Comparison of respiratory pathogens in children with community-acquired pneumonia before and during the COVID-19 pandemic

Altered microbiota of the lower respiratory tract and its association with COVID-19 severity analysed by metagenomics and metatranscriptomics

The interaction between gut and oropharyngeal microbiota plays a significant role in the viral infections like SARS-CoV-2, but role of the lower respiratory tract microbiota remains unclear. Our study utilized metatranscriptomics and metagenomics to analyze the microbial composition of bronchoalveolar lavage fluid and sputum samples from 116 COVID-19 patients, categorized into mild, severe, and critical groups. Our analysis revealed significant differences in viral genotypes across disease stages. As disease severity increased, the Chao index also rose. The mild group was predominantly dominated by Firmicutes, while the severe group showed an increase in Bacteroidetes. The critical group was characterized by a higher abundance of Actinobacteria and Proteobacteria. Notably, the abundance of Streptococcus and Rothia decreased as the disease progressed. Additionally, the Shannon index correlated with mortality risk, while the Chao index was associated with ICU admission, mechanical ventilation, and patient survival. These findings highlight the strong link between microbial composition and COVID-19 severity, providing valuable insights for assessing disease progression.

Comparative analysis of hospital-acquired and community-acquired infections at a tertiary hospital in China before and during COVID-19: A 7-year longitudinal study (2017-2023)

BACKGROUND

This 7-year longitudinal survey (2017-2023) assessed the point prevalence of hospital-acquired infections (HAIs) and community-acquired infections (CAIs) at a first-class tertiary hospital in China, both prior to and during the Corona Virus Disease 2019 (COVID-19) pandemic.

METHODS

Patients were stratified into prepandemic and pandemic periods, as well as into stringent and relaxed infection prevention and control (IPC) phases, to compare the point prevalence of HAIs and CAIs.

RESULTS

The overall point prevalence of HAIs was 1.50% (95% confidence interval [CI], 1.32%-1.71%), showing a significant downward trend (P = .021). Among patients receiving pathogen testing, the point prevalence of HAIs significantly declined during the pandemic (6.26% vs 9.89%, P < .001). The point prevalence of CAIs demonstrated a notable increase in 2023 compared with 2020 to 2022 among pathogen-tested patients (81.37% vs 74.18%, P = .001). Multivariate analysis identified hospitalization during the pandemic as a protective factor against HAIs (adjusted odds ratio 0.49, 95% CI, 0.36-0.67).

CONCLUSIONS

The comprehensive IPC strategy implemented during the COVID-19 pandemic at this tertiary hospital significantly reduced the point prevalence of HAIs. However, CAIs exhibited a rising trend following the relaxation of COVID-19 IPC measures.

Prevalence and distribution of respiratory pathogens in pediatric acute respiratory infections in Putian, China

BACKGROUND

Acute Respiratory Infections (ARIs) are a significant source of morbidity among pediatric populations. This study aimed to investigate the prevalence and distribution of respiratory pathogens in pediatric ARIs in Putian, China.

METHODS

This retrospective study included 3,790 pediatric patients with suspected ARIs, evaluated between March 2023 and February 2024. Nasopharyngeal swabs were obtained and analyzed via reverse-transcription polymerase chain reaction (RT-PCR) to detect eleven common respiratory pathogens. Statistical analyses were conducted to evaluate the distribution of these pathogens across various patient demographics, including gender, age, and season.

RESULTS

This study included 3,790 pediatric patients under 14 years (median age: 4.3 years, IQR: 1-7). Pathogen positivity was 78.9%, with higher rates in school-age children and during autumn and winter (P < 0.001), with Mycoplasma pneumoniae (Mp) as the most common pathogen (33.4%), followed by human rhinovirus (HRV; 15.0%) and human respiratory syncytial virus (HRSV; 12.1%). Single-pathogen detections dominated (81.9%), while co-detections (18.1%) were primarily dual-pathogen cases, with HRV + Mp as the leading combination. Pathogen distribution varied significantly by age: Mp detection rates escalated with age, peaking in school-age children, while HRSV and HRV predominated in infants and toddlers. Seasonal trends revealed distinct pathogen activity: Influenza A (InfA) peaked during spring, Mp during autumn and winter, and HRSV during summer (P < 0.001). Logistic regression analysis identified significant associations: InfA, human adenovirus (HADV), and Influenza B (InfB) were linked with acute upper respiratory infections (AURIs), while Mp, human metapneumovirus (HMPV), human parainfluenza virus (HPIV), and HRSV correlated with acute lower respiratory infections (ALRIs) (P < 0.05).

CONCLUSION

This study provides comprehensive insights into the prevalence and temporal patterns of respiratory pathogens among hospitalized children with ARIs in Putian, China. Mp, HRV, and HRSV were the predominant pathogens, with significant variations by age and season. Limitations include the one-year duration and the focus on hospitalized patients. Future studies should extend surveillance to outpatient and emergency settings to obtain a broader understanding of ARI epidemiology.

Analysis of respiratory pathogens in pediatric acute respiratory infections in Lanzhou, Northwest China, 2019-2024

Objective

This study aimed to assess the prevalence and distribution of respiratory pathogens in children under 18 years old with Acute Respiratory Infections (ARTIs) in Lanzhou, Northwest China, from July 2019 to January 2024.

