in the probability of patients to recover from respiratory distress during hospitalization between the RSV and non-RSV groups. However, time to recover from fever among patients in the RSV group was significantly longer than the non-RSV group [Log-Rank P < 0.001], as shown in [Figure 1]b.
Figure 1: Kaplan–Meier survival curve comparing (a) the recovery from respiratory distress and (b) the recovery from fever.

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  Discussion Top

The overall detection rate of viral respiratory pathogens with PCR technique in our study (75.6%) was comparable to other studies among children from developing countries including Bangladesh, Brazil, and Papua New Guinea, which ranges from 85% to 90% when using the comparable method with multiplex PCR technique.[4],[7],[8]

Our detection rate was higher than a previous population-based study in Northeastern Thailand by Hasan et al.[6] which reported an overall viral detection rate of 36.5% in hospitalized ALTI children. This is because of the detection technique using a combination of conventional and real-time reverse transcription-PCR. The previous studies also had a limitation in terms of viral strains detection, as previously mentioned that RSV, influenza A and B, and adenovirus were tested throughout the study from 2005 to 2010, but PIV, hMPV, rhinovirus, bocavirus, and coronavirus were tested partly.

The RSV positivity rate in our study (59.7%) was higher than in other studies, which ranges from 19%–42%.[4],[5],[6],[7],[8] There are two possible causes of this finding. First, our study was conducted between May and October, which is considered the rainy season in Thailand and is related to the peak season for RSV infection. Same as the report from Northeastern Thailand by Hasan et al.[6] that 87% of the RSV-detected ALTI cases occurred during June to October. However, our results were markedly different from a study conducted in Shenzhen, China, which reported that RSV was detected primarily during the spring and summer, particularly in March and September.[3] This difference in viral detection may be related to a region's climate and demographic factors.

Second, our population was mostly younger than 2 years (median age of 13 months), which related to the peak incidence of RSV infection in the first 2 years of life. Further, the population of hospitalized patients was related to the severity of disease in children, especially those younger than 6 months old.[9],[10],[11]

Atypical bacteria including M. pneumoniae and C. pneumoniae were not detected in our study, which is different from a previous study conducted in Northeast Brazil that reported the incidence of M. pneumoniae at 9.8% for children < 5 years old who presented with acute respiratory tract infection at the emergency department.[4] The difference in detection rate of atypical pathogens may be attributed to the technique for specimen collection. While Reznikov et al.[12] reported that the PCR for atypical bacterial detection, especially M. pneumoniae in nasopharyngeal aspiration and nasopharyngeal swab, had similar positivity percentages (45% and 50%, respectively), some previous studies [13],[14] argued that sputum samples from induced sputum technique were superior for the detection of M. pneumoniae because the number of bacteria is higher in the pulmonary alveolus than in the epithelium of the upper respiratory tract in patients with pneumonia.

Accordingly, the negative result of atypical bacterial infection by PCR detection method of our study could be also explained by a false negativity since the PCR technique is not a gold standard test. The currently accepted standard method for the diagnosis of M. pneumoniae infection is a combination of direct pathogen detection using molecular techniques and the serological testing.[15] The presence of organisms at numbers below the limits of detection of the assay due to previous antibiotic treatment could be another important contributing factor for probable false negative. Thus, we cannot conclude that the prevalence of atypical bacterial infection in our setting was low or negative.

Clinical characteristic comparison between viral pathogens cannot be determined due to the low detection rate of other viral pathogens besides RSV, so we stratified patients into the RSV and non-RSV groups to compare their clinical characteristics and the severity of disease estimated from median respiratory distress score on admission. We found no significant differences in clinical manifestations between these two groups.

Furthermore, respiratory distress score during hospitalization was not significantly different between the RSV and non-RSV groups, although the duration of fever was significantly longer in the RSV group. From previous studies, 60%–80% of the patients with a single RSV infection had fever (BT >38°C), which was not significantly different from other viral pathogens.[5],[9] However, a lack of bacterial co-infection study was a limitation for this study. A previous study of bacterial co-infection in hospitalized children with RSV bronchopulmonary infections found that pathogenic bacteria, including Haemophilus influenzae (43.9%), Streptococcus pneumoniae (36.6%), and Moraxella catarrhalis (29.3%), were predominantly isolated from 43.6% of the children hospitalized due to RSV bronchopulmonary infections, causing high-grade fever and severe respiratory illness.[16]

Our data suggested that respiratory viruses caused a large number of hospitalizations due to ALTI among children <5 years old. Due to the limitations of this study, which included short duration and small population, the results may be insufficient to accurately describe the epidemiological and seasonal distribution of respiratory pathogens in the southern region of Thailand. Larger populations and longer durations of study are recommended for further research concerning the epidemiologic data and seasonal patterns of viral pathogens, as understanding of seasonal patterns for respiratory viruses is essential for effective resource allocation and planning of preventive and therapeutic interventions including vaccine, medications, and personnel.

