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Zhang X, Tang X, Yi X, Lei Y, Lu S, Li T, Yue R, Pan L, Feng G, Huang X, Wang Y, Cheng D. Etiologic characteristics revealed by mNGS-mediated ultra-early and early microbiological identification in airway secretions from lung transplant recipients. Front Immunol 2023; 14:1271919. [PMID: 37809079 PMCID: PMC10551139 DOI: 10.3389/fimmu.2023.1271919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Background Post-operative etiological studies are critical for infection prevention in lung transplant recipients within the first year. In this study, mNGS combined with microbial culture was applied to reveal the etiological characteristics within one week (ultra-early) and one month (early) in lung transplant recipients, and the epidemiology of infection occurred within one month. Methods In 38 lung transplant recipients, deep airway secretions were collected through bronchofiberscope within two hours after the operation and were subjected to microbial identification by mNGS and microbial culture. The etiologic characteristics of lung transplant recipients were explored. Within one month, the infection status of recipients was monitored. The microbial species detected by mNGS were compared with the etiological agents causing infection within one month. Results The detection rate of mNGS in the 38 airway secretions specimens was significantly higher than that of the microbial culture (P<0.0001). MNGS identified 143 kinds of pathogenic microorganisms; bacterial pathogens account for more than half (72.73%), with gram-positive and -negative bacteria occupying large proportions. Fungi such as Candida are also frequently detected. 5 (50%) microbial species identified by microbial culture had multiple drug resistance (MDR). Within one month, 26 (68.42%) recipients got infected (with a median time of 9 days), among which 10 (38.46%) cases were infected within one week. In the infected recipients, causative agents were detected in advance by mNGS in 9 (34.62%) cases, and most of them (6, 66.67%) were infected within one week (ultra-early). In the infection that occurred after one week, the consistency between mNGS results and the etiological agents was decreased. Conclusion Based on the mNGS-reported pathogens in airway secretions samples collected within two hours, the initial empirical anti-infection regimes covering the bacteria and fungi are reasonable. The existence of bacteria with MDR forecasts the high risk of infection within 48 hours after transplant, reminding us of the necessity to adjust the antimicrobial strategy. The predictive role of mNGS performed within two hours in etiological agents is time-limited, suggesting continuous pathogenic identification is needed after lung transplant.
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Affiliation(s)
- Xiaoqin Zhang
- Department of Respiratory and Critical Care Medicine, West China Hospital, West China Clinical Medical School, Sichuan University, Chengdu, China
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuemei Tang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaoli Yi
- Medical Department, Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Yu Lei
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Sen Lu
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Tianlong Li
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Ruiming Yue
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Lingai Pan
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Gang Feng
- Department of Thoracic Surgery, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Xiaobo Huang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Yiping Wang
- Department of Critical Care Medicine, Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Deyun Cheng
- Department of Respiratory and Critical Care Medicine, West China Hospital, West China Clinical Medical School, Sichuan University, Chengdu, China
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Huang W, Hu S, Zhu Y, Liu S, Zhou X, Fang Y, Lu Y, Wang R. Metagenomic surveillance and comparative genomic analysis of Chlamydia psittaci in patients with pneumonia. Front Microbiol 2023; 14:1157888. [PMID: 37323913 PMCID: PMC10265514 DOI: 10.3389/fmicb.2023.1157888] [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: 02/03/2023] [Accepted: 05/12/2023] [Indexed: 06/17/2023] Open
Abstract
Chlamydia psittaci, a strictly intracellular bacterium, is an underestimated etiologic agent leading to infections in a broad range of animals and mild illness or pneumonia in humans. In this study, the metagenomes of bronchoalveolar lavage fluids from the patients with pneumonia were sequenced and highly abundant C. psittaci was found. The target-enriched metagenomic reads were recruited to reconstruct draft genomes with more than 99% completeness. Two C. psittaci strains from novel sequence types were detected and these were closely related to the animal-borne isolates derived from the lineages of ST43 and ST28, indicating the zoonotic transmissions of C. psittaci would benefit its prevalence worldwide. Comparative genomic analysis combined with public isolate genomes revealed that the pan-genome of C. psittaci possessed a more stable gene repertoire than those of other extracellular bacteria, with ~90% of the genes per genome being conserved core genes. Furthermore, the evidence for significantly positive selection was identified in 20 virulence-associated gene products, particularly bacterial membrane-embedded proteins and type three secretion machines, which may play important roles in the pathogen-host interactions. This survey uncovered novel strains of C. psittaci causing pneumonia and the evolutionary analysis characterized prominent gene candidates involved in bacterial adaptation to immune pressures. The metagenomic approach is of significance to the surveillance of difficult-to-culture intracellular pathogens and the research into molecular epidemiology and evolutionary biology of C. psittaci.
