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Zhang H, Tang M, Li D, Xu M, Ao Y, Lin L. Applications and advances in molecular diagnostics: revolutionizing non-tuberculous mycobacteria species and subspecies identification. Front Public Health 2024; 12:1410672. [PMID: 38962772 PMCID: PMC11220129 DOI: 10.3389/fpubh.2024.1410672] [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: 04/01/2024] [Accepted: 06/10/2024] [Indexed: 07/05/2024] Open
Abstract
Non-tuberculous mycobacteria (NTM) infections pose a significant public health challenge worldwide, affecting individuals across a wide spectrum of immune statuses. Recent epidemiological studies indicate rising incidence rates in both immunocompromised and immunocompetent populations, underscoring the need for enhanced diagnostic and therapeutic approaches. NTM infections often present with symptoms similar to those of tuberculosis, yet with less specificity, increasing the risk of misdiagnosis and potentially adverse outcomes for patients. Consequently, rapid and accurate identification of the pathogen is crucial for precise diagnosis and treatment. Traditional detection methods, notably microbiological culture, are hampered by lengthy incubation periods and a limited capacity to differentiate closely related NTM subtypes, thereby delaying diagnosis and the initiation of targeted therapies. Emerging diagnostic technologies offer new possibilities for the swift detection and accurate identification of NTM infections, playing a critical role in early diagnosis and providing more accurate and comprehensive information. This review delineates the current molecular methodologies for NTM species and subspecies identification. We critically assess the limitations and challenges inherent in these technologies for diagnosing NTM and explore potential future directions for their advancement. It aims to provide valuable insights into advancing the application of molecular diagnostic techniques in NTM infection identification.
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Affiliation(s)
- Haiyang Zhang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Maoting Tang
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Deyuan Li
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Min Xu
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Yusen Ao
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Liangkang Lin
- Department of Pediatrics, The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
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Quan Z, Li M, Chen Y, Liang J, Takiff H, Gao Q. Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection. Eur J Clin Microbiol Infect Dis 2024; 43:297-304. [PMID: 38041721 DOI: 10.1007/s10096-023-04720-8] [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: 08/22/2023] [Accepted: 11/16/2023] [Indexed: 12/03/2023]
Abstract
PURPOSE To evaluate the performance of core genome multilocus sequence typing (cgMLST) for genotyping Mycobacterium tuberculosis (M.tuberculosis) Strains in regions where the lineage 2 strains predominate. METHODS We compared clustering by whole-genome SNP typing with cgMLST clustering in the analysis of WGS data of 6240 strains from five regions of China. Using both the receiver operating characteristic (ROC) curve and epidemiological investigation to determine the optimal threshold for defining genomic clustering by cgMLST. The performance of cgMLST was evaluated by quantifying the sensitivity, specificity and concordance of clustering between two methods. Logistic regression was used to gauge the impact of strain genetic diversity and lineage on cgMLST clustering. RESULTS The optimal threshold for cgMLST to define genomic clustering was determined to be ≤ 10 allelic differences between strains. The overall sensitivity and specificity of cgMLST averaged 99.6% and 96.3%, respectively; the concordance of clustering between two methods averaged 97.1%. Concordance was significantly correlated with strain genetic diversity and was 3.99 times (95% CI, 2.94-5.42) higher in regions with high genetic diversity (π > 1.55 × 10-4) compared to regions with low genetic diversity. The difference missed statistical significance, while concordance for lineage 2 strains (96.8%) was less than that for lineage 4 strains (98.3%). CONCLUSION : cgMLST showed a discriminatory power comparable to whole-genome SNP typing and could be used to genotype clinical M.tuberculosis strains in different regions of China. The discriminative power of cgMLST was significantly correlated with strain genetic diversity and was slightly lower with strains from regions with low genetic diversity.
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Affiliation(s)
- Zhuo Quan
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Meng Li
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Yiwang Chen
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Jialei Liang
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Qian Gao
- Shanghai Institute of Infectious Disease and Biosecurity, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Fudan University, 131 Dongan Road, Shanghai, 200032, China.
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Bao S, Chen S, Zheng J, Ma J, Yang J, Huang H, Duan H. Efficacy of clofazimine-containing regimens for treatment of Mycobacterium avium complex-pulmonary disease in patients unsuitable for standard treatment regimen. Int J Antimicrob Agents 2024; 63:107061. [PMID: 38103753 DOI: 10.1016/j.ijantimicag.2023.107061] [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: 09/04/2023] [Revised: 11/28/2023] [Accepted: 12/08/2023] [Indexed: 12/19/2023]
Abstract
OBJECTIVES Patients with Mycobacterium avium complex-pulmonary disease (MAC-PD) can exhibit contraindications in applying the recommended treatment regimens by the guidelines. Clofazimine (CFZ) is considered a promising drug for MAC-PD treatment and is frequently included in alternative regimens; however, its efficacy remains unclear. METHODS MAC-PD patients, unsuitable for standard regimens, were enrolled continuously in a prospective study at Beijing Chest Hospital. The treatment response of the CFZ-containing regimen was monitored. RESULTS Fifty patients were enrolled in the initial treatment, and 25 patients had a history of anti-TB treatment. Nodular bronchiectasis was observed in 34 patients, while 8 patients exhibited fibrocavitary changes. Additionally, eight patients displayed a combination of both patterns. In a multivariate analysis, MAC-PD patients with CFZ MIC < 0.25 mg/L were significantly associated with culture conversion [OR 8.415, 95% CI (1.983-35.705); P = 0.004]. Among patients who had previous TB treatment history, patients with CFZ MIC < 0.25 mg/L had a higher chance of acquiring culture conversion outcomes [(OR 7.737, 95% CI 1.032-57.989); P = 0.046]. In contrast, among patients with no previous TB treatment history, the RIF-containing regimen had a higher chance of acquiring culture conversion outcomes [(OR 11.038, 95%CI 1.008-120.888); P = 0.049]. CONCLUSION MAC-PD patients unsuitable for standard regimens could benefit from a CFZ-containing regimen, especially for patients with previous TB treatment history and baseline CFZ MIC values lower than 0.25 mg/L.
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Affiliation(s)
- Shengjuan Bao
- Tuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing, China; National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Suting Chen
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Jifang Zheng
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Junke Ma
- The First Affiliated Hospital of Xinxiang Medical University, Xinxiang, Henan, China
| | - Jiali Yang
- Puer People's Hospital, Puer, Yunnan, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory for Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China.
| | - Hongfei Duan
- Tuberculosis Department, Beijing Chest Hospital, Capital Medical University, Beijing, China.
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Xie J, Meijer AH. Xenophagy receptors Optn and p62 and autophagy modulator Dram1 independently promote the zebrafish host defense against Mycobacterium marinum. Front Cell Infect Microbiol 2024; 13:1331818. [PMID: 38264729 PMCID: PMC10803470 DOI: 10.3389/fcimb.2023.1331818] [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: 11/01/2023] [Accepted: 12/18/2023] [Indexed: 01/25/2024] Open
Abstract
Anti-bacterial autophagy, also known as xenophagy, is a crucial innate immune process that helps maintain cellular homeostasis by targeting invading microbes. This defense pathway is widely studied in the context of infections with mycobacteria, the causative agents of human tuberculosis and tuberculosis-like disease in animal models. Our previous work in a zebrafish tuberculosis model showed that host defense against Mycobacterium marinum (Mm) is impaired by deficiencies in xenophagy receptors, optineurin (Optn) or sequestome 1 (p62), and Damage-regulated autophagy modulator 1 (Dram1). However, the interdependency of these receptors and their interaction with Dram1 remained unknown. In the present study, we used single and double knockout zebrafish lines in combination with overexpression experiments. We show that Optn and p62 can compensate for the loss of each other's function, as their overexpression restores the infection susceptibility of the mutant phenotypes. Similarly, Dram1 can compensate for deficiencies in Optn and p62, and, vice versa, Optn and p62 compensate for the loss of Dram1, indicating that these xenophagy receptors and Dram1 do not rely on each other for host defense against Mm. In agreement, Dram1 overexpression in optn/p62 double mutants restored the interaction of autophagosome marker Lc3 with Mm. Finally, optn/p62 double mutants displayed more severe infection susceptibility than the single mutants. Taken together, these results suggest that Optn and p62 do not function downstream of each other in the anti-mycobacterial xenophagy pathway, and that the Dram1-mediated defense against Mm infection does not rely on specific xenophagy receptors.
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Bakuła Z, Dziurzyński M, Decewicz P, Bakonytė D, Vasiliauskaitė L, Nakčerienė B, Krenke R, Stakėnas P, Jagielski T. Spoligotyping of Mycobacterium tuberculosis - Comparing in vitro and in silico approaches. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 115:105508. [PMID: 37757901 DOI: 10.1016/j.meegid.2023.105508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 09/29/2023]
Abstract
Spoligotyping is one of the molecular typing methods widely used for exploring the genetic variety of Mycobacterium tuberculosis. The aim of this study was to compare the spoligoprofiles of M. tuberculosis clinical isolates, obtained using in vitro and in silico approaches. The study included 230 M. tuberculosis isolates, recovered from Poland and Lithuania between 2018 and 2021. Spoligotyping in vitro was performed with a commercially available kit. Whole genome sequencing (WGS) was done with Illumina NovaSeq 6000 sequencer. Spoligotype International Types (SITs) were assigned according to the SITVIT2 database or using three different in silico tools, and based on WGS data, namely SpoTyping, SpolPred, and lorikeet. Upon in vitro spoligotyping, the isolates produced 65 different spoligotypes. Spoligotypes inferred from the WGS data were congruent with in vitro generated patterns in 81.7% (188/230) for lorikeet and 81.3% (187/230) for SpolPred and SpoTyping. Spacers 18 and 31 produced the highest ratio of discrepant results between in vitro and in silico approaches, with their signals discordantly assigned for 15 (6.5%) and 9 (3.9%) isolates, respectively. All three in silico approaches used were similarly efficient for M. tuberculosis spoligotype prediction. However, only SpoTyping could predict spoligotypes without a need for manual curation. Thus, we consider it as the most accurate tool. Its use is further advocated by the shortest time of analysis. A relatively high (ca. 20%) discordance between in vitro and in silico spoligotyping results was observed. While we discourage comparing conventional spoligotyping with in silico equivalents, we advise the use of the latter, as it improves the accuracy of spoligopatterns, and thus depicts the relatedness between the isolates more reliably.
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Affiliation(s)
- Zofia Bakuła
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland.
| | - Mikołaj Dziurzyński
- Department of Biology (DBIO), University of Florence, via Madonna del Piano 10, Sesto Fiorentino 50019, Italy.
| | - Przemysław Decewicz
- Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland.
| | - Daiva Bakonytė
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania.
| | - Laima Vasiliauskaitė
- Department of Physiology, Biochemistry, Microbiology and Laboratory Medicine, Institute of Biomedical Sciences, Vilnius University, Lithuania; Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania; Centre of Laboratory Medicine, Laboratory of Infectious Diseases and Tuberculosis, Vilnius University Hospital Santaros klinikos, Lithuania.
| | - Birutė Nakčerienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania; Department of Programs and State Tuberculosis Information System, Vilnius University Hospital Santaros klinikos, Vilnius, Lithuania.
| | - Rafał Krenke
- Department of Internal Medicine, Pulmonary Diseases & Allergy, Medical University of Warsaw, Warsaw, Poland.
| | - Petras Stakėnas
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania.
| | - Tomasz Jagielski
- Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Poland.