  Conclusions Top

Detection rate of respiratory pathogens in hospitalized ALTI patients in this study was 76% whereas RSV was the most commonly detected pathogen (60%) and RSV infected patients had significantly higher and longer duration of fever than non-RSV patients.


This study was granted by the Faculty of Medicine, Prince of Songkla University. We would like to thank all staff of the Immunology-Virology Unit and Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, for their assistance with data analysis and manuscript preparation.

Financial support and sponsorship

This study was financially supported by the Faculty of Medicine, Prince of Songkla University.

Conflicts of interest

There are no conflicts of interest.

  References Top

Nair H, Nokes DJ, Gessner BD, Dherani M, Madhi SA, Singleton RJ, et al. Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: A systematic review and meta-analysis. Lancet 2010;375:1545-55.  Back to cited text no. 1
Black RE, Cousens S, Johnson HL, Lawn JE, Rudan I, Bassani DG, et al. Global, regional, and national causes of child mortality in 2008: A systematic analysis. Lancet 2010;375:1969-87.  Back to cited text no. 2
Wang H, Zheng Y, Deng J, Wang W, Liu P, Yang F, et al. Prevalence of respiratory viruses among children hospitalized from respiratory infections in Shenzhen, China. Virol J 2016;13:39.  Back to cited text no. 3
Bezerra PG, Britto MC, Correia JB, Duarte Mdo C, Fonceca AM, Rose K, et al. Viral and atypical bacterial detection in acute respiratory infection in children under five years. PLoS One 2011;6:e18928.  Back to cited text no. 4
Sung CC, Chi H, Chiu NC, Huang DT, Weng LC, Wang NY, et al. Viral etiology of acute lower respiratory tract infections in hospitalized young children in Northern Taiwan. J Microbiol Immunol Infect 2011;44:184-90.  Back to cited text no. 5
Hasan R, Rhodes J, Thamthitiwat S, Olsen SJ, Prapasiri P, Naorat S, et al. Incidence and etiology of acute lower respiratory tract infections in hospitalized children younger than 5 years in rural Thailand. Pediatr Infect Dis J 2014;33:e45-52.  Back to cited text no. 6
Chidlow GR, Laing IA, Harnett GB, Greenhill AR, Phuanukoonnon S, Siba PM, et al. Respiratory viral pathogens associated with lower respiratory tract disease among young children in the highlands of Papua New Guinea. J Clin Virol 2012;54:235-9.  Back to cited text no. 7
Homaira N, Luby SP, Hossain K, Islam K, Ahmed M, Rahman M, et al. Viral etiology of pneumonia among severely malnourished under-five children in an urban hospital, Bangladesh. PLoS One 2016;11:e0147982.  Back to cited text no. 8
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Liu W, Chen D, Tan W, Xu D, Qiu S, Zeng Z, et al. Epidemiology and clinical presentations of respiratory syncytial virus subgroups A and B detected with multiplex real-time PCR. PLoS One 2016;11:e0165108.  Back to cited text no. 10
Yu X, Kou Y, Xia D, Li J, Yang X, Zhou Y, et al. Human respiratory syncytial virus in children with lower respiratory tract infections or influenza-like illness and its co-infection characteristics with viruses and atypical bacteria in Hangzhou, China. J Clin Virol 2015;69:1-6.  Back to cited text no. 11
Reznikov M, Blackmore TK, Finlay-Jones JJ, Gordon DL. Comparison of nasopharyngeal aspirates and throat swab specimens in a polymerase chain reaction-based test for Mycoplasma pneumoniae. Eur J Clin Microbiol Infect Dis 1995;14:58-61.  Back to cited text no. 12
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  [Figure 1]

  [Table 1], [Table 2]


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