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Trifonova I, Korsun N, Madzharova I, Alexiev I, Ivanov I, Levterova V, Grigorova L, Stoikov I, Donchev D, Christova I. Epidemiological and Genetic Characteristics of Respiratory Viral Coinfections with Different Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Viruses 2024; 16:958. [PMID: 38932250 PMCID: PMC11209099 DOI: 10.3390/v16060958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 06/07/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024] Open
Abstract
This study aimed to determine the incidence and etiological, seasonal, and genetic characteristics of respiratory viral coinfections involving severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Between October 2020 and January 2024, nasopharyngeal samples were collected from 2277 SARS-CoV-2-positive patients. Two multiplex approaches were used to detect and sequence SARS-CoV-2, influenza A/B viruses, and other seasonal respiratory viruses: multiplex real-time polymerase chain reaction (PCR) and multiplex next-generation sequencing. Coinfections of SARS-CoV-2 with other respiratory viruses were detected in 164 (7.2%) patients. The most common co-infecting virus was respiratory syncytial virus (RSV) (38 cases, 1.7%), followed by bocavirus (BoV) (1.2%) and rhinovirus (RV) (1.1%). Patients ≤ 16 years of age had the highest rate (15%) of mixed infections. Whole-genome sequencing produced 19 complete genomes of seasonal respiratory viral co-pathogens, which were subjected to phylogenetic and amino acid analyses. The detected influenza viruses were classified into the genetic groups 6B.1A.5a.2a and 6B.1A.5a.2a.1 for A(H1N1)pdm09, 3C.2a1b.2a.2a.1 and 3C.2a.2b for A(H3N2), and V1A.3a.2 for the B/Victoria lineage. The RSV-B sequences belonged to the genetic group GB5.0.5a, with HAdV-C belonging to type 1, BoV to genotype VP1, and PIV3 to lineage 1a(i). Multiple amino acid substitutions were identified, including at the antibody-binding sites. This study provides insights into respiratory viral coinfections involving SARS-CoV-2 and reinforces the importance of genetic characterization of co-pathogens in the development of therapeutic and preventive strategies.
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Affiliation(s)
- Ivelina Trifonova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Neli Korsun
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Iveta Madzharova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivailo Alexiev
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivan Ivanov
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Viktoria Levterova
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Lyubomira Grigorova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
| | - Ivan Stoikov
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Dean Donchev
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
| | - Iva Christova
- Department of Virology, National Centre of Infectious and Parasitic Diseases, 1233 Sofia, Bulgaria; (N.K.); (I.M.); (I.A.); (L.G.); (I.C.)
- Department of Microbiology, National Centre of Infectious and Parasitic Diseases, 1504 Sofia, Bulgaria; (I.I.); (V.L.); (I.S.); (D.D.)
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Pan Y, Xing Y, Lai Y, Dong H, Sheng H, Xu W. Metagenomic next-generation sequencing reveals co-infection with Legionella pneumophila and Fusobacterium necrophorum in a patient with severe pneumonia: a case report. BMC Pulm Med 2024; 24:279. [PMID: 38867173 PMCID: PMC11170816 DOI: 10.1186/s12890-024-03097-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 06/11/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Legionella pneumonia is one of the most severe types of atypical pneumonia, impairing multiple organ systems, posing a threat to life. Diagnosing Legionella pneumonia is challenging due to difficulties in culturing the bacteria and limitations in immunoassay sensitivity and specificity. CASE PRESENTATION This paper reports a rare case of sepsis caused by combined infection with Legionella pneumophila and Fusobacterium necrophorum, leading to respiratory failure, acute kidney injury, acute liver injury, myocardial damage, and electrolyte disorders. In addition, we systematically reviewed literature on patients with combined Legionella infections, analyzing their clinical features, laboratory results and diagnosis. CONCLUSIONS For pathogens that require prolonged incubation periods and are less sensitive to conventional culturing methods, metagenomic next-generation sequencing (mNGS) can be a powerful supplement to pathogen screening and plays a significant role in the auxiliary diagnosis of complex infectious diseases.
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Affiliation(s)
- Yunqi Pan
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Yi Xing
- Department of Hospital Infection Management, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Yanan Lai
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Huixing Dong
- Department of Respiratory and Critical Care Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Huiming Sheng
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Weihong Xu
- Department of Laboratory Medicine, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China.