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Bekele D, Aragie S, Alene KA, Dejene T, Warkaye S, Mezemir M, Abdena D, Kebebew T, Botore A, Mekonen G, Gutema G, Dufera B, Gemede K, Kenate B, Gobena D, Alemu B, Hailemariam D, Muleta D, Siu GKH, Tafess K. Spatiotemporal Distribution of Tuberculosis in the Oromia Region of Ethiopia: A Hotspot Analysis. Trop Med Infect Dis 2023; 8:437. [PMID: 37755898 PMCID: PMC10536582 DOI: 10.3390/tropicalmed8090437] [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: 07/28/2023] [Revised: 08/29/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023] Open
Abstract
Tuberculosis (TB) is a major public health concern in low- and middle-income countries including Ethiopia. This study aimed to assess the spatiotemporal distribution of TB and identify TB risk factors in Ethiopia's Oromia region. Descriptive and spatiotemporal analyses were conducted. Bayesian spatiotemporal modeling was used to identify covariates that accounted for variability in TB and its spatiotemporal distribution. A total of 206,278 new pulmonary TB cases were reported in the Oromia region between 2018 and 2022, with the lowest annual TB case notification (96.93 per 100,000 population) reported in 2020 (i.e., during the COVID-19 pandemic) and the highest TB case notification (106.19 per 100,000 population) reported in 2019. Substantial spatiotemporal variations in the distribution of notified TB case notifications were observed at zonal and district levels with most of the hotspot areas detected in the northern and southern parts of the region. The spatiotemporal distribution of notified TB incidence was positively associated with different ecological variables including temperature (β = 0.142; 95% credible interval (CrI): 0.070, 0.215), wind speed (β = -0.140; 95% CrI: -0.212, -0.068), health service coverage (β = 0.426; 95% CrI: 0.347, 0.505), and population density (β = 0.491; 95% CrI: 0.390, 0.594). The findings of this study indicated that preventive measures considering socio-demographic and health system factors can be targeted to high-risk areas for effective control of TB in the Oromia region. Further studies are needed to develop effective strategies for reducing the burden of TB in hotspot areas.
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Affiliation(s)
- Dereje Bekele
- Communicable and Non-Communicable Diseases Prevention and Control Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (D.A.); (G.M.); (K.G.); (B.A.); (D.H.)
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (S.A.); (G.G.); (B.D.)
| | - Solomon Aragie
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (S.A.); (G.G.); (B.D.)
| | - Kefyalew Addis Alene
- Geospatial and Tuberculosis Team, Telethon Kids Institute, Perth, WA 6009, Australia;
- School of Public Health, Faculty of Public Health Sciences, Curtin University, Perth, WA 6102, Australia
| | - Tariku Dejene
- Center for Population Studies, College of Development Studies, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia;
| | - Samson Warkaye
- Ethiopian Public Health Institute, National Data Management Center for Health, Addis Ababa P.O. Box 1242, Ethiopia;
| | - Melat Mezemir
- Health Promotion and Diseases Prevention Directorate, Addis Ababa City Administration Health Bureau, Addis Ababa P.O. Box 30738, Ethiopia;
| | - Dereje Abdena
- Communicable and Non-Communicable Diseases Prevention and Control Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (D.A.); (G.M.); (K.G.); (B.A.); (D.H.)
| | - Tesfaye Kebebew
- Public Health Emergency Management, Research, and Blood Bank Service Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (T.K.); (A.B.); (B.K.); (D.G.); (D.M.)
| | - Abera Botore
- Public Health Emergency Management, Research, and Blood Bank Service Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (T.K.); (A.B.); (B.K.); (D.G.); (D.M.)
| | - Geremew Mekonen
- Communicable and Non-Communicable Diseases Prevention and Control Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (D.A.); (G.M.); (K.G.); (B.A.); (D.H.)
| | - Gadissa Gutema
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (S.A.); (G.G.); (B.D.)
- National HIV/AIDS and TB Research Directorate, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia
| | - Boja Dufera
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (S.A.); (G.G.); (B.D.)
- Bacterial, Parasitic, and Zoonotic Research Directorate, Ethiopian Public Health Institute, Addis Ababa P.O. Box 1242, Ethiopia
| | - Kolato Gemede
- Communicable and Non-Communicable Diseases Prevention and Control Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (D.A.); (G.M.); (K.G.); (B.A.); (D.H.)
| | - Birhanu Kenate
- Public Health Emergency Management, Research, and Blood Bank Service Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (T.K.); (A.B.); (B.K.); (D.G.); (D.M.)
| | - Dabesa Gobena
- Public Health Emergency Management, Research, and Blood Bank Service Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (T.K.); (A.B.); (B.K.); (D.G.); (D.M.)
| | - Bizuneh Alemu
- Communicable and Non-Communicable Diseases Prevention and Control Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (D.A.); (G.M.); (K.G.); (B.A.); (D.H.)
| | - Dagnachew Hailemariam
- Communicable and Non-Communicable Diseases Prevention and Control Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (D.A.); (G.M.); (K.G.); (B.A.); (D.H.)
| | - Daba Muleta
- Public Health Emergency Management, Research, and Blood Bank Service Directorate, Oromia Region Health Bureau, Addis Ababa P.O. Box 24341, Ethiopia; (T.K.); (A.B.); (B.K.); (D.G.); (D.M.)
| | - Gilman Kit Hang Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong;
| | - Ketema Tafess
- Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, Adama P.O. Box 1888, Ethiopia;
- Institute of Pharmaceutical Science, Adama Science and Technology University, Adama P.O. Box 1888, Ethiopia
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Yu Q, Wang Y, Gao Z, Yang H, Liu S, Tan J, Yang L. DNA microarray chip assay in new use: early diagnostic value in cutaneous mycobacterial infection. Front Cell Infect Microbiol 2023; 13:1183078. [PMID: 37457951 PMCID: PMC10349391 DOI: 10.3389/fcimb.2023.1183078] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Introduction The clinical practicability of DNA microarray chip in detecting the presence of mycobacterial species/isolates directly in the skin tissues has not been evaluated, nor the efficacy of DNA microarray chip as a novel diagnostic tool for the early diagnosis of cutaneous mycobacterial infections is known. Methods The present study analyzed the incidence of cutaneous mycobacterial infections in Shanghai and explored the efficacy of a novel DNA microarray chip assay for the clinical diagnosis of the disease from skin tissue specimens compared to traditional detection methods. A total of 60 participants fulfilling the defined diagnostic criteria and confirmed positive for cutaneous mycobacterial infections from 2019 to 2021 were enrolled in the study. Subsequent to recording the participants' medical history and clinical characteristics, the skin tissue specimens were collected for analyses. The specimens underwent histopathological analyses, skin tissue culture, and DNA microarray chip assay. Results Increased incidence of cutaneous mycobacterial infection was detected from 2019 to 2021. The most common infecting pathogen was M. marinum followed by M. abscessus. The sensitivity, specificity and accuracy of the skin tissue culture method were 70%, 100% and 76.62%, respectively, while that of the DNA microarray chip assay were 91.67%, 100% and 93.51%, respectively. The sensitivity and accuracy of the DNA microarray chip assay were significantly higher than those of the skin tissue culture method. The positive likelihood and diagnostic odds ratio were >10 and >1, respectively for both the methods. The negative likelihood ratio was significantly higher (30% vs 8.33%) and the Youden's index was significantly lower (70.00% vs 91.67%) in the skin culture method compared to that of the DNA microarray chip assay. There was a significant association of false negative results with a history of antibiotic use in the skin tissue culture method. Discussion Given the increasing incidence of cutaneous mycobacterial infections, early diagnosis remains a prime clinical focus. The DNA microarray chip assay provides a simple, rapid, high-throughput, and reliable method for the diagnosis of cutaneous mycobacterial infections with potential for clinical application.
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Liu Y, Ren W, Xue Z, Miao Y, Wang W, Zhang X, Yao C, Shang Y, Li S, Mi F, Pang Y. Real-time recombinase-aided amplification assay for rapid amplification of the IS1081 gene of Mycobacterium tuberculosis. Eur J Clin Microbiol Infect Dis 2023:10.1007/s10096-023-04626-5. [PMID: 37256455 DOI: 10.1007/s10096-023-04626-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 05/23/2023] [Indexed: 06/01/2023]
Abstract
Mycobacterium tuberculosis (MTB), the etiological agent of tuberculosis (TB), is the leading cause of death due to a single infectious agent worldwide. Rapid and accurate diagnosis of MTB is critical for controlling TB especially in resource-limited countries, since any diagnosis delay increases the chances of transmission. Here, a real-time recombinase-aided amplification (RAA) assay targeting conserved positions in IS1081 gene of MTB, is successfully established to detect MTB. The intact workflow was completed within 30 min at 42 °C with no cross-reactivity observed for non-tuberculous mycobacteria and other clinical bacteria, and the detection limit for recombinant plasmid of MTB IS1081 was 163 copies/reaction at 95% probability, which was approximately 1.5-fold increase in analytical sensitivity for the detection of MTB, compared to conventional quantitative real-time PCR (qPCR; 244 copies/reaction). Furthermore, the result of clinical performance evaluation revealed an increased sensitivity of RAA assay relative to qPCR was majorly noted in the specimens with low bacteria loads. Our results demonstrate that the developed real-time RAA assay is a convenient, sensitive, and low-cost diagnostic tool for the rapid detection of MTB.
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Affiliation(s)
- Yuanyuan Liu
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Weicong Ren
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Zhongtan Xue
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuedong Miao
- Department of Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Wei Wang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Cong Yao
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Fengling Mi
- Department of Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China.
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Performances of bioinformatics tools for the analysis of sequencing data of Mycobacterium tuberculosis complex strains. Tuberculosis (Edinb) 2023; 139:102324. [PMID: 36848710 DOI: 10.1016/j.tube.2023.102324] [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: 10/11/2022] [Revised: 01/23/2023] [Accepted: 02/12/2023] [Indexed: 02/15/2023]
Abstract
Whole-genome sequencing of Mycobacterium tuberculosis complex (MTBC) strains is a rapidly growing tool to obtain results regarding the resistance and phylogeny of the strains. We evaluated the performances of two bioinformatics tools for the analysis of whole-genome sequences of MTBC strains. Two hundred and twenty-seven MTBC strains were isolated and whole-genome sequenced at the laboratory of Avicenne Hospital between 2015 and 2021. We investigated the resistance and susceptibility status of strains using two online tools, Mykrobe and PhyResSE. We compared the genotypic and phenotypic resistance results obtained by drug susceptibility testing. Unlike with the Mykrobe tool, sequencing quality data were obtained using PhyResSE: average coverage of 98% and average depth of 119X. We found a similar concordance between phenotypic and genotypic results when determining susceptibility to first-line anti-tuberculosis drugs (95%) with both tools. The sensitivity and specificity of each tool compared to the phenotypic method were respectively 72% [52-87] and 98% [96-99] for Mykrobe and 76% [57-90] and 97% [94-99] for PhyResSE. Mykrobe and PhyResSE were easy to use and efficient. These platforms are accessible to people not trained in bioinformatics and constitute a complementary approach to phenotypic methods for the study of MTBC strains.
