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Zhao M, Hou W, Pu D, Li Z, Tu L, Ow CJL, Tian J, Li W. Impact of Pulmonary microbiota on lung cancer treatment-related pneumonia. J Cancer 2024; 15:4503-4512. [PMID: 39006071 PMCID: PMC11242340 DOI: 10.7150/jca.93818] [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: 01/03/2024] [Accepted: 05/19/2024] [Indexed: 07/16/2024] Open
Abstract
Background: The use of immunotherapy is progressively expanding for the treatment of lung cancer, either alone or in combination with radiotherapy. However, treatment-related adverse events, especially pneumonia, significantly limit the drug's effectiveness in treating lung cancer. The occurrence of lung cancer, immunotherapy, and pulmonary radiotherapy can all contribute to the imbalance in the pulmonary microbiota, rendering the lungs more susceptible to inflammatory reactions. Methods: Mouse models of lung transplantation tumor were treated with either PD-1 monoclonal antibody or radiotherapy alone, or in combination. The differences in lung inflammation among the different treatment groups were regularly observed by micro-CT. Further, bronchoalveolar lavage fluid was extracted for macrogenomic and cytokine detection. The transcriptional genome of tumor-filled lung tissue was also sequenced. Results: When treated with a combination of PD-1 and radiotherapy, the CT scans showed more severe pulmonary inflammation. However, with the addition of continuously administered antibiotics, no exacerbation of pneumonia signs was observed. Moreover, the differential gene expression and cytokine profiles in the combination treatment group differed from those in the PD-1 monotherapy group and the radiotherapy monotherapy group. This discrepancy does not seem to be a straightforward superimposition of radiation-induced pneumonia and immune-related pneumonia. Further exploration of changes in pulmonary microbiota revealed specific bacterial interactions with DEGs and cytokines. Conclusions: The underlying causes of this susceptibility are intricate and may be associated with the complexity of pulmonary microbiota imbalance, along with fluctuations in the abundance of specific microbiota species.
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Affiliation(s)
- Maoyuan Zhao
- Lung cancer center, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Wang Hou
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dan Pu
- Lung cancer center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Zhixi Li
- Lung cancer center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Li Tu
- Lung cancer center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Calista Jia Ling Ow
- BSc (Hons) Biochemistry, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - Jie Tian
- Department of Thoracic Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Precision Medicine Research Center, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Research Units of West China, Chinese Academy of Medical Sciences, West China Hospital, Chengdu, Sichuan, China
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Toh SI, Elaine Keisha J, Wang YL, Pan YC, Jhu YH, Hsiao PY, Liao WT, Chen PY, Ko TM, Chang CY. Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin. Commun Biol 2023; 6:1282. [PMID: 38114770 PMCID: PMC10730852 DOI: 10.1038/s42003-023-05681-6] [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: 05/02/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
Metagenomic-based studies have predicted an extraordinary number of potential antibiotic-resistance genes (ARGs). These ARGs are hidden in various environmental bacteria and may become a latent crisis for antibiotic therapy via horizontal gene transfer. In this study, we focus on a resistance gene cph, which encodes a phosphotransferase (Cph) that confers resistance to the antituberculosis drug capreomycin (CMN). Sequence Similarity Network (SSN) analysis classified 353 Cph homologues into five major clusters, where the proteins in cluster I were found in a broad range of actinobacteria. We examine the function and antibiotics targeted by three putative resistance proteins in cluster I via biochemical and protein structural analysis. Our findings reveal that these three proteins in cluster I confer resistance to CMN, highlighting an important aspect of CMN resistance within this gene family. This study contributes towards understanding the sequence-structure-function relationships of the phosphorylation resistance genes that confer resistance to CMN.
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Affiliation(s)
- Shu-Ing Toh
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Johan Elaine Keisha
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Yung-Lin Wang
- Genomics Research Center, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Yi-Chi Pan
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Yu-Heng Jhu
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Po-Yun Hsiao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Wen-Ting Liao
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Po-Yuan Chen
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Tai-Ming Ko
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC
| | - Chin-Yuan Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC.
