Clinical Features and Value of Tracheal Aspirate Metagenomic Next-Generation Sequencing for Severe Pneumonia in Children in Pediatric Intensive Care Unit

Anteneh ZA, Arega HE, Mihretie KM. Validation of risk prediction for outcomes of severe community-acquired pneumonia among under-five children in Amhara region, Northwest Ethiopia. PLoS One. 2023 Feb;18 (2):e0281209. https://doi.org/10.1371/jour-nal.pone.0281209 Anteneh ZA Arega HE Mihretie KM. Validation of risk prediction for outcomes of severe community-acquired pneumonia among under-five children in Amhara region, Northwest Ethiopia . PLoS One . 2023 Feb ; 18 ( 2 ): e0281209 . https://doi.org/10.1371/jour-nal.pone.0281209 Search in Google Scholar

Biesbroek G, Tsivtsivadze E, Sanders EA, Montijn R, Veenhoven RH, Keijser BJ, Bogaert D. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children. Am J Respir Crit Care Med. 2014 Dec;190 (11):1283–1292. https://doi.org/10.1164/rccm.201407-1240oc Biesbroek G Tsivtsivadze E Sanders EA Montijn R Veenhoven RH Keijser BJ Bogaert D. Early respiratory microbiota composition determines bacterial succession patterns and respiratory health in children . Am J Respir Crit Care Med . 2014 Dec ; 190 ( 11 ): 1283 – 1292 . https://doi.org/10.1164/rccm.201407-1240oc Search in Google Scholar

Black RE, Cousens S, Johnson HL, Lawn JE, Rudan I, Bassani DG, Jha P, Campbell H, Walker CF, Cibulskis R, et al.; Child Health Epidemiology Reference Group of WHO and UNICEF. Global, regional, and national causes of child mortality in 2008: A systematic analysis. Lancet. 2010 Jun;375 (9730):1969–1987. https://doi.org/10.1016/S0140-6736 (10)60549-1 Black RE Cousens S Johnson HL Lawn JE Rudan I Bassani DG Jha P Campbell H Walker CF Cibulskis R .; Child Health Epidemiology Reference Group of WHO and UNICEF Global, regional, and national causes of child mortality in 2008: A systematic analysis . Lancet . 2010 Jun ; 375 ( 9730 ): 1969 – 1987 . https://doi.org/10.1016/S0140-6736 (10)60549-1 Search in Google Scholar

Blauwkamp TA, Thair S, Rosen MJ, Blair L, Lindner MS, Vil-fan ID, Kawli T, Christians FC, Venkatasubrahmanyam S, et al. Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease. Nat Microbiol. 2019 Apr;4 (4):663–674. https://doi.org/10.1038/s41564-018-0349-6 Blauwkamp TA Thair S Rosen MJ Blair L Lindner MS Vil-fan ID Kawli T Christians FC Venkatasubrahmanyam S Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease . Nat Microbiol . 2019 Apr ; 4 ( 4 ): 663 – 674 . https://doi.org/10.1038/s41564-018-0349-6 Search in Google Scholar

Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug;30 (15):2114–2120. https://doi.org/10.1093/bioinformatics/btu170 Bolger AM Lohse M Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data . Bioinformatics . 2014 Aug ; 30 ( 15 ): 2114 – 2120 . https://doi.org/10.1093/bioinformatics/btu170 Search in Google Scholar

Bradley JS, Byington CL, Shah SS, Alverson B, Carter ER, Harrison C, Kaplan SL, Mace SE, McCracken GH Jr, Moore MR, et al; Pediatric Infectious Diseases Society and the Infectious Diseases Society of America. The management of community-acquired pneumonia in infants and children older than 3 months of age: Clinical practice guidelines by the Pediatric Infectious Diseases Society and the Infectious Diseases Society of America. Clin Infect Dis. 2011 Oct;53 (7):e25–76. https://doi.org/10.1093/cid/cir531 Bradley JS Byington CL Shah SS Alverson B Carter ER Harrison C Kaplan SL Mace SE McCracken GH Jr Moore MR .; Pediatric Infectious Diseases Society and the Infectious Diseases Society of America The management of community-acquired pneumonia in infants and children older than 3 months of age: Clinical practice guidelines by the Pediatric Infectious Diseases Society and the Infectious Diseases Society of America . Clin Infect Dis . 2011 Oct ; 53 ( 7 ): e25 – 76 . https://doi.org/10.1093/cid/cir531 Search in Google Scholar

Cebey-López M, Herberg J, Pardo-Seco J, Gómez-Carballa A, Martinón-Torres N, Salas A, Martinón-Sánchez JM, Justicia A, Rivero-Calle I, Sumner E, et al.; GENDRES network. Does viral co-infection influence the severity of acute respiratory infection in children? PLoS One. 2016 Apr;11 (4):e0152481. https://doi.org/10.1371/journal.pone.0152481 Cebey-López M Herberg J Pardo-Seco J Gómez-Carballa A Martinón-Torres N Salas A Martinón-Sánchez JM Justicia A Rivero-Calle I Sumner E GENDRES network Does viral co-infection influence the severity of acute respiratory infection in children? PLoS One . 2016 Apr ; 11 ( 4 ): e0152481 . https://doi.org/10.1371/journal.pone.0152481 Search in Google Scholar