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He W, Tan Y, Song Z, Liu B, Wang Y, He P, Xia H, Huang F, Liu C, Zheng H, Pei S, Liu D, Ma A, Cao X, Zhao B, Ou X, Wang S, Zhao Y. Endogenous relapse and exogenous reinfection in recurrent pulmonary tuberculosis: A retrospective study revealed by whole genome sequencing. Front Microbiol 2023; 14:1115295. [PMID: 36876077 PMCID: PMC9981662 DOI: 10.3389/fmicb.2023.1115295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/02/2023] [Indexed: 02/19/2023] Open
Abstract
Background Tuberculosis may reoccur due to reinfection or relapse after initially successful treatment. Distinguishing the cause of TB recurrence is crucial to guide TB control and treatment. This study aimed to investigate the source of TB recurrence and risk factors related to relapse in Hunan province, a high TB burden region in southern China. Methods A population-based retrospective study was conducted on all culture-positive TB cases in Hunan province, China from 2013 to 2020. Phenotypic drug susceptibility testing and whole-genome sequencing were used to detect drug resistance and distinguish between relapse and reinfection. Pearson chi-square test and Fisher exact test were applied to compare differences in categorical variables between relapse and reinfection. The Kaplan-Meier curve was generated in R studio (4.0.4) to describe and compare the time to recurrence between different groups. p < 0.05 was considered statistically significant. Results Of 36 recurrent events, 27 (75.0%, 27/36) paired isolates were caused by relapse, and reinfection accounted for 25.0% (9/36) of recurrent cases. No significant difference in characteristics was observed between relapse and reinfection (all p > 0.05). In addition, TB relapse occurs earlier in patients of Tu ethnicity compared to patients of Han ethnicity (p < 0.0001), whereas no significant differences in the time interval to relapse were noted in other groups. Moreover, 83.3% (30/36) of TB recurrence occurred within 3 years. Overall, these recurrent TB isolates were predominantly pan-susceptible strains (71.0%, 49/69), followed by DR-TB (17.4%, 12/69) and MDR-TB (11.6%, 8/69), with mutations mainly in codon 450 of the rpoB gene and codon 315 of the katG gene. 11.1% (3/27) of relapse cases had acquired new resistance during treatment, with fluoroquinolone resistance occurring most frequently (7.4%, 2/27), both with mutations in codon 94 of gyrA. Conclusion Endogenous relapse is the main mechanism leading to TB recurrences in Hunan province. Given that TB recurrences can occur more than 4 years after treatment completion, it is necessary to extend the post-treatment follow-up period to achieve better management of TB patients. Moreover, the relatively high frequency of fluoroquinolone resistance in the second episode of relapse suggests that fluoroquinolones should be used with caution when treating TB cases with relapse, preferably guided by DST results.
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Affiliation(s)
- Wencong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yunhong Tan
- Hunan Provincial Chest Hospital, Tuberculosis Control Institution of Hunan Province, Changsha, Hunan, China
| | - Zexuan Song
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Binbin Liu
- Hunan Provincial Chest Hospital, Tuberculosis Control Institution of Hunan Province, Changsha, Hunan, China
| | - Yiting Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ping He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hui Xia
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Fei Huang
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Chunfa Liu
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huiwen Zheng
- Laboratory of Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing, China
| | - Dongxin Liu
- Shenzhen Third People's Hospital, Shenzhen, China
| | - Aijing Ma
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaolong Cao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xichao Ou
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shengfen Wang
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, China
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Shin JI, Ha JH, Kim KM, Choi JG, Park SR, Park HE, Park JS, Byun JH, Jung M, Baik SC, Lee WK, Kang HL, Yoo JW, Shin MK. A novel repeat sequence-based PCR (rep-PCR) using specific repeat sequences of Mycobacterium intracellulare as a DNA fingerprinting. Front Microbiol 2023; 14:1161194. [PMID: 37089534 PMCID: PMC10117815 DOI: 10.3389/fmicb.2023.1161194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/17/2023] [Indexed: 04/25/2023] Open
Abstract
Repetitive sequence-based PCR (rep-PCR) is a potential epidemiological technique that can provide high-throughput genotype fingerprints of heterogeneous Mycobacterium strains rapidly. Previously published rep-PCR primers, which are based on nucleotide sequences of Gram-negative bacteria may have low specificity for mycobacteria. Moreover, it was difficult to ensure the continuity of the study after the commercial rep-PCR kit was discontinued. Here, we designed a novel rep-PCR for Mycobacterium intracellulare, a major cause of nontuberculous mycobacterial pulmonary disease with frequent recurrence. We screened the 7,645 repeat sequences for 200 fragments from the genome of M. intracellulare ATCC 13950 in silico, finally generating five primers with more than 90% identity for a total of 226 loci in the genome. The five primers could make different band patterns depending on the genome of three different M. intracellulare strains using an in silico test. The novel rep-PCR with the five primers was conducted using 34 bacterial samples of 7 species containing 25 M. intracellulare clinical isolates, compared with previous published rep-PCRs. This shows distinguished patterns depending on species and blotting assay for 6 species implied the sequence specificity of the five primers. The Designed rep-PCR had a 95-98% of similarity value in the reproducibility test and showed 7 groups of fingerprints in M. intracellulare strains. Designed rep-PCR had a correlation value of 0.814 with VNTR, reference epidemiological method. This study provides a promising genotype fingerprinting method for tracing the recurrence of heterogeneous M. intracellulare.
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Affiliation(s)
- Jeong-Ih Shin
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Jong-Hun Ha
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Kyu-Min Kim
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Jeong-Gyu Choi
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Seo-Rin Park
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Hyun-Eui Park
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jin-Sik Park
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung-Hyun Byun
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Department of Laboratory Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Myunghwan Jung
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Seung-Chul Baik
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Woo-Kon Lee
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
| | - Hyung-Lyun Kang
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Jung-Wan Yoo
- Department of Internal Medicine, Gyeongsang National University Hospital, Jinju, Republic of Korea
- Jung-Wan Yoo,
| | - Min-Kyoung Shin
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
- Fastidious Specialized Pathogen Resources Bank, A Member of the National Culture Collection for Pathogens, Gyeongsang National University Hospital, Jinju, Republic of Korea
- *Correspondence: Min-Kyoung Shin,
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Ponce LC, Gallardo MJ, Marfil MJ, Petta A, Martínez Vivot M, Barandiaran S. Molecular detection of Mycobacterium tuberculosis complex in a captive aguará popé (Procyon cancrivorus) with macroscopic tuberculosis like-lesions. Indian J Tuberc 2023; 70:120-123. [PMID: 36740308 DOI: 10.1016/j.ijtb.2022.03.024] [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: 09/28/2021] [Revised: 03/13/2022] [Accepted: 03/26/2022] [Indexed: 02/07/2023]
Abstract
Tuberculosis is a chronic and contagious infectious disease caused by multi-host species of the genus Mycobacterium grouped within the Mycobacterium tuberculosis complex. These pathogenic bacteria mainly affect mammals, including humans. The most recognized species is Mycobacterium bovis, the causative agent of bovine tuberculosis in livestock. Although livestock is the main host of M. bovis, this species is frequently isolated from wild animals. Wild native mammals from Central and South America, as the crab-eating raccoon or "aguará popé" (Procyon cancrivorus), may act as a source of tuberculosis and may represent a human health risk, especially in captive scenarios, due to closer animal-human interaction. However, the only presence of infection in wild animals is not enough to determine their epidemiological role in the disease. Here we identify tuberculosis in a captive aguará popé with clinical signs and lung macroscopic tuberculosis-like lesions during necropsy. We detected tuberculosis by polymerase chain reaction assay. DNA was extracted directly from lung tissue and the amplification target was the insertion sequence 6110. This study contributes to investigate the presence of the disease in wild native animals of Argentina and supports the knowledge that wild mammals may act as a source of TB for humans and domestic animals.
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Affiliation(s)
- Loreana Carla Ponce
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Av. Chorroarín 280, C1427CWO, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Buenos Aires, Argentina.
| | - Mauro Julián Gallardo
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Av. Chorroarín 280, C1427CWO, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Patobiología Veterinaria, UEDD INTA-CONICET, Nicolás Repetto y De Los Reseros S/N, Hurlingham, Prov. de Buenos Aires, Argentina
| | - María Jimena Marfil
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Av. Chorroarín 280, C1427CWO, Buenos Aires, Argentina
| | - Adrián Petta
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Hospital Escuela, Chorroarín 280, C1427CWO, Buenos Aires, Argentina
| | - Marcela Martínez Vivot
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Av. Chorroarín 280, C1427CWO, Buenos Aires, Argentina
| | - Soledad Barandiaran
- Universidad de Buenos Aires, Facultad de Ciencias Veterinarias, Cátedra de Enfermedades Infecciosas, Av. Chorroarín 280, C1427CWO, Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Patobiología Veterinaria, UEDD INTA-CONICET, Nicolás Repetto y De Los Reseros S/N, Hurlingham, Prov. de Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Investigaciones en Producción Animal (INPA), Buenos Aires, Argentina
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13
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Korycka-Machała M, Kawka M, Lach J, Płocińska R, Bekier A, Dziadek B, Brzostek A, Płociński P, Strapagiel D, Szczesio M, Gobis K, Dziadek J. 2,4-Disubstituted pyridine derivatives are effective against intracellular and biofilm-forming tubercle bacilli. Front Pharmacol 2022; 13:1004632. [DOI: 10.3389/fphar.2022.1004632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 10/26/2022] [Indexed: 11/12/2022] Open
Abstract
It was recently reported that 4-substituted picolinohydrazonamides carrying hydrophilic cyclic amines, such as morpholine and pyrrolidine, at the end of their thiosemicarbazide chain have potent antimycobacterial activity in vitro at concentrations below 1 μg/ml. Here, two selected compounds, 2,4-disubstituted pyridine derivatives 11 and 15, revealed significant bactericidal activity against Mycobacterium tuberculosis localized intracellularly within human macrophages, as well as against biofilm-forming tubercle bacilli. Mutants were selected that were resistant to the investigated compounds at an efficiency similar to that identified in the presence of the first line antituberculosis drug rifampicin. The resistant mutants were viable in the presence of the tested compounds exclusively on solid media. Genome-wide sequencing of the mutants selected in the presence of compound 11 revealed the accumulation of nonsynonymous mutations in the mmpR5 gene encoding a transcriptional repressor of the MmpS5-MmpL5 efflux pump, whose upregulation has been associated with bedaquiline resistance. The depletion of MmpR5 in wild-type M. tuberculosis using CRISPR–Cas9 technology increased the resistance of this strain to compound 11. Mass spectrometry-based proteomics (LC–MS/MS) of wild-type tubercle bacilli growing in subinhibitory concentrations of compounds 11 or 15 revealed 15 overproduced proteins not detectable in the control cells, including virulence-related proteins.
