Through this retrospective study, we analyzed the epidemiological characteristics and the evolution of the pathogen spectrum of respiratory tract infections in children in Shandong, China, during and after the COVID-19 pandemic. We confirmed that the COVID-19 pandemic had a certain impact on the changes in the pathogen spectrum of respiratory tract infections in children, especially for pathogens such as MP, Bordetella pertussis, and some viruses, which showed more significant changes.

Some scholars analyzed the infection rates and case-fatality rates of the new coronavirus in different countries and regions from 2019 to 2023 using public data from the World Health Organization (WHO). The results showed that the Global prevalence of COVID-19 increased from 0.011 to 0.098, while the case-fatality rate decreased from 0.024 to 0.009. Europe reported the highest cumulative infection rate (0.326), and Africa the lowest (0.011) [12]. Some scholars analyzed Taiwan’s National Health Insurance database. After the announcement of NPIs for the novel coronavirus, the infection rates of other respiratory pathogens decreased significantly [13].Since the outbreak of the COVID-19 pandemic in 2019, multiple countries both domestically and internationally have implemented NPIs during the COVID-19 pandemic. These measures effectively curbed the spread of COVID-19 in 2020 and 2021, while also affecting the epidemiological patterns of other respiratory pathogens. Moreover, variations across regions, diverse pathogen detection methodologies, and differing diagnostic criteria for diseases may potentially influence the study outcomes.In 2022, as the domestic epidemic situation eased, people in low-risk areas had largely returned to normal work and life. With the lifting of NPIs, the incidence rates of various respiratory pathogens changed. Regarding viral pathogens, the “viral interference” mechanism between the novel coronavirus and other viruses can influence the epidemiological trends of some viruses. The current understanding of the mechanisms of viral interference includes the direct blocking of one virus from entering receptors by another virus and competition among viruses for host cells, as well as the induction of innate or adaptive immune responses by viruses to prevent infections from related or different viruses [14]. For bacterial pathogens, strict NPIs were implemented during the COVID-19 pandemic, but this also affected the vaccination rates of children. The delay or interruption of routine immunizations led to insufficient immune stimulation in the population, failing to build an effective immune protective barrier, resulting in what is known as an “immune gap” or “immune debt“ [15]. In the current domestic multi-child family model, infections of MP or Bordetella pertussis in children under 3 years old are mostly caused by cross-infections from older children in the family. Moreover, the emergence of drug-resistant strains is an important reason for the surge in MP and Bordetella pertussis in 2023.

It is well known that respiratory virus infections are the most common respiratory pathogens [16]. Studies have confirmed that in acute respiratory infections of children under 5 years old, the detection rate of viruses is the highest, among which IAV, RSV, and RV are the top three viral pathogens with the highest positive detection rates [17]. The results of this study also confirm the important status of these viruses in pediatric respiratory infections, but they have also been affected by the epidemic. As one of the most common viral pathogens in children, RSV is the most important viral pathogen for acute lower respiratory infections in children under 5 years old worldwide [17]. The results of this study show that the positive detection rate of RSV in all age groups in 2023 was significantly higher than that in 2022. However, there are differences in the incidence of RSV infections in different age groups. In 2023, the highest positive detection rate of RSV infection was found in children under 3 years old, followed by those aged 3–5 years, and the lowest in those aged 6–17 years. A recent birth cohort study also confirmed the differences in the incidence of RSV in different age groups, and that children under 3 years old are the most susceptible to RSV infections [18]. Due to the resumption of normal work and life in low-risk areas in the winter of 2022 and the lifting of NPIs in some areas, this may be the reason for the significant increase in the detection rate of RSV at the end of 2022 and in 2023. Domestic scholars’ research also believes that the surge in RSV infections is related to this [19]. In this study, it was found that in 2023, the detection rates of RV and RSV showed a trend of one rising and the other falling. A study on pathogen detection in infants also confirmed a negative correlation between the co-detection of RSV and rhinovirus, that is, immune defense can suppress RSV infections, but may simultaneously increase the risk of rhinovirus infections [20], which also supports the viral interference hypothesis. However, in this study, RV infections maintained their usual circulation levels. One reason is that medical masks can block the transmission of coronaviruses and influenza viruses, but cannot block RV transmitted through droplets and aerosols [21]. In addition, RV is a non-enveloped virus, so it may be inherently more difficult to inactivate with soap and water or alcohol-based hand sanitizers [22, 23]. Moreover, the poor handwashing quality of children also makes it difficult to prevent the spread of RV. After the lifting of NPIs, the global detection rate of influenza viruses has significantly increased, with IAV infections being predominant. WHO influenza surveillance data show that from October 2022 to February 2023, there was a significant peak in global influenza cases. Europe experienced a peak in November 2022, the United States in December 2022, and northern China in February 2023 [24]. The detection trend of influenza viruses in this study is consistent with the global influenza trend. At the end of 2022, China fully lifted NPIs, during which there was a surge in COVID-19 infection cases. However, in this study, the detection rate of influenza viruses in December 2022 was at a low level, which may be due to the “viral interference” mechanism between COVID-19 and influenza viruses mentioned earlier. Compared with other countries, the peak of influenza virus infections in China occurred later, which may be related to the strict and long-term implementation of NPIs in our country. The increase in the incidence of influenza viruses in China after the lifting of NPIs was also delayed, which may also be affected by the “viral interference” mechanism between the two [25]. The COVID-19 pandemic has changed people’s medical-seeking behaviors and increased their attention to non-pharmaceutical interventions. People have reduced the risk of infection through measures such as maintaining social distance, hand hygiene, and cough etiquette, leading to changes in the pathogen spectrum [26]. Therefore, continuous pathogen monitoring and a series of prevention and treatment measures for positive pathogens can affect the epidemiological characteristics of pathogens. Early intervention and treatment may reduce the incidence and prognosis of pediatric respiratory infections.

