{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T10:19:54Z","timestamp":1785406794713,"version":"3.56.0"},"reference-count":68,"publisher":"American Society for Microbiology","issue":"12","license":[{"start":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T00:00:00Z","timestamp":1764633600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T00:00:00Z","timestamp":1764633600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Microbiol Spectr"],"published-print":{"date-parts":[[2025,12,2]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:sec>\n                    <jats:title\/>\n                    <jats:p>\n                      Community-acquired pneumonia (CAP) has emerged as a significant health challenge for young children, especially after the relaxation of COVID-19 restrictions, which coincided with a sharp increase in CAP cases. While pathogen profiling is commonly performed, comprehensive studies examining the total infectome and its dynamic changes during disease progression and in relation to the pandemic remain scarce. To address this gap, we conducted a prospective cohort study involving 58 children hospitalized with CAP in Wuxi, China, during and after COVID-19 control measures. Sputum samples were analyzed using metagenomic and metatranscriptomic sequencing to characterize the total infectome. Results showed that RNA sequencing offers a more comprehensive view of the infectome, while DNA sequencing excels in detecting DNA viruses with greater sensitivity. Notable increases in\n                      <jats:italic toggle=\"yes\">Mycoplasma pneumoniae<\/jats:italic>\n                      , human respiratory syncytial virus (RSV), and\n                      <jats:italic toggle=\"yes\">Haemophilus influenzae<\/jats:italic>\n                      were observed after COVID-19 restrictions were lifted. During disease progression, some patients exhibited a decline in pathogen abundance, while others developed secondary infections, frequently involving co-infections, which might contribute to prolonged pneumonia or complicated disease course. Viral-bacterial co-infections were common, with\n                      <jats:italic toggle=\"yes\">M. pneumoniae<\/jats:italic>\n                      and RSV being the most prevalent combination. In summary, this study highlights the shifting respiratory infectome in children with CAP, both after the relaxation of COVID-19 control measures and throughout hospitalization. It emphasizes the need for comprehensive infectome monitoring to track dynamic changes across broader timeframes and during disease progression, offering insights for improved clinical management and future research.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>IMPORTANCE<\/jats:title>\n                    <jats:p>\n                      Community-acquired pneumonia (CAP) remains a leading threat to children\u2019s health globally, with shifting pathogen dynamics post-COVID-19 posing new challenges. This study reveals how pandemic control measures and their relaxation influenced the respiratory \u201cinfectome\u201d\u2014the full spectrum of pathogens\u2014in children with CAP. By integrating multi-sequencing technologies, we uncovered critical trends: a resurgence of virulent pathogens like\n                      <jats:italic toggle=\"yes\">Mycoplasma pneumoniae<\/jats:italic>\n                      and respiratory syncytial virus after restrictions eased, frequent viral-bacterial co-infections linked to prolonged pneumonia, and distinct infection patterns during hospitalization that predict recovery or complications. These findings highlight the need for dynamic, multi-pathogen surveillance to guide clinical decisions, particularly in managing co-infections and preventing secondary infections. Our work provides actionable insights for pediatricians and public health experts to anticipate post-pandemic pathogen behavior, tailor treatments, and mitigate risks during future outbreaks, ultimately improving care for vulnerable young patients.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1128\/spectrum.01450-25","type":"journal-article","created":{"date-parts":[[2025,10,27]],"date-time":"2025-10-27T12:00:33Z","timestamp":1761566433000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":2,"title":["Dynamics of the respiratory infectome in children with community-acquired pneumonia: insights from large and short time-scale analyses"],"prefix":"10.1128","volume":"13","author":[{"given":"Yuqi","family":"Liao","sequence":"first","affiliation":[{"name":"State key laboratory for biocontrol, Shenzhen Key Laboratory of Systems Medicine for inflammatory diseases, School of Medicine, Shenzhen 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