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14
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Al-Mutairi NM, Ahmad S, Mokaddas E, Al-Hajoj S. First insights into the phylogenetic diversity of Mycobacterium tuberculosis in Kuwait and evaluation of REBA MTB-MDR assay for rapid detection of MDR-TB. PLoS One 2022; 17:e0276487. [PMID: 36264939 PMCID: PMC9584360 DOI: 10.1371/journal.pone.0276487] [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: 03/16/2022] [Accepted: 10/07/2022] [Indexed: 11/06/2022] Open
Abstract
Early detection of Mycobacterium tuberculosis (Mtb) in clinical specimens, its susceptibility to anti-TB drugs and disruption of infection transmission to new hosts are essential components for global tuberculosis (TB) control efforts. This study investigated major Mtb genotypes circulating in Kuwait and evaluated the performance of REBA MTB-MDR (REBA) test in comparison to GenoType MTBDRplus (gMTBDR+) assay for rapid detection of resistance of Mtb to isoniazid and rifampicin (MDR-TB). M. tuberculosis isolates (n = 256) originating predominantly from expatriate patients during a 6-month period were tested by spoligotyping and a dendrogram was created by UPGMA using MIRU-VNTRplus software. Phenotypic drug susceptibility testing (DST) was performed by MGIT 960 system. Genotypic DST for isoniazid and rifampicin was done by REBA and gMTBDR+ assays. Spoligotyping assigned 188 (73.4%) isolates to specific spoligotype international type (SIT) while 68 isolates exhibited orphan patterns. All major M. tuberculosis lineages were detected and EAI, CAS and Beijing families were predominant. Phylogenetic tree showed 131 patterns with 105 isolates exhibiting a unique pattern while 151 isolates clustered in 26 patterns. Fifteen isolates were resistant to one/more drugs. REBA and gMTBDR+ detected isoniazid resistance in 11/12 and 10/12 and rifampicin resistance in 4/5 and 4/5 resistant isolates, respectively. The diversity of SIT patterns are highly suggestive of infection of most expatriate patients with unique Mtb strains, likely acquired in their native countries before their arrival in Kuwait. Both, REBA and gMTBDR+ assays performed similarly for detection of resistance of Mtb to isoniazid and rifampicin for rapid detection of MDR-TB.
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Affiliation(s)
- Noura M. Al-Mutairi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
| | - Suhail Ahmad
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- * E-mail: ,
| | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait
- Kuwait National TB Control Laboratory, Shuwaikh, Kuwait
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, Mycobacteriology Research Section, King Faisal Special Hospital and Research Center (KFSH & RC), Riyadh, Saudi Arabia
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15
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Xiao M, Yang S, Zhou A, Li T, Liu J, Chen Y, Luo Y, Qian C, Yang F, Tang B, Li C, Su N, Li J, Jiang M, Yang S, Lin H. MiR-27a-3p and miR-30b-5p inhibited-vitamin D receptor involved in the progression of tuberculosis. Front Microbiol 2022; 13:1020542. [PMID: 36304947 PMCID: PMC9593098 DOI: 10.3389/fmicb.2022.1020542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/20/2022] [Indexed: 11/28/2022] Open
Abstract
Background MicroRNAs (miRNAs) play a vital role in tuberculosis (TB). Vitamin D receptor (VDR), an miRNA target gene, and its ligand, vitamin D3 (VitD3), have been reported to exert protective effects against TB. However, whether miRNAs can affect the progression of TB by targeting VDR has not been reported. Materials and methods Research subjects were selected according to defined inclusion criteria. A clinical database of 360 samples was established, including the subjects’ demographic information, miRNA expression profiles and cellular experimental results. Two candidate miRNAs, miR-27a-3p, and miR-30b-5p, were identified by a high-throughput sequencing screen and validated by qRT–PCR assays. Univariate and multivariate statistical analyses were performed. VDR and NF-kB p65 protein levels were detected by Western blot assays. Proinflammatory cytokine expression levels were detected by enzyme-linked immunosorbent assay (ELISA). Luciferase assays and fluorescence-activated cell sorting (FACS) were further applied to elucidate the detailed mechanisms. Results Differential miRNA expression profiles were obtained, and miR-27a-3p and miR-30b-5p were highly expressed in patients with TB. These results showed that the two miRNAs were able to induce M1 macrophage differentiation and inhibit M2 macrophage differentiation. Further experiments showed that the two miRNAs decreased the VDR protein level and increased proinflammatory cytokine secretion by macrophages. Mechanistically, the miRNAs targeted the 3′ untranslated region (3′UTR) of the VDR mRNA and thereby downregulated VDR protein levels by post-transcriptional regulation. Then, due to the reduction in VDR protein levels, the NF-kB inflammatory cytokine signaling pathway was activated, thus promoting the progression of TB. Conclusion Our study not only identified differentially expressed miRNAs between the TB and control groups but also revealed that miR-27a-3p and miR-30b-5p regulate proinflammatory cytokine secretion and macrophage differentiation through VDR in macrophages. Thus, these two miRNAs influence the progression of TB.
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Affiliation(s)
- Min Xiao
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Song Yang
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - An Zhou
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Tongxin Li
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Jingjing Liu
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Yang Chen
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Ya Luo
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chunfang Qian
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Fuping Yang
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Bo Tang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Chunhua Li
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Na Su
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
| | - Jing Li
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
| | - Mingying Jiang
- Chongqing Public Health Medical Center, Southwest University, Chongqing, China
- *Correspondence: Mingying Jiang,
| | - Shiming Yang
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
- Shiming Yang,
| | - Hui Lin
- Department of Gastroenterology, Xinqiao Hospital, Army Medical University, Chongqing, China
- Hui Lin,
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Cheng L, Zhang F, Wang Y, Chen J, Yuan X. Association between IFNGR1 gene polymorphisms and tuberculosis susceptibility: A meta-analysis. Front Public Health 2022; 10:976221. [PMID: 36148347 PMCID: PMC9485675 DOI: 10.3389/fpubh.2022.976221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/15/2022] [Indexed: 01/25/2023] Open
Abstract
The association of IFN-γ receptor 1 (IFNGR1) gene polymorphisms with tuberculosis (TB) susceptibility has not been systematically studied. We therefore conducted a meta-analysis to assess their association. Literature search was conducted in PubMed, EMBASE, Web of Science, and the Cochrane Library. Odds ratio (OR) and 95% confidence interval (CI) was pooled by the random-effect model. Statistical analyses were performed using STATA 12.0 software. Fourteen studies involved 7,699 TB cases and 8,289 controls were included in this meta-analysis. A significant association was found between the IFNGR1 rs2234711 polymorphism and TB susceptibility among Africans in dominant model (OR = 1.24, 95%CI:1.01-1.52), and among Asians in allele model (OR = 0.89, 95%CI: 0.79-0.99), homozygote model (OR = 0.82, 95%CI: 0.70-0.98) and additive model (OR = 0.90, 95%CI: 0.83-0.97). In addition, a significant association was observed between the IFNGR1 rs7749390 polymorphism and TB susceptibility among Africans in allele model (OR = 0.89, 95%CI: 0.82-0.98). No significant association was found between the IFNGR1 rs1327474 polymorphism and TB susceptibility. In summary, IFNGR1 rs2234711 polymorphism was associated with increased TB susceptibility in Africans and decreased TB susceptibility in Asians, while IFNGR1 rs7749390 polymorphism was associated with decreased TB susceptibility in Africans.
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Affiliation(s)
- Liwei Cheng
- Office of Academic Research, Renmin Hospital of Wuhan University, Wuhan, China
| | - Fan Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan, China
| | - Ying Wang
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China
| | - Jing Chen
- Outpatient Department, Renmin Hospital of Wuhan University, Wuhan, China,*Correspondence: Xiaoping Yuan
| | - Xiaoping Yuan
- Department of Psychiatry, Renmin Hospital of Wuhan University, Wuhan, China,Jing Chen
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Morais FCL, Bello GL, Costi C, Schmid KB, Soares TDS, Barcellos RB, Unis G, Dias CF, da Silva PEA, Rossetti ML. Detection of non-tuberculosus mycobacteria (NTMs) in lung samples using 16S rRNA. Mem Inst Oswaldo Cruz 2022; 117:e220031. [PMID: 35920498 PMCID: PMC9337835 DOI: 10.1590/0074-02760220031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 07/11/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Non-tuberculous mycobacteria (NTMs) cause diseases known as mycobacteriosis
and are an important cause of morbidity and mortality. The diagnosis of
pulmonary disease caused by NTM is hampered by its clinical similarity with
tuberculosis (TB) and by the lack of an accurate and rapid laboratory
diagnosis. OBJECTIVES Detect DNA from NTMs directly from lung samples using real-time polymerase
chain reaction (qPCR) for amplification of 16S rRNA. Additionally, DNA
sequencing (hsp65 and rpoB genes) was used
to identify the species of MNTs. METHODS A total of 68 sputum samples (54 with suspected NTMs and 14 with TB) from
patients treated at a referral hospital were used. FINDINGS Of these, 27/54 (50%) were qPCR positive for NTMs and 14/14 TB patients
(controls) were qPCR negative with an almost perfect concordance
(Kappa of 0.93) with the Mycobacterium
spp. culture. Sequencing confirmed the presence of NTM in all positive
samples. The most common species was Mycobacterium gordonae
(33%), followed by Mycobacterium abscessus (26%),
Mycobacterium fortuitum (22%), Mycobacterium
avium (15%) and Mycobacterium peregrinum
(4%). MAIN CONCLUSIONS The qPCR technique for detecting NTMs targeting 16S rRNA has the potential
to detect NTMs and rapidly differentiate from Mycobacterium
tuberculosis. However, it is necessary to identify the species
to help in the differential diagnosis between disease and contamination, and
to guide the choice of the therapeutic scheme.