Chen D, Cao L, Li W. Etiological and clinical characteristics of severe pneumonia in pediatric intensive care unit (PICU). BMC Pediatr. 2023 Jul;23 (1):362. https://doi.org/10.1186/s12887-023-04175-y Chen D Cao L Li W. Etiological and clinical characteristics of severe pneumonia in pediatric intensive care unit (PICU) . BMC Pediatr . 2023 Jul ; 23 ( 1 ): 362 . https://doi.org/10.1186/s12887-023-04175-y Search in Google Scholar

Chen H, Zhang Y, Zheng J, Shi L, He Y, Niu Y, Lei J, Zhao Y, Xia H, Chen T. Application of mNGS in the etiological diagnosis of thoracic and abdominal infection in patients with end-stage liver disease. Front Cell Infect Microbiol. 2022 Jan;11:741220. https://doi.org/10.3389/fcimb.2021.741220 Chen H Zhang Y Zheng J Shi L He Y Niu Y Lei J Zhao Y Xia H Chen T. Application of mNGS in the etiological diagnosis of thoracic and abdominal infection in patients with end-stage liver disease . Front Cell Infect Microbiol . 2022 Jan ; 11 : 741220 . https://doi.org/10.3389/fcimb.2021.741220 Search in Google Scholar

Chen H, Zheng Y, Zhang X, Liu S, Yin Y, Guo Y, Wang X, Zhang Y, Zhao C, Gai W, et al. Clinical evaluation of cell-free and cellular metagenomic next-generation sequencing of infected body fluids. J Adv Res. 2024 Jan;55:119–129. https://doi.org/10.1016/j.jare.2023.02.018 Chen H Zheng Y Zhang X Liu S Yin Y Guo Y Wang X Zhang Y Zhao C Gai W Clinical evaluation of cell-free and cellular metagenomic next-generation sequencing of infected body fluids . J Adv Res . 2024 Jan ; 55 : 119 – 129 . https://doi.org/10.1016/j.jare.2023.02.018 Search in Google Scholar

Chen J, Hu P, Zhou T, Zheng T, Zhou L, Jiang C, Pei X. Epidemiology and clinical characteristics of acute respiratory tract infections among hospitalized infants and young children in Chengdu, West China, 2009–2014. BMC Pediatr. 2018 Jul;18 (1):216. https://doi.org/10.1186/s12887-018-1203-y Chen J Hu P Zhou T Zheng T Zhou L Jiang C Pei X. Epidemiology and clinical characteristics of acute respiratory tract infections among hospitalized infants and young children in Chengdu, West China, 2009–2014 . BMC Pediatr . 2018 Jul ; 18 ( 1 ): 216 . https://doi.org/10.1186/s12887-018-1203-y Search in Google Scholar

Chisti MJ, Salam MA, Smith JH, Ahmed T, Pietroni MA, Sha-hunja KM, Shahid AS, Faruque AS, Ashraf H, Bardhan PK, et al. Bubble continuous positive airway pressure for children with severe pneumonia and hypoxaemia in Bangladesh: An open, randomised controlled trial. Lancet. 2015 Sep;386 (9998):1057–1065. https://doi.org/10.1016/s0140-6736 (15)60249-5 Chisti MJ Salam MA Smith JH Ahmed T Pietroni MA Sha-hunja KM Shahid AS Faruque AS Ashraf H Bardhan PK Bubble continuous positive airway pressure for children with severe pneumonia and hypoxaemia in Bangladesh: An open, randomised controlled trial . Lancet . 2015 Sep ; 386 ( 9998 ): 1057 – 1065 . https://doi.org/10.1016/s0140-6736 (15)60249-5 Search in Google Scholar

Do Q, Dao TM, Nguyen TNT, Tran QA, Nguyen HT, Ngo TT. Procalcitonin identifies bacterial coinfections in Vietnamese children with severe respiratory syncytial virus pneumonia. Biomed Res Int. 2020 May;2020:7915158. https://doi.org/10.1155/2020/7915158 Do Q Dao TM Nguyen TNT Tran QA Nguyen HT Ngo TT. Procalcitonin identifies bacterial coinfections in Vietnamese children with severe respiratory syncytial virus pneumonia . Biomed Res Int . 2020 May ; 2020 : 7915158 . https://doi.org/10.1155/2020/7915158 Search in Google Scholar

Esposito S, Daleno C, Prunotto G, Scala A, Tagliabue C, Borzani I, Fossali E, Pelucchi C, Principi N. Impact of viral infections in children with community-acquired pneumonia: Results of a study of 17 respiratory viruses. Influenza Other Respir Viruses. 2013 Jan;7 (1):18–26. https://doi.org/10.1111/j.1750-2659.2012.00340.x Esposito S Daleno C Prunotto G Scala A Tagliabue C Borzani I Fossali E Pelucchi C Principi N. Impact of viral infections in children with community-acquired pneumonia: Results of a study of 17 respiratory viruses . Influenza Other Respir Viruses . 2013 Jan ; 7 ( 1 ): 18 – 26 . https://doi.org/10.1111/j.1750-2659.2012.00340.x Search in Google Scholar