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Affiliation(s)
- Weifeng Huang
- Department of Intensive Care Medicine, Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuqin Hu
- Department of Critical Care Medicine, Shanghai General Hospital of Nanjing Medical University, Shanghai, China
| | - Yongzhe Zhu
- Department of Microbiology, Navy Medical University, Shanghai, China
| | - Shijia Liu
- Department of Pulmonary Disease, PLA 905 Hospital, Shanghai, China
| | - Xingya Zhou
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc., Shanghai, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
- Shanghai Institute of Infectious Disease and Biosecurity, Shanghai, China
| | - Ruilan Wang
- Department of Critical Care Medicine, Shanghai General Hospital of Nanjing Medical University, Shanghai, China
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Zhou F, Zhang J, Gong L, Wang G, Khan A, Cui H. Infection caused by Lawsonella clevelandensis after breast augmentation with autologous fat grafting: a case report. BMC Infect Dis 2023; 23:124. [PMID: 36855087 PMCID: PMC9976391 DOI: 10.1186/s12879-022-07812-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 10/26/2022] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Lawsonella clevelandensis is one recently documented anaerobic, which is partially acid-fast. Nevertheless, it is rarely found to be associated with human infections, especially in scope of plastic and cosmetic surgery before our patient who was performed breast augmentation with autologous fat grafting. Breast augmentation is becoming popular, the most common post-surgery complication of which is bacterial infection. CASE PRESENTATION A 29-year-old female who was found swelling in her right breast and fever after breast augmentation surgery with autologous fat grafting was administered. Before administration, she had been treated with antibiotics (details unknown) for more than 1 month without any significant improvements. After administration, she was treated with intravenous antibiotic empirically and repeated debridement via Vaccuum Sealing Drainage (VSD). And samples of the necrotic tissues and pus collected in surgery were sent for microbiological testing. However, routine examination failed. Thus samples were further collected and sent to Genoxor Medical & Science Technology Inc. (Shanghai, China) to conduct Next-Generation Sequencing (NGS). Surprisingly Lawsonella clevelandensis was determined. Accordingly, sensitive antibiotic was applied in concert with thorough debridement and drainage and finally her condition was completely reversed with wound closure gradually. CONCLUSION Complications of breast augmentation with autologous fat graft are various, of which infection is most common. Rare pathogen such as Lawsonella clevelandensis infection in human is rare in clinical practice. Moreover, it is difficult to differentiate from non-tuberculous mycobacterium for its partial acid resistance, difficulty to culture and abscess formation. How to determine diagnosis of Lawsonella clevelandensis infection accurately come to be critical In our report, NGS is recommended as a useful method to identify the pathogen, which may provide us a novel tool for refractory wound.
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Affiliation(s)
- Feng Zhou
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Jun Zhang
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Lunli Gong
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Guobao Wang
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Aawrish Khan
- grid.412793.a0000 0004 1799 5032Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065 China
| | - Haiyan Cui
- Department of Plastic and Aesthetic Surgery, Tongji Hospital Affiliated to Tongji University, No. 389, Xincun Road, Putuo District, Shanghai, 200065, China.