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Guan Y, Yu C, Fei Y, Wang Q, Wang P, Zuo W, Wu H, Qi X, Shi Q. Case Report: Four cases of SARS-CoV-2-associated Guillain-Barré Syndrome with SARS-CoV-2-positive cerebrospinal fluid detected by metagenomic next-generation sequencing: a retrospective case series from China. Front Immunol 2023; 14:1258579. [PMID: 37701436 PMCID: PMC10493301 DOI: 10.3389/fimmu.2023.1258579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is often absent or at low levels in the cerebrospinal fluid (CSF) of patients with previous SARS-CoV-2-associated Guillain-Barré syndrome (GBS). This has led to speculation that SARS-CoV-2-associated GBS is more likely mediated by post-infectious immunity or a parainfection. This understanding has influenced the development of treatment regimens for SARS-CoV-2-associated GBS. This paper reports our experience with four Chinese patients with SARS-CoV-2-associated GBS who tested positive for SARS-CoV-2 RNA in the CSF. They developed symptoms of peripheral nerve damage 4-15 days after fever and confirmed SARS-CoV-2 infection, all of whom presented with progressive weakness of both lower limbs; three with autonomic nerve function impairment such as constipation and urination disorder; and one with polycranial neuritis and Miller-Fisher syndrome. Three patients were tested for anti-ganglioside antibodies, and one tested positive for GD1a-IgG. Four patients recovered well after treatment with anti-viral drugs combined with intravenous immunoglobulin. The present results showed that SARS-CoV-2 RNA can be detected via mNGS in the CSF of some patients with SARS-CoV-2-associated GBS, suggesting that SARS-CoV-2-associated GBS may have multiple pathogeneses.
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Affiliation(s)
- Yalin Guan
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Changshen Yu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Yunhan Fei
- Department of Emergency, Tianjin Huanhu Hospital, Tianjin, China
| | - Qiushi Wang
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, China
- Infection Business Unit, Novogene Co., Ltd., Beijing, China
| | - Pan Wang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Wenchao Zuo
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Hao Wu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Xuemei Qi
- Department of Neurology, The second hospital of tianjin medical university, Tianjin, China
| | - Qiyun Shi
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, China
- Infection Business Unit, Novogene Co., Ltd., Beijing, China
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Shen H, Liu T, Shen M, Zhang Y, Chen W, Chen H, Wang Y, Liu J, Tao J, He L, Lu G, Yan G. 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; 13:1200806. [PMID: 37655299 PMCID: PMC10466250 DOI: 10.3389/fcimb.2023.1200806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/27/2023] [Indexed: 09/02/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples. Methods A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data. Results Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the α-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%). Conclusions mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.
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Affiliation(s)
- Huili Shen
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Tingyan Liu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Meili Shen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Yi Zhang
- Department of Clinical Epidemiology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Weiming Chen
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Hanlin Chen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Yixue Wang
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Jing Liu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Jinhao Tao
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liming He
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Guoping Lu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Gangfeng Yan
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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Batool M, Galloway-Peña J. Clinical metagenomics-challenges and future prospects. Front Microbiol 2023; 14:1186424. [PMID: 37448579 PMCID: PMC10337830 DOI: 10.3389/fmicb.2023.1186424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Infections lacking precise diagnosis are often caused by a rare or uncharacterized pathogen, a combination of pathogens, or a known pathogen carrying undocumented or newly acquired genes. Despite medical advances in infectious disease diagnostics, many patients still experience mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Thus, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections. Compared to conventional diagnostics, metagenomic next-generation sequencing (mNGS) is a promising, culture-independent sequencing technology that is sensitive to detecting rare, novel, and unexpected pathogens with no preconception. Despite the fact that several studies and case reports have identified the effectiveness of mNGS in improving clinical diagnosis, there are obvious shortcomings in terms of sensitivity, specificity, costs, standardization of bioinformatic pipelines, and interpretation of findings that limit the integration of mNGS into clinical practice. Therefore, physicians must understand the potential benefits and drawbacks of mNGS when applying it to clinical practice. In this review, we will examine the current accomplishments, efficacy, and restrictions of mNGS in relation to conventional diagnostic methods. Furthermore, we will suggest potential approaches to enhance mNGS to its maximum capacity as a clinical diagnostic tool for identifying severe infections.