Gonapaladeniya M, Dissanayake T, Liyanage G. Burden of respiratory syncytial virus associated severe pneumonia in hospitalized children. Int J Pediatr. 2021 Jun 30;2021:8269400. https://doi.org/10.1155/2021/8269400 Gonapaladeniya M Dissanayake T Liyanage G. Burden of respiratory syncytial virus associated severe pneumonia in hospitalized children . Int J Pediatr . 2021 Jun 30 ; 2021 : 8269400 . https://doi.org/10.1155/2021/8269400 Search in Google Scholar

Gu W, Miller S, Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection. Annu Rev Pathol. 2019 Jan;14:319–338. https://doi.org/10.1146/annurev-pathmechdis-012418-012751 Gu W Miller S Chiu CY. Clinical metagenomic next-generation sequencing for pathogen detection . Annu Rev Pathol . 2019 Jan ; 14 : 319 – 338 . https://doi.org/10.1146/annurev-pathmechdis-012418-012751 Search in Google Scholar

Hurst JH, McCumber AW, Aquino JN, Rodriguez J, Heston SM, Lugo DJ, Rotta AT, Turner NA, Pfeiffer TS, Gurley TC, et al. Age-related changes in the nasopharyngeal microbiome are associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and symptoms among children, adolescents, and young adults. Clin Infect Dis. 2022 Aug;75 (1):e928–e937. https://doi.org/10.1093/cid/ciac184 Hurst JH McCumber AW Aquino JN Rodriguez J Heston SM Lugo DJ Rotta AT Turner NA Pfeiffer TS Gurley TC Age-related changes in the nasopharyngeal microbiome are associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and symptoms among children, adolescents, and young adults . Clin Infect Dis . 2022 Aug ; 75 ( 1 ): e928 – e937 . https://doi.org/10.1093/cid/ciac184 Search in Google Scholar

Kalantar KL, Moazed F, Christenson SC, Wilson J, Deiss T, Belzer A, Vessel K, Caldera S, Jauregui A, Bolourchi S, et al. Metag-enomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota. Am J Physiol Lung Cell Mol Physiol. 2019 Mar;316 (3):L578-L584. https://doi.org/10.1152/ajplung.00476.2018 Kalantar KL Moazed F Christenson SC Wilson J Deiss T Belzer A Vessel K Caldera S Jauregui A Bolourchi S Metag-enomic comparison of tracheal aspirate and mini-bronchial alveolar lavage for assessment of respiratory microbiota . Am J Physiol Lung Cell Mol Physiol . 2019 Mar ; 316 ( 3 ): L578 – L584 . https://doi.org/10.1152/ajplung.00476.2018 Search in Google Scholar

Kalil AC, Metersky ML, Klompas M, Muscedere J, Sweeney DA, Palmer LB, Napolitano LM, O’Grady NP, Bartlett JG, Carratalà J, et al. Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society. Clin Infect Dis. 2016 Sep;63 (5):e61–e111. https://doi.org/10.1093/cid/ciw353 Kalil AC Metersky ML Klompas M Muscedere J Sweeney DA Palmer LB Napolitano LM O’Grady NP Bartlett JG Carratalà J Management of adults with hospital-acquired and ventilator-associated pneumonia: 2016 Clinical Practice Guidelines by the Infectious Diseases Society of America and the American Thoracic Society . Clin Infect Dis . 2016 Sep ; 63 ( 5 ): e61 – e111 . https://doi.org/10.1093/cid/ciw353 Search in Google Scholar

Katayama Y, Minami H, Enomoto M, Takano T, Hayashi S, Lee YK. Usefulness of Gram staining of tracheal aspirates in initial therapy for ventilator-associated pneumonia in extremely preterm neonates. J Perinatol. 2010 Apr;30 (4):270–274. https://doi.org/10.1038/jp.2009.144 Katayama Y Minami H Enomoto M Takano T Hayashi S Lee YK. Usefulness of Gram staining of tracheal aspirates in initial therapy for ventilator-associated pneumonia in extremely preterm neonates . J Perinatol . 2010 Apr ; 30 ( 4 ): 270 – 274 . https://doi.org/10.1038/jp.2009.144 Search in Google Scholar

Khuri-Bulos N, Lawrence L, Piya B, Wang L, Fonnesbeck C, Faouri S, Shehabi A, Vermund SH, Williams JV, Halasa NB. Severe outcomes associated with respiratory viruses in newborns and infants: A prospective viral surveillance study in Jordan. BMJ Open. 2018 May;8 (5):e021898. https://doi.org/10.1136/bmjop-en-2018-021898 Khuri-Bulos N Lawrence L Piya B Wang L Fonnesbeck C Faouri S Shehabi A Vermund SH Williams JV Halasa NB. Severe outcomes associated with respiratory viruses in newborns and infants: A prospective viral surveillance study in Jordan . BMJ Open . 2018 May ; 8 ( 5 ): e021898 . https://doi.org/10.1136/bmjop-en-2018-021898 Search in Google Scholar