- Center for Intelligent Drug Systems and Smart Bio-devices, National Yang Ming Chiao Tung University, Hsinchu, 30010, Taiwan, ROC.
- Department of Biomedical Science and Environment Biology, Kaohsiung Medical University, Hsinchu, 80708, Taiwan, ROC.
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Alam MS, Guan P, Zhu Y, Zeng S, Fang X, Wang S, Yusuf B, Zhang J, Tian X, Fang C, Gao Y, Khatun MS, Liu Z, Hameed HMA, Tan Y, Hu J, Liu J, Zhang T. Comparative genome analysis reveals high-level drug resistance markers in a clinical isolate of Mycobacterium fortuitum subsp . fortuitum MF GZ001. Front Cell Infect Microbiol 2023; 12:1056007. [PMID: 36683685 PMCID: PMC9846761 DOI: 10.3389/fcimb.2022.1056007] [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: 09/28/2022] [Accepted: 12/05/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction Infections caused by non-tuberculosis mycobacteria are significantly worsening across the globe. M. fortuitum complex is a rapidly growing pathogenic species that is of clinical relevance to both humans and animals. This pathogen has the potential to create adverse effects on human healthcare. Methods The MF GZ001 clinical strain was collected from the sputum of a 45-year-old male patient with a pulmonary infection. The morphological studies, comparative genomic analysis, and drug resistance profiles along with variants detection were performed in this study. In addition, comparative analysis of virulence genes led us to understand the pathogenicity of this organism. Results Bacterial growth kinetics and morphology confirmed that MF GZ001 is a rapidly growing species with a rough morphotype. The MF GZ001 contains 6413573 bp genome size with 66.18 % high G+C content. MF GZ001 possesses a larger genome than other related mycobacteria and included 6156 protein-coding genes. Molecular phylogenetic tree, collinearity, and comparative genomic analysis suggested that MF GZ001 is a novel member of the M. fortuitum complex. We carried out the drug resistance profile analysis and found single nucleotide polymorphism (SNP) mutations in key drug resistance genes such as rpoB, katG, AAC(2')-Ib, gyrA, gyrB, embB, pncA, blaF, thyA, embC, embR, and iniA. In addition, the MF GZ001strain contains mutations in iniA, iniC, pncA, and ribD which conferred resistance to isoniazid, ethambutol, pyrazinamide, and para-aminosalicylic acid respectively, which are not frequently observed in rapidly growing mycobacteria. A wide variety of predicted putative potential virulence genes were found in MF GZ001, most of which are shared with well-recognized mycobacterial species with high pathogenic profiles such as M. tuberculosis and M. abscessus. Discussion Our identified novel features of a pathogenic member of the M. fortuitum complex will provide the foundation for further investigation of mycobacterial pathogenicity and effective treatment.
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Affiliation(s)
- Md Shah Alam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Ping Guan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Yuting Zhu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, China
| | - Sanshan Zeng
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Xiange Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- National Clinical Research Center for Infectious Diseases, Guangdong Provincial Clinical Research Center for Tuberculosis, Shenzhen Third People's Hospital, Shenzhen, China
| | - Buhari Yusuf
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Jingran Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Xirong Tian
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Cuiting Fang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Yamin Gao
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Mst Sumaia Khatun
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Zhiyong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Jinxing Hu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Chest Hospital, Guangzhou, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Diseases, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, China
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Alemayehu A, Kebede A, Neway S, Tesfaye E, Zerihun B, Getu M, Petros B. A glimpse into the genotype and clinical importance of non tuberculous mycobacteria among pulmonary tuberculosis patients: The case of Ethiopia. PLoS One 2022; 17:e0275159. [PMID: 36155559 PMCID: PMC9512186 DOI: 10.1371/journal.pone.0275159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 09/11/2022] [Indexed: 12/02/2022] Open
Abstract
Laboratory identification of nontuberculous mycobacteria (NTM) species is not regularly performed while, they have a public health importance with a prevalence of more than 5% among pulmonary tuberculosis (PTB) patients in Ethiopia. Hence, this study aimed to identify the NTM species and their clinical significance among PTB patients. A retrospective study was conducted at the Ethiopian Public Health Institution’s (EPHI’s) national TB referral laboratory. Stored NTM isolates were genotyped using GenoType Mycobacterium CM/AS kit (Hain Life science, Germany). Data pertinent to the study was extracted from the EPHI’s database and patients’ medical records. Between January 2 & December 28 of 2017, a total of 3,834 samples were processed from 698 TB patients of whom 50% were female. Among 3,317 samples with mycobacterial culture results 7.3% were NTM and majority of them were identified from smear negative TB patients. M. simiae was the /predominant NTM among the genotyped isolates. All the studied NTM species were not clinically important however, considering the similarity of clinical and radiologic findings between NTM and MTBC infected patients, integrating NTM species identification in the routine TB laboratory diagnosis may augment clinicians’ decision particularly in DR-TB patients. Additional similar prospective study with a larger sample size is recommended. Moreover, urgent improvements on patients’ record keeping practice are required in the studied hospitals.