Research by domestic scholars on the etiology and epidemiological characteristics of acute respiratory infections indicates that, in terms of bacterial positive detection rates, Streptococcus pneumoniae is the most common bacterium, followed by Haemophilus influenzae and Klebsiella pneumoniae. In terms of age distribution, the top three bacterial pathogens in preschool children are Streptococcus pneumoniae, Haemophilus influenzae, and Staphylococcus aureus. In school-age children, MP ranks first, followed by Streptococcus pneumoniae and Haemophilus influenzae [16]. This study found that the most common bacteria in 2022 and 2023 were Streptococcus pneumoniae and Haemophilus influenzae. The World Health Organization’s 2008 “Global Action Plan for the Prevention and Control of Pneumonia” listed the immunization coverage rates for Haemophilus influenzae and Streptococcus pneumoniae, as well as immunizations for pertussis and measles, as primary prevention strategies. Given that our country does not routinely use vaccines covering these two bacteria, Haemophilus influenzae and Streptococcus pneumoniae, the infection rates of pneumococcal and Haemophilus influenzae infections in children are relatively high [27]. In this study, the positive detection rates of Haemophilus influenzae in all age groups in 2023 were significantly higher than those in 2022. Moreover, the positive detection rates of Streptococcus pneumoniae and Haemophilus influenzae both peaked at the end of 2022. The possible reasons are that during the NPIs period, the microbial exposure of people in different age groups was reduced, the proportion of susceptible children increased, and the group immunity decreased due to the delay or interruption of immunizations, forming an “immune debt” during the COVID-19 pandemic [28]. In the post-epidemic period, as people’s epidemic prevention measures were relaxed and NPIs were gradually lifted, a peak in bacterial detection rates occurred when the COVID-19 pandemic was about to be fully lifted in 2022.