Kloepfer KM, Kennedy JL. Childhood respiratory viral infections and the microbiome. J Allergy Clin Immunol. 2023 Oct;152 (4):827–834. https://doi.org/10.1016/j.jaci.2023.08.008 Kloepfer KM Kennedy JL. Childhood respiratory viral infections and the microbiome . J Allergy Clin Immunol . 2023 Oct ; 152 ( 4 ): 827 – 834 . https://doi.org/10.1016/j.jaci.2023.08.008 Search in Google Scholar

Kumpitsch C, Koskinen K, Schöpf V, Moissl-Eichinger C. The microbiome of the upper respiratory tract in health and disease. BMC Biol. 2019 Nov;17 (1):87. https://doi.org/10.1186/s12915-019-0703-z Kumpitsch C Koskinen K Schöpf V Moissl-Eichinger C. The microbiome of the upper respiratory tract in health and disease . BMC Biol . 2019 Nov ; 17 ( 1 ): 87 . https://doi.org/10.1186/s12915-019-0703-z Search in Google Scholar

Langelier C, Kalantar KL, Moazed F, Wilson MR, Crawford ED, Deiss T, Belzer A, Bolourchi S, Caldera S, Fung M, et al. Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults. Proc Natl Acad Sci USA. 2018 Dec;115 (52):E12353–E12362. https://doi.org/10.1073/pnas.1809700115 Langelier C Kalantar KL Moazed F Wilson MR Crawford ED Deiss T Belzer A Bolourchi S Caldera S Fung M Integrating host response and unbiased microbe detection for lower respiratory tract infection diagnosis in critically ill adults . Proc Natl Acad Sci USA . 2018 Dec ; 115 ( 52 ): E12353 – E12362 . https://doi.org/10.1073/pnas.1809700115 Search in Google Scholar

Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012 Mar;9 (4):357–359. https://doi.org/10.1038/nmeth.1923 Langmead B Salzberg SL. Fast gapped-read alignment with Bowtie 2 . Nat Methods . 2012 Mar ; 9 ( 4 ): 357 – 359 . https://doi.org/10.1038/nmeth.1923 Search in Google Scholar

Li D, Gai W, Zhang J, Cheng W, Cui N, Wang H. Metagenomic next-generation sequencing for the microbiological diagnosis of abdominal sepsis patients. Front Microbiol. 2022a Feb;13:816631. https://doi.org/10.3389/fmicb.2022.816631 Li D Gai W Zhang J Cheng W Cui N Wang H. Metagenomic next-generation sequencing for the microbiological diagnosis of abdominal sepsis patients . Front Microbiol . 2022a Feb ; 13 : 816631 . https://doi.org/10.3389/fmicb.2022.816631 Search in Google Scholar

Li D, Gai W, Zhang J, Cheng W, Cui N, Wang H. Multisite metag-enomic next-generation sequencing improved diagnostic performance for sepsis-associated lymphopenia patients. Microbiol Spectr. 2022b Dec;10 (6):e0353222. https://doi.org/10.1128/spec-trum.03532-22 Li D Gai W Zhang J Cheng W Cui N Wang H. Multisite metag-enomic next-generation sequencing improved diagnostic performance for sepsis-associated lymphopenia patients . Microbiol Spectr . 2022b Dec ; 10 ( 6 ): e0353222 . https://doi.org/10.1128/spec-trum.03532-22 Search in Google Scholar

Li M, Wang J, Yao Z, Liao H, Su S, Yang X, Xie M, Zheng Y. Metag-enomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit. Front Public Health. 2023 Jun 15;11:1177069. https://doi.org/10.3389/fpubh.2023.1177069 Li M Wang J Yao Z Liao H Su S Yang X Xie M Zheng Y. Metag-enomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit . Front Public Health . 2023 Jun 15 ; 11 : 1177069 . https://doi.org/10.3389/fpubh.2023.1177069 Search in Google Scholar

Li Z, Gu W, Zhu F, Han E, Yan Y, Sun H, Xu W, Zhang X, Huang L, Gao S, et al. Clinical characteristics and risk factors of severe pneumonia caused by human bocavirus in children. BMC Infect Dis. 2025 Jan;25 (1):58. https://doi.org/10.1186/s12879-025-10465-w Li Z Gu W Zhu F Han E Yan Y Sun H Xu W Zhang X Huang L Gao S Clinical characteristics and risk factors of severe pneumonia caused by human bocavirus in children . BMC Infect Dis . 2025 Jan ; 25 ( 1 ): 58 . https://doi.org/10.1186/s12879-025-10465-w Search in Google Scholar

Liu L, Oza S, Hogan D, Perin J, Rudan I, Lawn JE, Cousens S, Mathers C, Black RE. Global, regional, and national causes of child mortality in 2000–13, with projections to inform post-2015 priorities: An updated systematic analysis. Lancet. 2015 Jan;385 (9966):430–440. https://doi.org/10.1016/s0140-6736 (14)61698-6 Liu L Oza S Hogan D Perin J Rudan I Lawn JE Cousens S Mathers C Black RE. Global, regional, and national causes of child mortality in 2000–13, with projections to inform post-2015 priorities: An updated systematic analysis . Lancet . 2015 Jan ; 385 ( 9966 ): 430 – 440 . https://doi.org/10.1016/s0140-6736 (14)61698-6 Search in Google Scholar