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Affiliation(s)
- Franciele Costa Leite Morais
- Universidade Luterana do Brasil, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil
| | - Graziele Lima Bello
- Instituto Nacional de Ciência e Tecnologia em Tuberculose, Programa Institutos Nacionais de Ciência e Tecnologia, Porto Alegre, RS, Brasil
| | - Cíntia Costi
- Secretaria da Saúde do Rio Grande do Sul, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Karen Barros Schmid
- Secretaria da Saúde do Rio Grande do Sul, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
| | - Tainá Dos Santos Soares
- Universidade Luterana do Brasil, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil.,Secretaria da Saúde do Rio Grande do Sul, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil
| | - Regina Bones Barcellos
- Secretaria da Saúde do Rio Grande do Sul, Centro de Desenvolvimento Científico e Tecnológico, Porto Alegre, RS, Brasil.,Universidade Federal do Rio de Janeiro, Programa de Pós-Graduação em Clínica Médica, Rio de Janeiro, RJ, Brasil
| | - Gisela Unis
- Secretaria da Saúde do Rio Grande do Sul, Hospital Sanatório Partenon, Porto Alegre, RS, Brasil
| | - Claudia Fontoura Dias
- Secretaria da Saúde do Rio Grande do Sul, Hospital Sanatório Partenon, Porto Alegre, RS, Brasil
| | - Pedro Eduardo Almeida da Silva
- Universidade Federal do Rio Grande, Faculdade de Medicina, Centro de Pesquisas em Microbiologia Médica, Rio Grande, RS, Brasil
| | - Maria Lucia Rossetti
- Universidade Luterana do Brasil, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, RS, Brasil.,Instituto Nacional de Ciência e Tecnologia em Tuberculose, Programa Institutos Nacionais de Ciência e Tecnologia, Porto Alegre, RS, Brasil.,Universidade Federal do Rio Grande do Sul, Programa de Pós-Graduação em Biologia Celular e Molecular, Porto Alegre, RS, Brasil
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18
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Meghdadi H, Khosravi AD, Hashemzadeh M, Tabandeh MR. New design of multilocus sequence analysis of rpoB, ssrA, tuf, atpE, ku, and dnaK for identification of Mycobacterium species. Mol Biol Rep 2022; 49:7967-7977. [PMID: 35717471 DOI: 10.1007/s11033-022-07638-0] [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: 04/10/2022] [Revised: 05/20/2022] [Accepted: 05/24/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Differentiating Mycobacterium tuberculosis (MTB) from nontuberculous mycobacteria (NTM) is very important in the treatment process of patients. According to the American Thoracic Society guideline (ATS), NTM clinical isolates should be identified at the species level proper treatment and patient management. This study aimed to identify NTM clinical isolates by evaluationg rpoB, ssrA, tuf, atpE, ku, and dnaK genes, and use multilocus sequence analysis (MLSA) to concatenate the six genes. METHODS Ninety-six Mycobacterium isolates, including 86 NTM and 10 MTB isolates, from all the patients referred to the certain TB Reference Centres were included. All isolates were evaluated by PCR amplification of rpoB, ssrA, tuf, ku, atpE, and dnaK genes and MLSA. RESULTS Out of 96 isolates, 91 (94.8%), 87 (90.6%), 72 (75%), 84 (87.5%) and 79 (82.3%) were differentiated to the species level by rpoB, tuf, ssrA, dnaK and atpE genes, respectively. The ku gene was able to identify 69 (80.2%) isolates of the 86 NTM isolates to the species level. We could identify 100% of the isolates to the species level by MLSA. CONCLUSIONS None of the PCR targets used in this study were able to completely differentiate all species. The MLSA technique used to concatenate the six genes could increase the identification of clinical Mycobacterium isolates and all 16 species were well-differentiated.
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Affiliation(s)
- Hossein Meghdadi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Azar Dokht Khosravi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Reza Tabandeh
- Department of Basic Sciences, Division of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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19
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Synthesis and in vitro studies for structure-based design of novel chalcones as antitubercular agents targeting InhA. Future Med Chem 2022; 14:851-866. [PMID: 35548879 DOI: 10.4155/fmc-2022-0052] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background: The authors aimed to estimate the therapeutic potential of novel chalcones against tuberculosis. Methods: 11 synthesized compounds were tested for in vitro antimycobacterial activity against Mycobacterium tuberculosis (H37RV; American Type Culture Collection number: 27294) using the microplate alamarBlue assay. Molecular docking and pharmacokinetic parameter analyses were then performed. Results: The most potent compounds, (2E)-1-(4-bromophenyl) (2E)-1-(2-nitrophenyl) prop-2-en-1-one, -3-(2-nitrophenyl) prop-2-en-1-one (4-bromophenyl) (2E)-1-(3-phenoxyphenyl)prop-2-en-1-one, 3-(phenoxyphenyl)prop-2-en-1-one (4-bromophenyl) prop-2-en-1-one and (2E)-1-(4-bromophenyl)-3-(5-chloro-2-hydroxyphenyl)-prop-2-en-1-one, showed in vitro activity, with a minimum inhibitory concentration (MIC) of 6.25 μg/ml. Conclusion: Compounds LSD2, LSD12, LSD13 and LSD15 showed strong in vitro antimycobacterial activity at a concentration of 6.25 μg/ml.
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20
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Abstract
Whole-genome sequencing (WGS) has shown tremendous potential in rapid diagnosis of drug-resistant tuberculosis (TB). In the current study, we performed WGS on drug-resistant Mycobacterium tuberculosis isolates obtained from Shanghai (n = 137) and Russia (n = 78). We aimed to characterise the underlying and high-frequency novel drug-resistance-conferring mutations, and also create valuable combinations of resistance mutations with high predictive sensitivity to predict multidrug- and extensively drug-resistant tuberculosis (MDR/XDR-TB) phenotype using a bootstrap method. Most strains belonged to L2.2, L4.2, L4.4, L4.5 and L4.8 lineages. We found that WGS could predict 82.07% of phenotypically drug-resistant domestic strains. The prediction sensitivity for rifampicin (RIF), isoniazid (INH), ethambutol (EMB), streptomycin (STR), ofloxacin (OFL), amikacin (AMK) and capreomycin (CAP) was 79.71%, 86.30%, 76.47%, 88.37%, 83.33%, 70.00% and 70.00%, respectively. The mutation combination with the highest sensitivity for MDR prediction was rpoB S450L + rpoB H445A/P + katG S315T + inhA I21T + inhA S94A, with a sensitivity of 92.17% (0.8615, 0.9646), and the mutation combination with highest sensitivity for XDR prediction was rpoB S450L + katG S315T + gyrA D94G + rrs A1401G, with a sensitivity of 92.86% (0.8158, 0.9796). The molecular information presented here will be of particular value for the rapid clinical detection of MDR- and XDR-TB isolates through laboratory diagnosis.
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21
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Osei-Wusu S, Morgan P, Asare P, Adams G, Musah AB, Siam IM, Gillespie SH, Sabiiti W, Yeboah-Manu D. Bacterial Load Comparison of the Three Main Lineages of Mycobacterium tuberculosis Complex in West Africa. Front Microbiol 2021; 12:719531. [PMID: 34777274 PMCID: PMC8578714 DOI: 10.3389/fmicb.2021.719531] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/29/2021] [Indexed: 11/13/2022] Open
Abstract
Studies have shown an association between bacterial load and virulence; however, not much is known about the diversity in this phenotypic characteristic of Mycobacterium tuberculosis complex (MTBC). This study was therefore aimed to determine the differences in bacterial load of the three most prevalent MTBC genotypes (L4, L5, and L6) in West Africa at the time of diagnosis. A total of 170 paired fresh sputum samples were collected; one part in guanidinium thiocyanate (GTC) was used for RNA extraction and tuberculosis molecular bacterial load assay (TB-MBLA), and the other part without GTC was confirmed for TB positivity using GeneXpert MTB/RIF, smear microscopy grading, and culture on Löwenstein-Jensen media slants. The 170 sputum samples comprised 155 new cases, three follow-up cases, and 12 TB negative sputum samples. The time-to-culture positivity (TTP) and degree of culture positivity (DCP) were recorded. All 122 isolates obtained were spoligotyped for lineage (L) classification, but spoligotypes were obtained from 120 isolates. Of the typed isolates, 70.0, 10.8, 10.8, 4.2, 2.5, 0.8, and 0.8% were lineages 4, 5, 6, 2, 3, 1, and Mycobacterium bovis, respectively. Further analysis of the three most prevalent lineages showed significantly shorter TTP and higher DCP by L4 compared to L5 and L6, respectively: TTP 20.8, vs. 26.5, and 28.2 days; p-value = 0.005 and DCP 1.27, vs. 0.81 and 0.29, p < 0.001. The average TB-MBLA measured bacterial load of L4 was 3.82 Log10eCFU/ml which was not significantly different from 3.81 and 3.80 Log10eCFU/ml of L5 and L6, respectively, p = 0.84. Degrees of smear microscopy L4 = 1.20, L5 = 1.20, and L6 = 0.92 and GeneXpert Cq values L4 = 17.08, L5 = 18.37, and L6 = 17.59 showed no significant difference between the lineages, p = 0.72 and p = 0.48, respectively. Retrospective analysis of a larger sample confirmed the difference in TTP, p < 0.001. In conclusion, the observed shorter TTP and high DCP of L4 could signify high growth rate in culture that is independent of total bacterial load at diagnosis.
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Affiliation(s)
- Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.,West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
| | - Portia Morgan
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Prince Asare
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Godfrey Adams
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Abdul Basit Musah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ishaque Mintah Siam
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Stephen Henry Gillespie
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Wilber Sabiiti
- Division of Infection and Global Health, School of Medicine, University of St Andrews, St Andrews, United Kingdom
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana.,West African Center for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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22
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Merid Y, Hailu E, Habtamu G, Tilahun M, Abebe M, Hailu M, Hailu T, Datiko DG, Woldeamanuel Y, Aseffa A. Molecular Epidemiology of Mycobacterium tuberculosis strains isolated from pulmonary tuberculosis patients in south Ethiopia. J Infect Dev Ctries 2021; 15:1299-1307. [PMID: 34669600 PMCID: PMC8556644 DOI: 10.3855/jidc.14742] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 03/04/2021] [Indexed: 01/22/2023] Open
Abstract
Introduction: Understanding the epidemiology of tuberculosis is limited by lack of genotyping data. We sought to characterize the drug susceptibility testing patterns and genetic diversity of M. tuberculosis isolates in southern Ethiopia. Methodology: A cross-sectional study was conducted among newly diagnosed sputum smear positive patients with tuberculosis visiting nine health facilities in southern Ethiopia from June 2015 to May 2016. Three consecutive sputum samples (spot-morning-spot) per patient were examined using acid-fast bacilli smear microscopy with all smear positive specimens having acid-fast bacilli cultures performed. M. tuberculosis isolates had drug susceptibility testing performed using indirect proportion method and were genotyped with RD9 deletion analysis and spoligotyping. Mapping of strain was made using geographic information system. Results: Among 250 newly diagnosed patients with tuberculosis, 4% were HIV co-infected. All 230 isolates tested were M. tuberculosis strains belonging to three lineages: Euro-American, 187 (81%), East-African-Indian, 31 (14%), and Lineage 7 (Ethiopian lineage), 8 (4%); categorized into 63 different spoligotype patterns, of which 85% fell into 28 clusters. M. tuberculosis strains were clustered by geographic localities. The dominant spoligotypes were SIT149 (21%) and SIT53 (19%). Drug susceptibility testing found that 14% of isolates tested were resistant to ≥ 1 first line anti- tuberculosis drugs and 11% to INH. SIT 149 was dominant among drug resistant isolates. Conclusions: The study revealed several clusters and drug resistant strains of M. tuberculosis in the study area, suggesting recent transmission including of drug resistant tuberculosis. Wider monitoring of drug susceptibility testing and geospatial analysis of transmission trends is required to control tuberculosis in southern Ethiopia.
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Affiliation(s)
- Yared Merid
- College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia.
| | - Elena Hailu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Getnet Habtamu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Melaku Tilahun
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Mesay Hailu
- College of Medicine and Health Sciences, Hawassa University, Hawassa, Ethiopia
| | - Tsegaye Hailu
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | | | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
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23
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Tabassum R, Ashfaq M, Oku H. Current Pharmaceutical Aspects of Synthetic Quinoline Derivatives. Mini Rev Med Chem 2021; 21:1152-1172. [PMID: 33319670 DOI: 10.2174/1389557520999201214234735] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 10/06/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022]
Abstract
Quinoline derivatives are considered broad-spectrum pharmacological compounds that exhibit a wide range of biological activities. Integration of quinoline moiety can improve its physical and chemical properties and also pharmacological behavior. Due to its wide range of pharmaceutical applications, it is a very popular compound to design new drugs for the treatment of multiple diseases like cancer, dengue fever, malaria, tuberculosis, fungal infections, AIDS, Alzheimer's disease and diabetes. In this review, our major focus is to pay attention to the biological activities of quinoline compounds in the treatment of these diseases such as anti-viral, anti-cancer, anti-malarial, antibacterial, anti-fungal, anti-tubercular and anti-diabetic.
