Aims of the study

Analyzing data obtained from clinical microbiology tests for atypical viruses and bacteria through routine Multiplex Real-time Polymerase Chain Reaction (MLP rPCR) conducted in a laboratory equipped with capable devices. The analytical data will shed light on the roles of atypical viruses and bacteria in hospitalized children with LRTI and simultaneously examine the circulation rates to predict outbreaks.

Materials and methods

Samples collected were nasotracheal aspirates (NTA) from pediatric patients with LRTI. After reliability evaluation using the Barlett scoring system, the specimens underwent total nucleic acid extraction. The extraction products were then placed in PCR tubes containing MPL-rPCR mixes targeting atypical viruses and bacteria associated with LRTI. Developed by Vietnam’s Clinical Microbiology Research Institute, the MPL real-time PCR reagent set demonstrated high sensitivity (detecting 1 copy/reaction) and 100% specificity, without cross-reaction with non-target agents. MPL-rPCR reactions were conducted in real-time PCR devices (ABI7500 fast or CFX-96 touch screen), with results recorded in Excel for subsequent analysis.

Results and discussion

In 2023, 1,541 respiratory samples were examined. The results revealed a 59.2% detection rate for viral agents, peaking at 70.8% in the first quarter and 64% in the last quarter. Adenovirus (14.9%), Epstein-Barr virus (11.6%), Rhinovirus (11.4%), RSV (10.7%), and Parainfluenza 3 virus (10.5%) were the most prevalent. hMPV, SARS-CoV-2, and parainfluenza 1 had low detection rates (2.1%, 1.3%, and 1.1%, respectively). Influenzae C virus (0.4%), parainfluenza 2 (0.4%), and Human-corona virus (0.1%) showed very low detection rates. Seasonal variations were observed for certain viruses. Adenovirus showed high detection rates in the first three months of the year (20.5%) and the last three months of the year (19.5%). Epstein-Barr virus had a lower detection rate in the last three months of the year (9.5%) compared to the first nine months (13.8% and 13.4%). Other viruses displayed diverse seasonal trends. For atypical bacteria, the detection rate was 16.7%, highest in the last three months (19.4%) and lowest in the first three months of the year (8.7%). The atypical bacteria with the highest detection rate was M. pneumoniae (14.5%), with a high detection rate from March to December. Additionally, there were a few cases where B. pertussis (3 cases), B. parapertussis (1 case), C. trachomatis (6 cases), and C. pneumoniae (1 case) were detected.

Conclusions

Thanks to the availability of real-time PCR technology and the ability to rountinely detect atypical viruses and bacteria in respiratory samples, this study has been conducted. Our findings have revealed a significant role of these two groups of agents in pediatric LRTI, while also analyzing the seasonal distribution of these agents. This routine testing can be used to analyze the epidemiological situation of respiratory infections and the risk of an agent evolving into a pandemic.

Figure 1: MPL-rPCR method to detect the atypical bacteria and virus from lower respiratory tract samples

Graph 1: The detection rate of the atypical bacteria and the virus from the lower respiratory tract samples

Graph 2: The detection rate of the species of the atypical bacteria from the lower respiratory tract samples

Graph 3: The detection rate of the species of the virus from the lower respiratory tract samples

REFERENCES

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