Liu YN, Zhang YF, Xu Q, Qiu Y, Lu QB, Wang T, Zhang XA, Lin SH, Lv CL, Jiang BG, et al; Chinese Center for Disease Control and Prevention Etiology Surveillance Study Team of Acute Respiratory Infections. Infection and co-infection patterns of community-acquired pneumonia in patients of different ages in China from 2009 to 2020: A national surveillance study. Lancet Microbe. 2023 May;4 (5):e330–e339. https://doi.org/10.1016/s2666-5247(23)00031-9 Liu YN Zhang YF Xu Q Qiu Y Lu QB Wang T Zhang XA Lin SH Lv CL Jiang BG Chinese Center for Disease Control and Prevention Etiology Surveillance Study Team of Acute Respiratory Infections Infection and co-infection patterns of community-acquired pneumonia in patients of different ages in China from 2009 to 2020: A national surveillance study . Lancet Microbe . 2023 May ; 4 ( 5 ): e330 – e339 . https://doi.org/10.1016/s2666-5247(23)00031-9 Search in Google Scholar

Lyu J, Deng Q, Li R, Tian B, Zhao Y, Hu X, Zhou M, Gu B. Pneumonia caused by coinfection with cytomegalovirus and Pneumocystis jirovecii in an HIV-negative infant diagnosed by metagenomic next-generation sequencing. Infect Drug Resist. 2022 Jun;15:3417–3425. https://doi.org/10.2147/idr.s364241 Lyu J Deng Q Li R Tian B Zhao Y Hu X Zhou M Gu B. Pneumonia caused by coinfection with cytomegalovirus and Pneumocystis jirovecii in an HIV-negative infant diagnosed by metagenomic next-generation sequencing . Infect Drug Resist . 2022 Jun ; 15 : 3417 – 3425 . https://doi.org/10.2147/idr.s364241 Search in Google Scholar

McCauley K, Durack J, Valladares R, Fadrosh DW, Lin DL, Calatroni A, LeBeau PK, Tran HT, Fujimura KE, LaMere B, et al; National Institute of Allergy and Infectious Diseases–spon-sored Inner-City Asthma Consortium. Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma. J Allergy Clin Immunol. 2019 Nov;144 (5):1187–1197. https://doi.org/10.1016/j.jaci.2019.05.035 McCauley K Durack J Valladares R Fadrosh DW Lin DL Calatroni A LeBeau PK Tran HT Fujimura KE LaMere B National Institute of Allergy and Infectious Diseases–spon-sored Inner-City Asthma Consortium Distinct nasal airway bacterial microbiotas differentially relate to exacerbation in pediatric patients with asthma . J Allergy Clin Immunol . 2019 Nov ; 144 ( 5 ): 1187 – 1197 . https://doi.org/10.1016/j.jaci.2019.05.035 Search in Google Scholar

McCauley KE, Flynn K, Calatroni A, DiMassa V, LaMere B, Fad-rosh DW, Lynch KV, Gill MA, Pongracic JA, Khurana Hershey GK, et al; National Institute of Allergy and Infectious Diseas-es–sponsored Inner-City Asthma Consortium. Seasonal airway microbiome and transcriptome interactions promote childhood asthma exacerbations. J Allergy Clin Immunol. 2022 Jul;150 (1):204–213. https://doi.org/10.1016/j.jaci.2022.01.020 McCauley KE Flynn K Calatroni A DiMassa V LaMere B Fad-rosh DW Lynch KV Gill MA Pongracic JA Khurana Hershey GK National Institute of Allergy and Infectious Diseas-es–sponsored Inner-City Asthma Consortium . Seasonal airway microbiome and transcriptome interactions promote childhood asthma exacerbations . J Allergy Clin Immunol . 2022 Jul ; 150 ( 1 ): 204 – 213 . https://doi.org/10.1016/j.jaci.2022.01.020 Search in Google Scholar

Men Z, Chen Z, Gu X, Wang Y, Zhang X, Fang F, Shen M, Huang S, Wu S, Zhou L, et al. Clinical relevance of lung microbiota composition in critically ill children with acute lower respiratory tract infections: insights from a retrospective analysis of metagenomic sequencing. Eur J Clin Microbiol Infect Dis. 2025 Jan;441):83–98. https://doi.org/10.1007/s10096-024-04980-y Men Z Chen Z Gu X Wang Y Zhang X Fang F Shen M Huang S Wu S Zhou L Clinical relevance of lung microbiota composition in critically ill children with acute lower respiratory tract infections: insights from a retrospective analysis of metagenomic sequencing . Eur J Clin Microbiol Infect Dis . 2025 Jan ; 441 ): 83 – 98 . https://doi.org/10.1007/s10096-024-04980-y Search in Google Scholar

Meskill SD, O’Bryant SC. Respiratory virus co-infection in acute respiratory infections in children. Curr Infect Dis Rep. 2020 Jan;22 (1):3. https://doi.org/10.1007/s11908-020-0711-8 Meskill SD O’Bryant SC. Respiratory virus co-infection in acute respiratory infections in children . Curr Infect Dis Rep . 2020 Jan ; 22 ( 1 ): 3 . https://doi.org/10.1007/s11908-020-0711-8 Search in Google Scholar