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Wang L, Li S, Qin J, Tang T, Hong J, Tung TH, Xu C, Yu S, Qian J. Clinical Diagnosis Application of Metagenomic Next-Generation Sequencing of Plasma in Suspected Sepsis. Infect Drug Resist 2023; 16:891-901. [PMID: 36820080 PMCID: PMC9938705 DOI: 10.2147/idr.s395700] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/02/2023] [Indexed: 02/16/2023] Open
Abstract
Purpose We analyzed the clinical concordance of mNGS test results from blood samples and improved the clinical efficiency of mNGS in the diagnosis of suspected sepsis pathogens. Patients and Methods In this study, 99 samples of suspected blood flow infection were included for plasma mNGS, and the correlation between mNGS results and blood culture results, serum inflammatory indices, clinical symptoms and antibiotic treatment was analyzed, as well as the comparison with the detection rate of BALF pathogens, as well as the classification of different pathogens in the mNGS results were analyzed. Results The mNGS pathogen detection rate was higher than that of traditional blood culture (83.02% vs 35.82%). The rate of the mNGS results being consistent with the clinical diagnosis was also higher than that of traditional blood culture (58.49% vs 20.75%). This study shows that bacteria and fungi are the main pathogens in sepsis, and viral sepsis is very rare. In this study, 32% of sepsis patients were secondary to pneumonia. Compared with the pathogen detection rate using alveolar lavage fluid, the detection rate from plasma mNGS was 62.5%. Samples were also easy to sample, noninvasive, and more convenient for clinical application. Conclusion This study shows that compared with blood culture, the detection rate of mNGS pathogen that meets the diagnosis of sepsis is higher. We need a combination of multiple indicators to monitor the early diagnosis and treatment of sepsis.
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Affiliation(s)
- Lisha Wang
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Shixiao Li
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Jiajia Qin
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Tianbin Tang
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Jiawen Hong
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Tao-Hsin Tung
- Evidence-Based Medicine Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People’s Republic of China
| | - Chunyan Xu
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
| | - Sufei Yu
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China,Correspondence: Sufei Yu; Jiao Qian, Email ;
| | - Jiao Qian
- Department of Laboratory Medicine, Taizhou Hospital of Zhejiang Province Affiliated to Wenzhou Medical University, Linhai, People’s Republic of China
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Metagenomic Insights into Pathogenic Characterization of ST410 Acinetobacter nosocomialis Prevalent in China. Pathogens 2022; 11:pathogens11080838. [PMID: 36014959 PMCID: PMC9414201 DOI: 10.3390/pathogens11080838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2022] [Revised: 07/16/2022] [Accepted: 07/25/2022] [Indexed: 02/01/2023] Open
Abstract
Acinetobacter nosocomialis is a prevalent opportunistic pathogen that causes hospital-acquired infections. The increasing threats from A. nosocomialis infections have led to attention from the scientific and medical communities. Metagenomic next-generation sequencing (mNGS) was performed for an exudate specimen collected from an ICU patient with wound infection, followed by sepsis, in Tongji Hospital. Three assembly strategies were employed to recover the genome of A. nosocomialis in the metagenomic sample. Together with publicly available genomes of A. nosocomialis, the features of population genetics and molecular epidemiology were deeply analyzed. A draft genome was reconstructed for the metagenomic strain WHM01, derived from the ST410 A. nosocomialis dominating the microbial community, thereby prompting its highly pathogenic risk, which is associated with infection and persistence. The structure of the bacterial pangenome was characterized, including the 1862 core and 11,815 accessory genes present in the 157 strains. The genetic diversity of the genes coding for the 128 virulence factors assigned to 14 functional categories was uncovered in this nosocomial pathogen, such as the lipooligosaccharide, capsule, type IV pilus, and outer membrane proteins. Our work revealed genomic properties of ST410 A. nosocomialis, which is prevalent in China, and further highlighted that metagenomic surveillance may be a prospective application for evaluating the pathogenic characteristics of the nosocomial opportunistic pathogens.
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