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Affiliation(s)
- Alem Alemayehu
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Adds Ababa University, Addis Ababa, Ethiopia
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
- College of Health and Medical Sciences, School of Medial Laboratory Science, Haramaya University, Dire Dawa, Ethiopia
- * E-mail: ,
| | - Abebaw Kebede
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Adds Ababa University, Addis Ababa, Ethiopia
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Sebsib Neway
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Efrem Tesfaye
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | | | - Melak Getu
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Beyene Petros
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Adds Ababa University, Addis Ababa, Ethiopia
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Lange C, Böttger EC, Cambau E, Griffith DE, Guglielmetti L, van Ingen J, Knight SL, Marras TK, Olivier KN, Santin M, Stout JE, Tortoli E, Wagner D, Winthrop K, Daley CL, Lange C, Andrejak C, Böttger E, Cambau E, Griffith D, Guglielmetti L, van Ingen J, Knight S, Leitman P, Marras TK, Olivier KN, Santin M, Stout JE, Tortoli E, Wagner D, Wallace RJ, Winthrop K, Daley C. Consensus management recommendations for less common non-tuberculous mycobacterial pulmonary diseases. THE LANCET INFECTIOUS DISEASES 2022; 22:e178-e190. [DOI: 10.1016/s1473-3099(21)00586-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/08/2021] [Accepted: 09/01/2021] [Indexed: 12/18/2022]
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Identification of Nontuberculous Mycobacteria in Drinking Water in Cali, Colombia. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 18:ijerph18168451. [PMID: 34444201 PMCID: PMC8392123 DOI: 10.3390/ijerph18168451] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 08/03/2021] [Accepted: 08/05/2021] [Indexed: 11/29/2022]
Abstract
Nontuberculous mycobacteria (NTM) are ubiquitous microorganisms naturally resistant to antibiotics and disinfectants that can colonize drinking water supply systems. Information regarding the spread of NTM in specifically South America and Colombia is limited. We aimed to identify and characterize NTM present in tap water samples from Cali, Colombia. Drinking water samples and faucet biofilm swabs were collected in 18 places, including the city’s three main water treatment plants (WTPs). Filter-trapped material and eluates (0.45 μm) from swab washes were plated in 7H11 agar plates. Suspected colonies were evaluated microscopically, and NTM species were identified based on the rpoB gene. Antibiotic susceptibility testing was also performed. Fifty percent (9/18) of sampling points were positive for NTM (including two WTPs), from which 16 different isolates were identified: Mycobacterium mucogenicum (8/16), M. phocaicum (3/16), M. chelonae (2/16), M. mageritense (2/16), and M. fortuitum (1/16), all rapidly growing mycobacteria. A susceptibility profile was obtained from 68.75% (11/16) of the isolates. M. chelonae was the most resistant species. All NTM isolated are potentially responsible for human diseases; our findings might provide a baseline for exploring NTM transmission dynamics and clinical characterization, as well as potential associations between NTM species found in drinking water and isolates from patients.
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