Mick E, Tsitsiklis A, Kamm J, Kalantar KL, Caldera S, Lyden A, Tan M, Detweiler AM, Neff N, Osborne CM, et al. Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children. J Clin Invest. 2023 Apr;133 (7):e165904. https://doi.org/10.1172/jci165904 Mick E Tsitsiklis A Kamm J Kalantar KL Caldera S Lyden A Tan M Detweiler AM Neff N Osborne CM Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children . J Clin Invest . 2023 Apr ; 133 ( 7 ): e165904 . https://doi.org/10.1172/jci165904 Search in Google Scholar

Muhlebach MS, Zorn BT, Esther CR, Hatch JE, Murray CP, Turkovic L, Ranganathan SC, Boucher RC, Stick SM, Wolfgang MC. Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children. PLoS Pathog. 2018 Jan;14 (1):e1006798. https://doi.org/10.1371/journal.ppat.1006798 Muhlebach MS Zorn BT Esther CR Hatch JE Murray CP Turkovic L Ranganathan SC Boucher RC Stick SM Wolfgang MC. Initial acquisition and succession of the cystic fibrosis lung microbiome is associated with disease progression in infants and preschool children . PLoS Pathog . 2018 Jan ; 14 ( 1 ): e1006798 . https://doi.org/10.1371/journal.ppat.1006798 Search in Google Scholar

Ning G, Wang X, Wu D, Yin Z, Li Y, Wang H, Yang W. The etiology of community-acquired pneumonia among children under 5 years of age in mainland China, 2001–2015: A systematic review. Hum Vaccin Immunother. 2017 Nov;13 (11):2742–2750. https://doi.org/10.1080/21645515.2017.1371381 Ning G Wang X Wu D Yin Z Li Y Wang H Yang W. The etiology of community-acquired pneumonia among children under 5 years of age in mainland China, 2001–2015: A systematic review . Hum Vaccin Immunother . 2017 Nov ; 13 ( 11 ): 2742 – 2750 . https://doi.org/10.1080/21645515.2017.1371381 Search in Google Scholar

Ogunbayo AE, Mogotsi MT, Sondlane H, Sabiu S, Nyaga MM. Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa. J Med Virol. 2023 May;95 (5):e28753. https://doi.org/10.1002/jmv.28753 Ogunbayo AE Mogotsi MT Sondlane H Sabiu S Nyaga MM. Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa . J Med Virol . 2023 May ; 95 ( 5 ): e28753 . https://doi.org/10.1002/jmv.28753 Search in Google Scholar

Pettigrew MM, Gent JF, Kong Y, Wade M, Gansebom S, Bramley AM, Jain S, Arnold SL, McCullers JA. Association of sputum microbiota profiles with severity of community-acquired pneumonia in children. BMC Infect Dis. 2016 Jul;16:317. https://doi.org/10.1186/s12879-016-1670-4 Pettigrew MM Gent JF Kong Y Wade M Gansebom S Bramley AM Jain S Arnold SL McCullers JA. Association of sputum microbiota profiles with severity of community-acquired pneumonia in children . BMC Infect Dis . 2016 Jul ; 16 : 317 . https://doi.org/10.1186/s12879-016-1670-4 Search in Google Scholar

Renz H, Adkins BD, Bartfeld S, Blumberg RS, Farber DL, Garssen J, Ghazal P, Hackam DJ, Marsland BJ, McCoy KD, et al. The neonatal window of opportunity-early priming for life. J Allergy Clin Immunol. 2018 Apr;141 (4):1212–1214. https://doi.org/10.1016/j.jaci.2017.11.019 Renz H Adkins BD Bartfeld S Blumberg RS Farber DL Garssen J Ghazal P Hackam DJ Marsland BJ McCoy KD The neonatal window of opportunity-early priming for life . J Allergy Clin Immunol . 2018 Apr ; 141 ( 4 ): 1212 – 1214 . https://doi.org/10.1016/j.jaci.2017.11.019 Search in Google Scholar

Rudan I, Boschi-Pinto C, Biloglav Z, Mulholland K, Campbell H. Epidemiology and etiology of childhood pneumonia. Bull World Health Organ. 2008 May;86 (5):408–416. https://doi.org/10.2471/blt.07.048769 Rudan I Boschi-Pinto C Biloglav Z Mulholland K Campbell H. Epidemiology and etiology of childhood pneumonia . Bull World Health Organ . 2008 May ; 86 ( 5 ): 408 – 416 . https://doi.org/10.2471/blt.07.048769 Search in Google Scholar

Rudan I, O’Brien KL, Nair H, Liu L, Theodoratou E, Qazi S, Lukšić I, Fischer Walker CL, Black RE, Campbell H; Child Health Epidemiology Reference Group (CHERG). Epidemiology and etiology of childhood pneumonia in 2010: Estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries. J Glob Health. 2013 Jun;3 (1):010401. https://doi.org/10.7189/jogh.03.010401 Rudan I O’Brien KL Nair H Liu L Theodoratou E Qazi S Lukšić I Fischer Walker CL Black RE Campbell H Child Health Epidemiology Reference Group (CHERG) Epidemiology and etiology of childhood pneumonia in 2010: Estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries . J Glob Health . 2013 Jun ; 3 ( 1 ): 010401 . https://doi.org/10.7189/jogh.03.010401 Search in Google Scholar