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Huang PH, Huang YT, Lee PH, Tseng CH, Liu PY, Liu CW. Diagnosis of Legionnaires' Disease Assisted by Next-Generation Sequencing in a Patient with COVID-19. Infect Drug Resist 2023; 16:355-362. [PMID: 36714349 PMCID: PMC9880021 DOI: 10.2147/idr.s396254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/03/2023] [Indexed: 01/21/2023] Open
Abstract
Coinfection in COVID-19 patients is associated with worsening outcome. Among patients with COVID-19, Legionella pneumophila, a common cause of pneumonia, has been reported as a co-occurring respiratory infection. A nonspecific clinical presentation, however, makes an early diagnosis difficult. Bronchoalveolar lavage fluid was collected from a patient suffering from COVID-19 and presenting with pneumonia and sent for metagenomic analysis. Differential abundance analysis was carried out by comparing each taxon reads per million between the bronchoalveolar lavage fluid sample and the negative control. Two replicates of metagenomic sequencing were conducted on bronchoalveolar lavage fluid samples. Within each replicated sequencing, one negative control was sequenced for comparison of taxon abundance in the BALF sample. In both replicates, Legionella pneumophila was the only taxon with significantly higher abundance when compared with the negative control. PCR of the bronchoalveolar further confirmed the presence of L. pneumophila. Several studies have estimated that the incidence of Legionnaires' disease co-infection in patients with COVID-19 infection is approximately 0% to 1.5%. There are some common characteristics of COVID-19 and co-infection with Legionnaires' disease, making it difficult to diagnose bacterial infection early. The diagnosis of these cases is important due to the different treatments used. Current diagnostic tests for Legionnaires' disease include conventional culture, urinary antigen for L. pneumophila serogroup 1, polymerase chain reaction, direct fluorescent antibody stain, and paired serology. The current study demonstrated that metagenomics is a promising approach that facilitated the diagnosis of Legionnaires' disease.
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Affiliation(s)
- Po-Hsiu Huang
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi, Taiwan
| | - Po-Hsin Lee
- Division of Chest Medicine, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,College of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan,Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan,Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan,Correspondence: Po-Yu Liu; Chia-Wei Liu, Tel +886 4 2359 2525, Fax +886 4 2359 2525 2111, Email ;
| | - Chia-Wei Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan
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Clark JA, Conway Morris A, Curran MD, White D, Daubney E, Kean IRL, Navapurkar V, Bartholdson Scott J, Maes M, Bousfield R, Török ME, Inwald D, Zhang Z, Agrawal S, Kanaris C, Khokhar F, Gouliouris T, Baker S, Pathan N. The rapid detection of respiratory pathogens in critically ill children. Crit Care 2023; 27:11. [PMID: 36627688 PMCID: PMC9831374 DOI: 10.1186/s13054-023-04303-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
PURPOSE Respiratory infections are the most common reason for admission to paediatric intensive care units (PICU). Most patients with lower respiratory tract infection (LRTI) receive broad-spectrum antimicrobials, despite low rates of bacterial culture confirmation. Here, we evaluated a molecular diagnostic test for LRTI to inform the better use of antimicrobials. METHODS The Rapid Assay for Sick Children with Acute Lung infection Study was a single-centre, prospective, observational cohort study of mechanically ventilated children (> 37/40 weeks corrected gestation to 18 years) with suspected community acquired or ventilator-associated LRTI. We evaluated the use of a 52-pathogen custom TaqMan Array Card (TAC) to identify pathogens in non-bronchoscopic bronchoalveolar lavage (mini-BAL) samples. TAC results were compared to routine microbiology testing. Primary study outcomes were sensitivity and specificity of TAC, and time to result. RESULTS We enrolled 100 patients, all of whom were tested with TAC and 91 of whom had matching culture samples. TAC had a sensitivity of 89.5% (95% confidence interval (CI95) 66.9-98.7) and specificity of 97.9% (CI95 97.2-98.5) compared to routine bacterial and fungal culture. TAC took a median 25.8 h (IQR 9.1-29.8 h) from sample collection to result. Culture was significantly slower: median 110.4 h (IQR 85.2-141.6 h) for a positive result and median 69.4 h (IQR 52.8-78.6) for a negative result. CONCLUSIONS TAC is a reliable and rapid adjunct diagnostic approach for LRTI in critically ill children, with the potential to aid early rationalisation of antimicrobial therapy.