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Affiliation(s)
- Rukhsana Tabassum
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, 36100, Pakistan
| | - Muhammad Ashfaq
- Department of Chemistry, The Islamia University of Bahawalpur, Bahawalpur, 36100, Pakistan
| | - Hiroyuki Oku
- Division of Molecular Science, Graduate School of Science & Engineering Gunma University, Gunma 376-8515, Japan
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24
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Bordin A, Pandey S, Coulter C, Syrmis M, Pardo C, Hackett H, Bell SC, Wainwright CE, Nimmo GR, Jennison AV, Clark JE, Whiley DM. Rapid macrolide and amikacin resistance testing for Mycobacterium abscessus in people with cystic fibrosis. J Med Microbiol 2021; 70. [PMID: 33909552 DOI: 10.1099/jmm.0.001349] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Introduction. Mycobacterium abscessus complex (MABSC) is an environmental organism and opportunistic pathogen. MABSC pulmonary infections in people with cystic fibrosis are of growing clinical concern. Resistance data guide the use of macrolides and amikacin in MABSC pulmonary disease treatment. MABSC can acquire resistance against macrolides or amikacin via 23S or 16S rRNA gene mutations, respectively.Gap Statement. Current culture-based methods for MABSC detection and antibiotic resistance characterization are typically prolonged, limiting their utility to directly inform treatment or clinical trials. Culture-independent molecular methods may help address this limitation.Aim. To develop real-time PCR assays for characterization of key 23S or 16S rRNA gene mutations associated with constitutive resistance in MABSC.Methodology. We designed two real-time PCR assays to detect the key 23S and 16S rRNA gene mutations. The highly conserved nature of rRNA genes was a major design challenge. To reduce potential cross-reactivity, primers included non-template bases and targeted single-nucleotide polymorphisms unique to MABSC. We applied these assays, as well as a previously developed real-time PCR assay for MABSC detection, to 968 respiratory samples from people with cystic fibrosis. The results from the molecular methods were compared to those for gold standard culture methods and 23S and 16S rRNA gene sequencing.Results.The real-time PCR MABSC detection assay provided a sensitivity of 83.8 % and a specificity of 97.8 % compared to culture. The results from the real-time PCR resistance detection assays were mostly concordant (>77.4 %) with cultured isolate sequencing. The real-time PCR resistance detection assays identified several samples harbouring both resistant and susceptible MABSC, while culture-dependent methods only identified susceptible MABSC in these samples.Conclusion. Using the molecular methods described here, results for health care providers or researchers could be available days or weeks earlier than is currently possible via culture-based antibiotic susceptibility testing.
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Affiliation(s)
- Amanda Bordin
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Sushil Pandey
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Christopher Coulter
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Melanie Syrmis
- Queensland Mycobacterium Reference Laboratory, Pathology Queensland, Brisbane, Queensland, Australia.,The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Carolyn Pardo
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Hazel Hackett
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia
| | - Scott C Bell
- Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia.,Lung Bacteria Group, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.,The Prince Charles Hospital, Department of Thoracic Medicine, Brisbane, Queensland, Australia
| | - Claire E Wainwright
- Respiratory and Sleep Medicine Department, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - Graeme R Nimmo
- Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
| | - Amy V Jennison
- Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Julia E Clark
- Infection Management and Prevention Service, Queensland Children's Hospital, Brisbane, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| | - David M Whiley
- The University of Queensland Centre for Clinical Research, University of Queensland, Brisbane, Queensland, Australia.,Central Laboratory, Pathology Queensland, Brisbane, Queensland, Australia
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25
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Chen W, Dong B, Liu W, Liu Z. Recent Advances in Peptide Nucleic Acids as Antibacterial Agents. Curr Med Chem 2021; 28:1104-1125. [PMID: 32484766 DOI: 10.2174/0929867327666200602132504] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 11/22/2022]
Abstract
The emergence of antibiotic-resistant bacteria and the slow progress in searching for new antimicrobial agents makes it hard to treat bacterial infections and cause problems for the healthcare system worldwide, including high costs, prolonged hospitalizations, and increased mortality. Therefore, the discovery of effective antibacterial agents is of great importance. One attractive alternative is antisense peptide nucleic acid (PNA), which inhibits or eliminates gene expression by binding to the complementary messenger RNA (mRNA) sequence of essential genes or the accessible and functionally important regions of the ribosomal RNA (rRNA). Following 30 years of development, PNAs have played an extremely important role in the treatment of Gram-positive, Gram-negative, and acidfast bacteria due to their desirable stability of hybrid complex with target RNA, the strong affinity for target mRNA/rRNA, and the stability against nucleases. PNA-based antisense antibiotics can strongly inhibit the growth of pathogenic and antibiotic-resistant bacteria in a sequence-specific and dose-dependent manner at micromolar concentrations. However, several fundamental challenges, such as intracellular delivery, solubility, physiological stability, and clearance still need to be addressed before PNAs become broadly applicable in clinical settings. In this review, we summarize the recent advances in PNAs as antibacterial agents and the challenges that need to be overcome in the future.
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Affiliation(s)
- Wei Chen
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
| | - Bo Dong
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
| | - Wenen Liu
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha 410008, China
| | - Zhengchun Liu
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics Central South University, Changsha 410083, China
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26
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Occupational exposure and challenges in tackling M. bovis at human-animal interface: a narrative review. Int Arch Occup Environ Health 2021; 94:1147-1171. [PMID: 33725176 PMCID: PMC7961320 DOI: 10.1007/s00420-021-01677-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 01/12/2021] [Indexed: 01/09/2023]
Abstract
Zoonotic tuberculosis caused by Mycobacterium bovis (M. bovis), a member of Mycobacterium tuberculosis complex (MTBC) has increasingly gathered attention as a public health risk, particularly in developing countries with higher disease prevalence. M. bovis is capable of infecting multiple hosts encompassing a number of domestic animals, in particular cattle as well as a broad range of wildlife reservoirs. Humans are the incidental hosts of M. bovis whereby its transmission to humans is primarily through the consumption of cattle products such as unpasteurized milk or raw meat products that have been contaminated with M. bovis or the transmission could be due to close contact with infected cattle. Also, the transmission could occur through aerosol inhalation of infective droplets or infected body fluids or tissues in the presence of wound from infected animals. The zoonotic risk of M. bovis in humans exemplified by miscellaneous studies across different countries suggested the risk of occupational exposure towards M. bovis infection, especially those animal handlers that have close and unreserved contact with cattle and wildlife populations These animal handlers comprising of livestock farmers, abattoir workers, veterinarians and their assistants, hunters, wildlife workers as well as other animal handlers are at different risk of contracting M. bovis infection, depending on the nature of their jobs and how close is their interaction with infected animals. It is crucial to identify the underlying transmission risk factors and probable transmission pathways involved in the zoonotic transmission of M. bovis from animals to humans for better designation and development of specific preventive measures and guidelines that could reduce the risk of transmission and to protect these different occupational-related/populations at risk. Effective control and disease management of zoonotic tuberculosis caused by M. bovis in humans are also hindered by various challenges and factors involved at animal–human interface. A closer look into factors affecting proper disease control and management of M. bovis are therefore warranted. Hence, in this narrative review, we have gathered a number of different studies to highlight the risk of occupational exposure to M. bovis infection and addressed the limitations and challenges underlying this context. This review also shed lights on various components and approaches in tackling M. bovis infection at animal–human interface.
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27
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Kock R, Michel AL, Yeboah-Manu D, Azhar EI, Torrelles JB, Cadmus SI, Brunton L, Chakaya JM, Marais B, Mboera L, Rahim Z, Haider N, Zumla A. Zoonotic Tuberculosis - The Changing Landscape. Int J Infect Dis 2021; 113 Suppl 1:S68-S72. [PMID: 33713812 PMCID: PMC8672060 DOI: 10.1016/j.ijid.2021.02.091] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 02/06/2023] Open
Abstract
Globally, Zoonotic TB remains a poorly monitored and an important unaddressed burden. Zoonotic TB primarily from consumption M. bovis contaminated unpasteurized dairy products. Novel zoonotic TB strains (e.g. M. orygis), warrants more attention and intervention. Early detection and control of M. bovis in cattle remains the mainstay of reducing zoonotic TB risk. Reverse zoonosis to animals of treatment resistant TB strains is a threat to eliminating TB.
Despite slow reductions in the annual burden of active human tuberculosis (TB) cases, zoonotic TB (zTB) remains a poorly monitored and an important unaddressed global problem. There is a higher incidence in some regions and countries, especially where close association exists between growing numbers of cattle (the major source of Mycobacterium bovis) and people, many suffering from poverty, and where dairy products are consumed unpasteurised. More attention needs to be focused on possible increased zTB incidence resulting from growth in dairy production globally and increased demand in low income countries in particular. Evidence of new zoonotic mycobacterial strains in South Asia and Africa (e.g. M. orygis), warrants urgent assessment of prevalence, potential drivers and risk in order to develop appropriate interventions. Control of M. bovis infection in cattle through detect and cull policies remain the mainstay of reducing zTB risk, whilst in certain circumstances animal vaccination is proving beneficial. New point of care diagnostics will help to detect animal infections and human cases. Given the high burden of human tuberculosis (caused by M. tuberculosis) in endemic areas, animals are affected by reverse zoonosis, including multi-drug resistant strains. This, may create drug resistant reservoirs of infection in animals. Like COVID-19, zTB is evolving in an ever-changing global landscape.
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Affiliation(s)
- Richard Kock
- Pathobiology and Population Sciences Department, Royal Veterinary College, Hatfield, AL9 7TA, UK.
| | - Anita L Michel
- Department of Veterinary Tropical Diseases, Bovine Tuberculosis and Brucellosis Research Programme, Faculty of Veterinary Sciences, University of Pretoria, Onderstepoort, Pretoria, South Africa.
| | - Dorothy Yeboah-Manu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Ghana.
| | - Esam I Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, and Medical Laboratory Technology Department, Faculty of Applied Medical Sciences, King Abdulaziz University, Jeddah, Saudi Arabia.
| | - Jordi B Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Simeon I Cadmus
- Department of Veterinary Public Health and Preventive Medicine, University of Ibadan, Ibadan, Nigeria.
| | - Lucy Brunton
- Pathobiology and Population Sciences Department, Royal Veterinary College, Hatfield, AL9 7TA, UK.
| | - Jeremiah M Chakaya
- Department of Medicine, Therapeutics, Dermatology and Psychiatry, Kenyatta University, Nairobi, Kenya; Department of Clinical Sciences, Liverpool School of Tropical Medicine UK.
| | - Ben Marais
- Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, NSW, Australia.
| | - Leonard Mboera
- SACIDS Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania.
| | - Zeaur Rahim
- International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Mohakhali, Dhaka, 1212, Bangladesh.
| | - Najmul Haider
- Pathobiology and Population Sciences Department, Royal Veterinary College, Hatfield, AL9 7TA, UK.
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London, London, UK; National Institute for Health Research Biomedical Research Centre, University College London Hospitals National Health Service Foundation Trust, London, UK.