Shen H, Liu T, Shen M, Zhang Y, Chen W, Chen H, Wang Y, Liu J, Tao J, He L, et al. Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: Results from a large real-world cohort. Front Cell Infect Microbiol. 2023 Aug;13:1200806. https://doi.org/10.3389/fcimb.2023.1200806 Shen H Liu T Shen M Zhang Y Chen W Chen H Wang Y Liu J Tao J He L Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: Results from a large real-world cohort . Front Cell Infect Microbiol . 2023 Aug ; 13 : 1200806 . https://doi.org/10.3389/fcimb.2023.1200806 Search in Google Scholar

Shi T, Chen C, Huang L, Fan H, Lu G, Yang D, Zhao C, Zhang D. Risk factors for mortality from severe community-acquired pneumonia in hospitalized children transferred to the pediatric intensive care unit. Pediatr Neonatol. 2020 Dec;61 (6):577–583. https://doi.org/10.1016/j.pedneo.2020.06.005 Shi T Chen C Huang L Fan H Lu G Yang D Zhao C Zhang D. Risk factors for mortality from severe community-acquired pneumonia in hospitalized children transferred to the pediatric intensive care unit . Pediatr Neonatol . 2020 Dec ; 61 ( 6 ): 577 – 583 . https://doi.org/10.1016/j.pedneo.2020.06.005 Search in Google Scholar

Shin EJ, Kim Y, Jeong JY, Jung YM, Lee MH, Chung EH. The changes of prevalence and etiology of pediatric pneumonia from National Emergency Department Information System in Korea, between 2007 and 2014. Korean J Pediatr. 2018 Sep;61 (9):291–300. https://doi.org/10.3345/kjp.2017.06100 Shin EJ Kim Y Jeong JY Jung YM Lee MH Chung EH. The changes of prevalence and etiology of pediatric pneumonia from National Emergency Department Information System in Korea, between 2007 and 2014 . Korean J Pediatr . 2018 Sep ; 61 ( 9 ): 291 – 300 . https://doi.org/10.3345/kjp.2017.06100 Search in Google Scholar

Vayssier-Taussat M, Albina E, Citti C, Cosson JF, Jacques MA, Lebrun MH, Le Loir Y, Ogliastro M, Petit MA, Roumagnac P, et al. Shifting the paradigm from pathogens to pathobiome: New concepts in the light of meta-omics. Front Cell Infect Microbiol. 2014 Mar 5;4:29. https://doi.org/10.3389/fcimb.2014.00029 Vayssier-Taussat M Albina E Citti C Cosson JF Jacques MA Lebrun MH Le Loir Y Ogliastro M Petit MA Roumagnac P Shifting the paradigm from pathogens to pathobiome: New concepts in the light of meta-omics . Front Cell Infect Microbiol . 2014 Mar 5 ; 4 : 29 . https://doi.org/10.3389/fcimb.2014.00029 Search in Google Scholar

Wickham H. ggplot2: Elegant graphics for data analysis. New York (USA): Springer International Publishing; 2016. https://doi.org/10.1007/978-3-319-24277-4 Wickham H. ggplot2: Elegant graphics for data analysis . New York (USA) : Springer International Publishing ; 2016 . https://doi.org/10.1007/978-3-319-24277-4 Search in Google Scholar

Williams AJ, Duong T, McNally LM, Tookey PA, Masters J, Miller R, Lyall EG, Gibb DM. Pneumocystis carinii pneumonia and cytomegalovirus infection in children with vertically acquired HIV infection. AIDS. 2001 Feb;15 (3):335–339. https://doi.org/10.1097/00002030-200102160-00006 Williams AJ Duong T McNally LM Tookey PA Masters J Miller R Lyall EG Gibb DM. Pneumocystis carinii pneumonia and cytomegalovirus infection in children with vertically acquired HIV infection . AIDS . 2001 Feb ; 15 ( 3 ): 335 – 339 . https://doi.org/10.1097/00002030-200102160-00006 Search in Google Scholar

Williams DJ, Zhu Y, Grijalva CG, Self WH, Harrell FE Jr, Reed C, Stockmann C, Arnold SR, Ampofo KK, Anderson EJ, et al. Predicting severe pneumonia outcomes in children. Pediatrics. 2016 Oct;138 (4):e20161019. https://doi.org/10.1542/peds.2016-1019 Williams DJ Zhu Y Grijalva CG Self WH Harrell FE Jr Reed C Stockmann C Arnold SR Ampofo KK Anderson EJ Predicting severe pneumonia outcomes in children . Pediatrics . 2016 Oct ; 138 ( 4 ): e20161019 . https://doi.org/10.1542/peds.2016-1019 Search in Google Scholar