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Affiliation(s)
- John A Clark
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK. .,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.
| | - Andrew Conway Morris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Division of Anaesthesia, Department of Medicine, University of Cambridge, Cambridge, UK.,Division of Immunology, Department of Pathology, University of Cambridge, Cambridge, UK
| | - Martin D Curran
- Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge, UK
| | - Deborah White
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Esther Daubney
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Iain R L Kean
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Vilas Navapurkar
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Josefin Bartholdson Scott
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Rachel Bousfield
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge, UK
| | - M Estée Török
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Division of Infectious Diseases, Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Inwald
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Zhenguang Zhang
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | - Shruti Agrawal
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Constantinos Kanaris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Blizard Institute, Queen Mary University of London, London, UK
| | - Fahad Khokhar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Theodore Gouliouris
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK.,Clinical Microbiology and Public Health Laboratory, United Kingdom Health Security Agency, Cambridge, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge, Cambridge, UK
| | - Nazima Pathan
- Department of Paediatrics, Addenbrooke's Hospital, University of Cambridge, Level 8, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK.,Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
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Yu C, Guo W, Zhang Z, Ma Y, Cao X, Sun N, Cui Y, Wang Y, Cui W, Xu Y, Zhan J. The Impact of mNGS Technology in the Etiological Diagnosis of Severe Pneumonia in Children During the Epidemic of COVID-19. Infect Drug Resist 2023; 16:2395-2402. [PMID: 37113527 PMCID: PMC10128870 DOI: 10.2147/idr.s403851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Purpose Metagenomic next-generation sequencing (mNGS) is an emerging technique for pathogen detection. However, most literature on the clinical application of pediatrics generally comprises case reports or small-scale cohort studies. Patients and Methods A total of 101 children with community-acquired severe pneumonia admitted to Tianjin Children's Hospital from November 2021 to February 2022 were included. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS. The performances of mNGS and conventional tests on pulmonary infection diagnosis and pathogen identification were compared. Results According to our data, mNGS had a broader spectrum for pathogen detection. The mNGS results of BALF showed that the number of children with severe pneumonia hospitalized for mycoplasma pneumoniae infection was more than that for other bacterial infections during the COVID-19 epidemic. In addition, 43 cases (42.6%) had been identified with mixed infection, including 36 cases (35.6%) of Mycoplasma pneumoniae mixed with other pathogenic bacteria. Analytically, the mNGS exhibited significantly enhanced detection in the BALF as compared with the conventional laboratory pathogenic detection approaches (P < 0.05). The Pearson correlation analysis revealed positive correlation between the time of fever during hospitalization and the number of mycoplasma sequences (P < 0.05). Conclusion Compared with traditional methods, mNGS has a higher etiological detection rate and can comprehensively detect various pathogens of severe pneumonia. Therefore, mNGS of bronchoalveolar lavage fluid should be performed in children with severe pneumonia, which is of great significance for guiding treatment.
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Affiliation(s)
- Changjiang Yu
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
| | - Wei Guo
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
- Graduate School of Tianjin Medical University, Tianjin, People’s Republic of China
| | - Zhulai Zhang
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
| | - Yuting Ma
- Department of Infection, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
| | - Xiaobei Cao
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
| | - Na Sun
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
| | - Yingyao Cui
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
| | - Yunshen Wang
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
| | - Wenyu Cui
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
| | - Yongsheng Xu
- Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
- Correspondence: Yongsheng Xu, Department of Pediatric Respiratory Medicine, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, 300134, People’s Republic of China, Email
| | - Jianghua Zhan
- Graduate School of Tianjin Medical University, Tianjin, People’s Republic of China
- Department of Pediatric Surgery, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, People’s Republic of China
- Jianghua Zhan, Graduate School of Tianjin Medical University, Department of Pediatric Surgery, Tianjin Children’s Hospital, Tianjin University Children’s Hospital, Tianjin, 300134, People’s Republic of China, Email
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