In China’s immunization schedule for children, the pertussis vaccine is given at 3 months, 4 months, 5 months, and 18 months after birth [29], and influenza and pneumococcal vaccines are not included in the routine immunization program.According to data from the WHO, from 2019 to 2021, the coverage rate of the DTP (diphtheria, pertussis, and tetanus) vaccine for children decreased by 5%, with the global DTP vaccine coverage rate dropping to 81%. NPIs reduced the spread of Bordetella pertussis among children, leading to a decrease of about 90% in the number of infection cases [30]. In this study, the positive detection rates of Bordetella pertussis in all age groups in 2023 were significantly lower than those in 2022, which may be related to the fact that children under 3 years old did not receive the pertussis vaccine on time during the COVID-19 period, and the antibody levels against pertussis in children over 5 years old gradually decreased. Studies have shown that after the cancellation of NPIs in our country, the number of reported pertussis cases increased from 1,512 in June 2023 to a significant surge at the beginning of 2024, reaching 97,669 cases by May 2024 [31]. This study has not yet statistically analyzed the detection rates of Bordetella pertussis in this region for 2024. Factors such as increased awareness among healthcare professionals, strengthened surveillance measures, decreased vaccination rates in specific areas, insufficient vaccine efficacy, and the emergence of macrolide-resistant Bordetella pertussis are associated with the resurgence of pertussis [32]. The pertussis vaccination strategy in China mainly targets infants and young children, and the national immunization program does not include vaccination for infants under 3 months and children over 6 years old. Studies have shown that pertussis infections in infants under 3 months are more likely to develop into severe infections with higher mortality rates [33]. Given the high-density contact environment in schools, the risk of transmission of Bordetella pertussis among school-age children is higher. Research in Germany and the United Kingdom has shown that administering a booster dose at the age of 4–6 can reduce the incidence of pertussis in the entire population and prevent household transmission [34, 35].

MP is one of the most common pathogens of respiratory infections in children and adolescents, accounting for 40% of community-acquired pneumonia in children over 5 years old [36]. The research results of this study in 2023 showed that the most common pathogen in school-age children was MP. From September to December 2023, the detection rate of MP remained high. It has been reported that in the autumn and winter of 2023, there was a significant increase in the prevalence of MP in northern China, the Netherlands, and the United States [37,38,39]. The sharp increase in MP infections from October to November 2023 attracted close attention from the World Health Organization [40]. The epidemic of MP pneumonia (MPP) is cyclical, with regional outbreaks occurring every 3 to 7 years, and each outbreak can last for 1 to 1.5 years [41] In this study, the positive detection rates of MP in children under 3 years old and those aged 6–17 years in 2023 were significantly higher than those in 2022. This may be related to the inherent cyclical pattern of MPP and the potential “immune debt“ [15]. Since 2000, macrolide-resistant M.pneumoniae (MRMP) infections have become more prevalent around the world, especially in East Asia, where the isolation rate of MRMP has reached as high as 70–90%. This high prevalence has posed significant challenges for pediatricians. In the absence of effective antibiotics, MRMP infections inevitably bring a series of clinical problems, including prolonged fever and hospitalization, an increase in severe cases, and difficulties in antibiotic selection. The emergence of MRMP in 2023 was also one of the reasons for this result [37, 42].

In our study, we employed tNGS for pathogen detection. While tNGS offers high sensitivity for pathogen detection, this advantage comes with inherent challenges. Due to the fact that NGS includes a pre-amplification step prior to sequencing, plus the sequencing being a sequencing-by-synthesis method, the technique’s high sensitivity increases the risk of false positives from environmental contaminants (e.g., reagent microbes or aerosols). The implementation of standardized tNGS protocols incorporating negative controls, external positive controls during extraction, and non-template controls in sequencing procedures effectively addresses this limitation. Future studies should expand to multicenter cohorts with larger sample sizes to improve the generalizability of the findings. Additionally, there are numerous other point-of-care (POC) technologies available for pathogen detection [43]. Nucleic Acid Amplification Tests (NAATs) enable rapid diagnosis and are widely used in clinical practice, with the capability to simultaneously detect multiple viruses. These methods are susceptible to contamination, relatively high in cost, and unable to provide quantitative viral load measurements [44]. Immunoassays feature user-friendly operation and deliver rapid results, with the additional capability for multiplex viral detection. The utility is constrained by an inability to quantify viral loads, stringent storage requirements (particularly refrigeration needs for specific assays), and potential cross-reactivity issues [45].

This article compares the epidemiological characteristics of common pathogens in respiratory infections among children in China during the COVID-19 pandemic and after the full reopening. Nevertheless, several limitations should be noted in this study. First, this study was conducted in a single center, which may lead to bias in the selection of patients. Second, during the pandemic, many public health interventions were implemented, some of which (such as wearing masks) still existed in some populations later on. Therefore, the sample size should be further expanded, and pathogens should be assessed for at least two years before and after COVID-19 to check which of these measures may be the most effective in preventing the spread of respiratory pathogens.Third, the detection of respiratory pathogens (including viruses and bacteria) relied solely on a single testing methodology, which may yield false-negative results. Furthermore, potential contamination risks during sample transportation and processing could compromise the accuracy of test results.