Methods

The respiratory pathogens studied were FluA, FluB, PIV, RSV, ADV, MP, CP, CB, and LP, detected by indirect immunofluorescence assay (IIF). Data were obtained from the laboratory information system (LIS) of the Lanzhou University Second Hospital. As in Lanzhou, NPIs were implemented in January 2020, and were lifted in December 2022, data were divided into pre-NPIs (July 2019 to December 2019), NPIs (January 2020 to December 2022) and post-NPIs (January 2023 to January 2024) periods for analysis. Pearson's chi-square test, ANOVA, and Fisher's exact test were used to evaluate statistical significance in variable differences, with P < 0.05 considered significant.

Results

A total of 29,659 children diagnosed with ARTIs were included in the study, with 13030(43.93%) test positive for at least one pathogen. Single-pathogen infections predominated (33.10%), while co-detection of MP and PIV was the most common among multi-pathogen cases (52.96%). Pathogen detection rates were notably higher in female children (50.62%) and preschool-aged children (53.45%) and exhibited seasonal variations, with a pronounced increase in winter (47.61%) and a peak in November (48.92%). MP had the highest detection rate (38.59%), followed by PIV (10.18%). Detection rates significantly increased following the lifting of NPIs, rising from 33.82% (SD ± 13.13) during NPIs to 64.42% (SD ± 4.67) (P < 0.001), with 2023 showing the highest detection rate (64.61%) and largest participant count (9,591). In November 2023, detection rates reached their highest level at 73.09%. Post-NPI, most pathogens, except CB and LP, demonstrated significantly higher prevalence (P<0.001).

Conclusion

In the Lanzhou region, MP and PIV were identified as the most prevalent respiratory pathogens among children with ARTIs, with peak detection rates during the winter season. Boys and school-age children exhibited higher susceptibility to these infections. NPIs played a critical role in reducing respiratory pathogen transmission. Once NPIs were lifted, a marked resurgence in pathogen incidence highlighted their impact on controlling infection spread.

Ten different viral agents infecting and co-infecting children with acute gastroenteritis in Southern Italy: Role of known pathogens and emerging viruses during and after COVID-19 pandemic

Acute gastroenteritis (AGE) represents a world public health relevant problem especially in children. Enteric viruses are the pathogens mainly involved in the episodes of AGE, causing about 70.00% of the cases. Apart from well-known rotavirus (RVA), adenovirus (AdV) and norovirus (NoV), there are various emerging viral pathogens potentially associated with AGE episodes. In this study, the presence of ten different enteric viruses was investigated in 152 fecal samples collected from children hospitalized for gastroenteritis. Real time PCR results showed that 49.3% of them were positive for viral detection with the following prevalence: norovirus GII 19.7%, AdV 15.8%, RVA 10.5%, human parechovirus (HPeV) 5.3%, enterovirus (EV) 3.3%, sapovirus (SaV) 2.6%. Salivirus (SalV), norovirus GI and astrovirus (AstV) 1.3% each, aichivirus (AiV) found in only one patient. In 38.2% of feces only one virus was detected, while co-infections were identified in 11.8% of the cases. Among young patients, 105 were ≤5 years old and 56.0% tested positive for viral detection, while 47 were >5 years old with 40.0% of them infected. Results obtained confirm a complex plethora of viruses potentially implicated in gastroenteritis in children, with some of them previously known for other etiologies but detectable in fecal samples. Subsequent studies should investigate the role of these viruses in causing gastroenteritis and explore the possibility that other symptoms may be ascribed to multiple infections.

Impact of normalized COVID-19 prevention and control measures on lower respiratory tract infection pathogenesis in hospitalized children

Objective

This study aimed to investigate the epidemiological characteristics of common pathogens contributing to childhood lower respiratory tract infections (LRTIs) in Xiangtan City, Hunan Province before and during the coronavirus disease 2019 (COVID-19) pandemic.

Methods

A total of 11,891 enrolled patients, aged 1 month to 14 years, diagnosed with LRTIs and admitted to Xiangtan Central Hospital from January 2018 to December 2021 were retrospectively reviewed in this study. Specifically, the epidemiological characteristics of these pathogens before and during the COVID-19 pandemic were analyzed.

Results

There was a significant decrease in the number of children hospitalized with LRTIs during the COVID-19 pandemic (2020-2021) compared to data from 2018 to 2019 (before the COVID-19 pandemic). Of these cases, 60.01% (7,136/11,891) were male and 39.99% (4,755/11,891) were female. 78.9% (9,381/11,891) cases occurred in children under 4 years of age. The average pathogen detection rate among 11,891 hospitalized LRTIs children was 62.19% (7,395/11,891), with the average pathogen detection rate of 60.33% (4,635/7,682) and 65.57% (2,670/4,209) before and during COVID-19 pandemic, respectively. The detection rates of adenovirus (ADV), bordetella pertussis (BP) and moraxella catarrhalis (M. catarrhalis) decreased dramatically, while the detection rates of influenza viruses (IFV), parainfluenza viruses (PIV), respiratory syncytial virus (RSV), haemophilus influenzae (H. influenzae), streptococcus pneumoniae (S. pneumoniae), and staphylococcus aureus (S. aureus) increased significantly during the COVID-19 pandemic. Overall, RSV, mycoplasma pneumoniae (MP), H. influenzae, and IFV were the major pathogens causing LRTIs in hospitalized children before and during the COVID-19 pandemic.

Conclusion

Public health interventions for COVID-19 prevention are beneficial to reduce the incidence of LRTIs in children by limiting the prevalence of ADV, MP, BP, and M. catarrhalis, but which have limited restrictive effects on other common LRTIs-associated pathogens. Collectively, the data in this study comprehensively investigated the effects of COVID-19 pandemic on the epidemiological characteristics of respiratory pathogens, which will be beneficial for improving early preventive measures.