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Jbara S, Herranz M, Sola-Campoy PJ, Rodríguez-Grande C, Chiner-Oms Á, Comas I, Muñoz P, García de Viedma D, Pérez-Lago L. Overlapping prison/community tuberculosis outbreaks in Costa Rica revealed by alternative analysis of suboptimal material. Transbound Emerg Dis 2021; 69:1065-1072. [PMID: 33687788 DOI: 10.1111/tbed.14063] [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: 11/09/2020] [Revised: 02/15/2021] [Accepted: 03/05/2021] [Indexed: 11/29/2022]
Abstract
Costa Rica has a low incidence of tuberculosis. Thus, identifying transmission hotspots is key to implement interventions. A tuberculosis outbreak was suspected in a prison in Costa Rica. Given the suboptimal quality of the samples received in our laboratory in Madrid, we applied alternative schemes for their analysis. In the first scheme, we bypassed the standard approach of applying systematic mycobacterial interspersed repetitive units-variable number of tandem repeats (MIRU-VNTR) and used a strain-specific polymerase chain reaction (PCR) that allowed identifying a cluster involving six cases (C1). The second scheme followed the canonical MIRU-VNTR path coupled with a whole-genomic amplification step, by which a second unsuspected overlapping cluster (C2), was detected in the same prison. These findings justified the implementation of a surveillance programme adapted to local resources based on a tailored multiplex allele-specific oligonucleotide (ASO)-PCR targeting C1 and C2. Presence of the C2 strain at a different prison was determined. ASO-PCR was applied extensively and alerted to the active circulation of one of the strains within and beyond prisons. Our study shows that alternative methodological strategies may provide useful data in settings with lack of resources for performing systematic standard molecular epidemiology programmes and/or with suboptimal material for analysis.
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Affiliation(s)
- Sarah Jbara
- Centro Nacional de Referencia de Micobacteriología, Inciensa, Tres Ríos, Costa Rica
| | - Marta Herranz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades respiratorias, CIBERES, Spain
| | - Pedro J Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Cristina Rodríguez-Grande
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Álvaro Chiner-Oms
- Unidad Mixta Genómica y Salud, Centro Superior de Investigación en Salud Pública (FISABIO), Universitat de València, Valencia, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain.,CIBER en Epidemiología y Salud Pública (CIBERESP), Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades respiratorias, CIBERES, Spain.,Department of Medicine, Universidad Complutense de Madrid, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades respiratorias, CIBERES, Spain
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
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Venske Bierhals D, Busatto C, Silveira MDPDR, da Matta Talaier E, Silva ABS, Reis AJ, von Groll A, da Silva PEA, Ramis IB. Tuberculosis cases in a prison in the extreme south of Brazil. J Med Microbiol 2021; 70. [PMID: 33555247 DOI: 10.1099/jmm.0.001319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) control is a challenge, especially in vulnerable populations, such as prisoners.Hypothesis. In prison houses, the transmission of micro-organisms that cause infectious diseases can occur due to the susceptibility and immune compromise of prisoners, and due to the precarious physical conditions of the prison houses. However, strategies such as monitoring by health professionals, can mitigate the transmission of these micro-organisms, as well as, reduce the number of coinfections and antimicrobials resistance.Aim. This study attempted to analyse the dynamics of transmission and the antimicrobial resistance profile of Mycobacterium tuberculosis strains obtained from prisoners and to characterize the epidemiological, clinical and laboratory profiles of prisoners diagnosed with TB.Methodology. A cross-sectional and retrospective study was conducted with sputum samples collected from 228 distinct prisoners who were treated at the Health Unit located in the Regional Penitentiary of Rio Grande, Rio Grande do Sul, Brazil. The antimicrobial resistance profile of the strains was evaluated using the Resazurin Microtiter Assay and the transmission dynamics was investigated using 15-loci MIRU-VNTR.Results. Thirty-five patients (15.4 %) were diagnosed with TB, and when a TB/HIV coinfection was assessed, 8.6 % (3/35) of the patients were positive. In addition, all patients with results available for HBV, HCV, syphilis and diabetes mellitus were negative. Based on the genotypic profile, 55.9 % of the clinical isolates were grouped into five groups. One isolate with mono-resistance to isoniazid and two with mono-resistance to streptomycin were found.Conclusion. The presence of a Health Unit may have influenced the low numbers of TB/HIV, TB/HBV, TB/HCV, TB/syphilis coinfections and TB cases resistant to antimicrobials. Recent M. tuberculosis transmission can be inferred based on the high percentage of formatting of clusters. This situation stresses the need to improve active and passive detection, the screening of individuals for TB upon entrance into prison for early detection, and the implementation of prophylactic measures to reduce M. tuberculosis transmission.
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Affiliation(s)
- Dienefer Venske Bierhals
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Caroline Busatto
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | | | - Edilon da Matta Talaier
- Rio Grande City Hall, Basic Prison Health Unit - SMS/PERG, Rio Grande, Rio Grande do Sul, Brazil
| | - Ana Bárbara Scholante Silva
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Ana Julia Reis
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Andrea von Groll
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Pedro Eduardo Almeida da Silva
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Ivy Bastos Ramis
- Medical Microbiology Research Center, Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
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30
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Tian S, Yang D, Long Q, Ling M. Proteomic Analysis of Differentially Expressed Proteins in Mycobacterium Tuberculosis-Infected Macrophages. CURR PROTEOMICS 2021. [DOI: 10.2174/1570164617666191218112128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
Mycobacterium tuberculosis (MTB) and Mycobacterium avium (MA) are intracellular
parasitic bacteria. The biological characteristics of MA and MTB are very similar and need
to be identified.
Objective:
The study aims to better understand how MTB survives in macrophages and the different
pathogenic mechanisms of MTB and MA.
Methods:
The Tandem Mass Tag (TMT) and liquid chromatography-tandem mass spectrometry (LCMS/
MS) were used for analysis of the differentially expressed proteins in MTB-infected macrophages
and MA-infected macrophages.
Results:
A total of 682 proteins were found to be differentially expressed in MTB-infected cells in
comparison with MA-infected cells. Among these, 10 proteins (O60812, P06576, O43660-2, E9PL10,
O00442, M0R050, Q9H8H0, Q9BSJ8, P41240 and Q8TD57-3) were down-regulated in MTB-infected
cells, and M0R050, O00442, Q9H8H0, O60812 and O43660 are interactive proteins which participate
in a multitude of cellular RNA processing.
Conclusion:
The five down-regulated proteins (M0R050, O00442, Q9H8H0, O60812 and O43660)
might repress the synthesis of some resistant proteins in MTB-infected cells to promote MTB survival
in macrophages.
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Affiliation(s)
- Shuang Tian
- Department of Biotechnology, Key Laboratory of Biological Molecular Medicine, Research of Guangxi University, School of Basic Medicine Sciences, Guangxi Medical University, Nanning, China
| | - Dongjun Yang
- Department of Biotechnology, Key Laboratory of Biological Molecular Medicine, Research of Guangxi University, School of Basic Medicine Sciences, Guangxi Medical University, Nanning, China
| | - Qian Long
- Department of Biotechnology, Key Laboratory of Biological Molecular Medicine, Research of Guangxi University, School of Basic Medicine Sciences, Guangxi Medical University, Nanning, China
| | - Min Ling
- Department of Biotechnology, Key Laboratory of Biological Molecular Medicine, Research of Guangxi University, School of Basic Medicine Sciences, Guangxi Medical University, Nanning, China
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31
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Marín AV, Rastogi N, Couvin D, Mape V, Murcia MI. First approach to the population structure of Mycobacterium tuberculosis complex in the indigenous population in Puerto Nariño-Amazonas, Colombia. PLoS One 2021; 16:e0245084. [PMID: 33411781 PMCID: PMC7790298 DOI: 10.1371/journal.pone.0245084] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/21/2020] [Indexed: 11/18/2022] Open
Abstract
Introduction Tuberculosis affects vulnerable groups to a greater degree, indigenous population among them. Objective To determine molecular epidemiology of clinical isolates of Mycobacterium tuberculosis circulating in an indigenous population through Spoligotyping and 24-loci MIRU-VNTR. Methodology A descriptive cross-sectional study was conducted in 23 indigenous communities of Puerto Nariño-Amazonas, Colombia. Recovered clinical isolates were genotyped. For genotyping analyzes global SITVIT2 database and the MIRU-VNTRplus web portal were used. Results 74 clinical isolates were recovered. Genotyping of clinical isolates by spoligotyping determined 5 different genotypes, all of them belonged to Euro-American lineage. By MIRU-VNTR typing, a total of 14 different genotypes were recorded. Furthermore, polyclonal infection was found in two patients from the same community. The combination of the two methodologies determined the presence of 19 genotypes, 8 formed clusters with 63 clinical isolates in total. Based on epidemiological information, it was possible to establish a potential chain of active transmission in 10/63 (15.9%) patients. Conclusions High genomic homogeneity was determined in the indigenous population suggesting possible chains of active transmission. The results obtained showed that specific genotypes circulating among the indigenous population of Colombia are significantly different from those found in the general population.
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Affiliation(s)
- Alejandro Vega Marín
- MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Viviana Mape
- MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Martha Isabel Murcia
- MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
- * E-mail:
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Peixoto ADS, Montenegro LML, Lima AS, Melo FL, Barbosa Júnior WL, Neves MMC, Ramos JP, Schindler HC, Medeiros ZM. Identification of nontuberculous mycobacteria species by multiplex real-time PCR with high-resolution melting. Rev Soc Bras Med Trop 2020; 53:e20200211. [PMID: 33174954 PMCID: PMC7670742 DOI: 10.1590/0037-8682-0211-2020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 09/02/2020] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION: Nontuberculous mycobacteria (NTM) species, as human pathogens,
are increasing in the world, as is the difficulty of accurately identifying
them. Differential diagnosis, especially between the M.
tuberculosis complex and NTM species, and the characterization
of NTM species is important. This study aimed to evaluate the performance of
a molecular system based on multiplex real-time PCR with high-resolution
melting (HRM) for the identification and differentiation of NTM species of
clinical importance of an endemic area for tuberculosis in northeastern
Brazil. METHODS: The technical protocol of the molecular system was based on multiplex
real-time PCR-HRM, and evaluated the sensitivity and specificity of the
detection of NTM species in mycobacterial clinical isolates from the studied
region. The gold standard method was specific gene sequencing. RESULTS: The sensitivity and specificity of multiplex real-time PCR-HRM modified for
differentiation between NTM and M. tuberculosis were 90%
and 100%, respectively. The PCR-HRM sensitivities for the characterization
of NTM species (M. kansasii, M. abscesses, M. avium, and M.
fortuitum) were 94.59%, 80%, 57.14%, and 54%, respectively.
CONCLUSIONS The multiplex real-time PCR-HRM modified assay has the potential to rapidly
and efficiently identify nontuberculous mycobacteria of clinical importance,
which is crucial for immediate implementation of the appropriate therapy and
thus avoiding complications and sequelae in patients.