Wood DE, Lu J, Langmead B. Improved metagenomic analysis with Kraken 2. Genome Biol. 2019 Nov;20 (1):257. https://doi.org/10.1186/s13059-019-1891-0 Wood DE Lu J Langmead B. Improved metagenomic analysis with Kraken 2 . Genome Biol . 2019 Nov ; 20 ( 1 ): 257 . https://doi.org/10.1186/s13059-019-1891-0 Search in Google Scholar

Wu HX, Wei FL, Zhang W, Han J, Guo S, Wang Z, Chen DX, Hou W, Hu ZJ. Clinical evaluation of metagenomic next-generation sequencing method for the diagnosis of suspected ascitic infection in patients with liver cirrhosis in a clinical laboratory. Microbiol Spectr. 2023 Feb;11 (1):e0294622. https://doi.org/10.1128/spec-trum.02946-22 Wu HX Wei FL Zhang W Han J Guo S Wang Z Chen DX Hou W Hu ZJ. Clinical evaluation of metagenomic next-generation sequencing method for the diagnosis of suspected ascitic infection in patients with liver cirrhosis in a clinical laboratory . Microbiol Spectr . 2023 Feb ; 11 ( 1 ): e0294622 . https://doi.org/10.1128/spec-trum.02946-22 Search in Google Scholar

Yi X, Gao J, Wang Z. The human lung microbiome – a hidden link between microbes and human health and diseases. iMeta. 2022 Jun;1 (3):e33. https://doi.org/10.1002/imt2.33 Yi X Gao J Wang Z. The human lung microbiome – a hidden link between microbes and human health and diseases . iMeta . 2022 Jun ; 1 ( 3 ): e33 . https://doi.org/10.1002/imt2.33 Search in Google Scholar

Zhang C, Liu T, Wang Y, Chen W, Liu J, Tao J, Zhang Z, Zhu X, Zhang Z, Ming M, et al. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid from children with severe pneumonia in pediatric intensive care unit. Front Cell Infect Microbiol. 2023 Mar;13:1082925. https://doi.org/10.3389/fcimb.2023.1082925 Zhang C Liu T Wang Y Chen W Liu J Tao J Zhang Z Zhu X Zhang Z Ming M Metagenomic next-generation sequencing of bronchoalveolar lavage fluid from children with severe pneumonia in pediatric intensive care unit . Front Cell Infect Microbiol . 2023 Mar ; 13 : 1082925 . https://doi.org/10.3389/fcimb.2023.1082925 Search in Google Scholar

Zhang H, Ai JW, Yang W, Zhou X, He F, Xie S, Zeng W, Li Y, Yu Y, Gou X, et al. Metatranscriptomic characterization of coronavirus disease 2019 identified a host transcriptional classifier associated with immune signaling. Clin Infect Dis. 2021 Aug;73 (3):376–385. https://doi.org/10.1093/cid/ciaa663 Zhang H Ai JW Yang W Zhou X He F Xie S Zeng W Li Y Yu Y Gou X Metatranscriptomic characterization of coronavirus disease 2019 identified a host transcriptional classifier associated with immune signaling . Clin Infect Dis . 2021 Aug ; 73 ( 3 ): 376 – 385 . https://doi.org/10.1093/cid/ciaa663 Search in Google Scholar

Zhang X, Chen Z, Gu W, Ji W, Wang Y, Hao C, He Y, Huang L, Wang M, Shao X, et al. Viral and bacterial co-infection in hospitalised children with refractory Mycoplasma pneumoniae pneumonia. Epidemiol Infect. 2018 Aug;146 (11):1384–1388. https://doi.org/10.1017/s0950268818000778 Zhang X Chen Z Gu W Ji W Wang Y Hao C He Y Huang L Wang M Shao X Viral and bacterial co-infection in hospitalised children with refractory Mycoplasma pneumoniae pneumonia . Epidemiol Infect . 2018 Aug ; 146 ( 11 ): 1384 – 1388 . https://doi.org/10.1017/s0950268818000778 Search in Google Scholar

Zhao Y, Lu R, Shen J, Xie Z, Liu G, Tan W. Comparison of viral and epidemiological profiles of hospitalized children with severe acute respiratory infection in Beijing and Shanghai, China. BMC Infect Dis. 2019 Aug;19 (1):729. https://doi.org/10.1186/s12879-019-4385-5 Zhao Y Lu R Shen J Xie Z Liu G Tan W. Comparison of viral and epidemiological profiles of hospitalized children with severe acute respiratory infection in Beijing and Shanghai, China . BMC Infect Dis . 2019 Aug ; 19 ( 1 ): 729 . https://doi.org/10.1186/s12879-019-4385-5 Search in Google Scholar

Zhu W, Wu Y, Liu H, Jiang C, Huo L. Gut-lung axis: Microbial crosstalk in pediatric respiratory tract infections. Front Immunol. 2021 Nov;12:741233. https://doi.org/10.3389/fimmu.2021.741233 Zhu W Wu Y Liu H Jiang C Huo L. Gut-lung axis: Microbial crosstalk in pediatric respiratory tract infections . Front Immunol . 2021 Nov ; 12 : 741233 . https://doi.org/10.3389/fimmu.2021.741233 Search in Google Scholar