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Affiliation(s)
- Aline Dos Santos Peixoto
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Recife, PE, Brasil.,Universidade de Pernambuco, Pós-Graduação em Ciências da Saúde, Recife, PE, Brasil
| | | | - Andrea Santos Lima
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Imunologia, Recife, PE, Brasil
| | - Fábio Lopes Melo
- Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Parasitologia, Recife, PE, Brasil
| | | | | | - Jesus Pais Ramos
- Centro de Referência Professor Hélio Fraga, Escola Nacional de Saúde Pública, Laboratório Nacional de Referência para Tuberculose, Rio de Janeiro, RJ, Brasil
| | | | - Zulma Maria Medeiros
- Universidade de Pernambuco, Pós-Graduação em Ciências da Saúde, Recife, PE, Brasil.,Fundação Oswaldo Cruz, Instituto Aggeu Magalhães, Departamento de Parasitologia, Recife, PE, Brasil
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Rodríguez-Castillo JG, Llerena C, Argoty-Chamorro L, Guerra J, Couvin D, Rastogi N, Murcia MI. Population structure of multidrug-resistant Mycobacterium tuberculosis clinical isolates in Colombia. Tuberculosis (Edinb) 2020; 125:102011. [PMID: 33137696 DOI: 10.1016/j.tube.2020.102011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 10/09/2020] [Accepted: 10/16/2020] [Indexed: 11/19/2022]
Abstract
Emergence of multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) isolates is a major public health problem that threatens progress made in tuberculosis (TB) care and control worldwide. In Colombia, the prevalence of MDR tuberculosis (MDR-TB) has increased slowly but steadily since 2001. However, the population structure of the MDR-TB strains circulating in Colombia is sparsely known. In this work, 203 MDR isolates isolated in 2012-2013 were collected, and characterized by spoligotyping, followed by 24-loci MIRU-VNTR (data available for 190 isolates). The most prevalent genotypes corresponded to SIT42/LAM9 (12.81%), SIT62/H1 (10.34%), and SIT190/Beijing (10.34%). A fine analysis showed that although the MDR strains came from 29 of the 33 departments of Colombia, the distribution of these main lineages was not at random and depended on the city of isolation (p-value <0.000001). Both LAM and Beijing lineage strains were significantly associated with MDR-TB (p-value <0.0001): LAM lineage was associated with 2 patterns of MDR, namely combined resistance to INH + Rifampin (HR), and to SHRE (Streptomycin + INH + Rifampin + Ethambutol), while the Beijing lineage strains were essentially associated with MDR (SHRE). Interestingly, distribution of genotypic lineages in function of drug resistance information (e.g. pansusceptible vs. MDR) was different in our setting as compared to other countries in Latin America. However, MIRU-VNTR patterns were unique for all strains, an observation that did not support active transmission of circulating MDR clones.
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Affiliation(s)
- Juan Germán Rodríguez-Castillo
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Carrera 30 45 - 03, Facultad de Medicina, Edifcio 471, Bogotá, D.C, Colombia
| | - Claudia Llerena
- Grupo de Micobacterias, Red Nacional de Laboratorios, Instituto Nacional de Salud, Avenida calle 26 No. 51-20 - Zona 6 CAN, Bogotá, D.C, Colombia
| | - Lorena Argoty-Chamorro
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Carrera 30 45 - 03, Facultad de Medicina, Edifcio 471, Bogotá, D.C, Colombia
| | - Julio Guerra
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Carrera 30 45 - 03, Facultad de Medicina, Edifcio 471, Bogotá, D.C, Colombia
| | - David Couvin
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Morne Jolivière, BP484, F97183 Abymes Cedex, Abymes, Guadeloupe, France
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Morne Jolivière, BP484, F97183 Abymes Cedex, Abymes, Guadeloupe, France.
| | - Martha Isabel Murcia
- Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Carrera 30 45 - 03, Facultad de Medicina, Edifcio 471, Bogotá, D.C, Colombia.
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Molecular epidemiology of clinical Mycobacterium tuberculosis complex isolates in South Omo, Southern Ethiopia. BMC Infect Dis 2020; 20:750. [PMID: 33050903 PMCID: PMC7557052 DOI: 10.1186/s12879-020-05394-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 09/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is caused by Mycobacterium tuberculosis complex (MTBC). Mapping the genetic diversity of MTBC in high TB burden country like Ethiopia is important to understand principles of the disease transmission and to strengthen the regional TB control program. The aim of this study was to investigate the genetic diversity of Mycobacterium tuberculosis complex (MTBC) isolates circulating in the South Omo, southern Ethiopia. METHODS MTBC isolates (N = 156) were genetically analyzed using spacer oligotyping (spoligotyping) and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing. Major lineages and lineages were identified using MTBC databases. Logistic regression was used to correlate patient characteristics with strain clustering. RESULTS The study identified Euro-American (EA), East-African-Indian (EAI), Indo-Oceanic (IO), Lineage_7/Aethiops vertus, Mycobacterium bovis and Mycobacterium africanum major lineages in proportions of 67.3% (105/156), 22.4% (35/156), 6.4% (10/156), 1.9% (3/156), 1.3% (2/156) and 0.6% (1/156), respectively. Lineages identified were Delhi/CAS 23.9% (37/155), Ethiopia_2 20.6% (32/155), Haarlem 14.2% (22/155), URAL 14.2%(22/155), Ethiopia_3 8.4% (13/155), TUR 6.5% (10/155), Lineage_7/Aethiops vertus 1.9% (3/155), Bovis 1.3% (2/155), LAM 1.3% (2/155), EAI 0.6% (1/155), X 0.6% (1/155) and Ethiopia H37Rv-like strain 0.6% (1/155). Of the genotyped isolates 5.8% (9/155) remained unassigned. The recent transmission index (RTI) was 3.9%. Orphan strains compared to shared types (AOR: 0.09, 95% CI: 0.04-0.25) were associated with reduced odds of clustering. The dominant TB lineage in pastoral areas was EAI and in non-pastoral areas was EA. CONCLUSION The epidemiological data, highly diverse MTBC strains and a low RTI in South Omo, provide information contributing to the TB Control Program of the country.
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dos Anjos LRB, Parreira PL, Torres PPTS, Kipnis A, Junqueira-Kipnis AP, Rabahi MF. Non-tuberculous mycobacterial lung disease: a brief review focusing on radiological findings. Rev Soc Bras Med Trop 2020; 53:e20200241. [PMID: 32935786 PMCID: PMC7491562 DOI: 10.1590/0037-8682-0241-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 06/29/2020] [Indexed: 12/12/2022] Open
Abstract
The incidence and prevalence of lung disease caused by non-tuberculous mycobacteria (NTM-LD) has increased worldwide and its diagnosis represents a complex challenge. This article aims to review the tomographic findings of NTM-LD in order to facilitate their definitive diagnosis. The search for publications on the subject was performed in PMC and Scielo using the keywords 'non-tuberculous mycobacteria', 'lung disease and computed tomography (CT)' and 'radiological findings'. The radiological findings described by 18 articles on mycobacteriosis were reviewed. In addition, CT images of patients diagnosed with NTM-LD were considered to represent radiological findings. Eighteen publications were used whose main findings were pulmonary cavitation (88.9%), bronchiectasis (77.8%), and pulmonary nodules (55.6%). Despite the overlaps in imaging-related analysis of myocobacterioses with other pulmonary infections, such as tuberculosis, the predominant involvement of the middle lobe and lingula should raise suspicion for NTM-LD.
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Affiliation(s)
- Laura Raniere Borges dos Anjos
- Universidade Federal de Goiás, Instituto de Patologia Tropical e Saúde Pública, Departamento de Biociências e Tecnologia, Goiânia, GO, Brasil
| | - Poliana Lopes Parreira
- Universidade Federal de Goiás, Faculdade de Medicina, Departamento de Clínica Médica, Goiânia, GO, Brasil
| | | | - André Kipnis
- Universidade Federal de Goiás, Instituto de Patologia Tropical e Saúde Pública, Departamento de Biociências e Tecnologia, Goiânia, GO, Brasil
| | - Ana Paula Junqueira-Kipnis
- Universidade Federal de Goiás, Instituto de Patologia Tropical e Saúde Pública, Departamento de Biociências e Tecnologia, Goiânia, GO, Brasil
| | - Marcelo Fouad Rabahi
- Universidade Federal de Goiás, Faculdade de Medicina, Departamento de Clínica Médica, Goiânia, GO, Brasil
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Diagnostic tools for bacterial infections in travellers: Current and future options. Travel Med Infect Dis 2020; 37:101856. [PMID: 32841728 DOI: 10.1016/j.tmaid.2020.101856] [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: 04/03/2019] [Revised: 04/30/2020] [Accepted: 08/19/2020] [Indexed: 11/22/2022]
Abstract
International travel has increased dramatically over the past 50 years, and travel destinations have diversified. Although physicians are more familiar with the panel of aetiological agents responsible for illnesses of returning travellers, thanks to regular epidemiological studies, the spectrum of pathogens potentially encountered in various travel destinations is nevertheless increasing. In addition, the wide array of approaches currently available and addressed in this paper could render the procedures for microbiological analyses increasingly complex. As the time to result is crucial to adequately manage patients, modern approaches have been developed to shorten diagnosis delays. The syndromic approach, which consists of simultaneously testing a wide panel of microorganisms, substantially increases the diagnostic yield with significant time savings, particularly when coupled with point-of-care laboratories. The tools commonly used for this purpose are immunochromatographic tests, mainly targeting bacterial antigens, and multiplex real-time PCR. The emergence of next-generation sequencing technologies, which enable random amplification of genetic material of any microbe present in a clinical specimen, provides further exciting perspectives in the diagnosis of infectious diseases.
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Rodríguez-Sánchez B, Cercenado E, Coste AT, Greub G. Review of the impact of MALDI-TOF MS in public health and hospital hygiene, 2018. ACTA ACUST UNITED AC 2020; 24. [PMID: 30696525 PMCID: PMC6351997 DOI: 10.2807/1560-7917.es.2019.24.4.1800193] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Introduction MALDI-TOF MS represents a new technological era for microbiology laboratories. Improved sample processing and expanded databases have facilitated rapid and direct identification of microorganisms from some clinical samples. Automated analysis of protein spectra from different microbial populations is emerging as a potential tool for epidemiological studies and is expected to impact public health. Aim To demonstrate how implementation of MALDI-TOF MS has changed the way microorganisms are identified, how its applications keep increasing and its impact on public health and hospital hygiene. Methods A review of the available literature in PubMED, published between 2009 and 2018, was carried out. Results Of 9,709 articles retrieved, 108 were included in the review. They show that rapid identification of a growing number of microorganisms using MALDI-TOF MS has allowed for optimisation of patient management through prompt initiation of directed antimicrobial treatment. The diagnosis of Gram-negative bacteraemia directly from blood culture pellets has positively impacted antibiotic streamlining, length of hospital stay and costs per patient. The flexibility of MALDI-TOF MS has encouraged new forms of use, such as detecting antibiotic resistance mechanisms (e.g. carbapenemases), which provides valuable information in a reduced turnaround time. MALDI-TOF MS has also been successfully applied to bacterial typing. Conclusions MALDI-TOF MS is a powerful method for protein analysis. The increase in speed of pathogen detection enables improvement of antimicrobial therapy, infection prevention and control measures leading to positive impact on public health. For antibiotic susceptibility testing and bacterial typing, it represents a rapid alternative to time-consuming conventional techniques.
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Affiliation(s)
- Belén Rodríguez-Sánchez
- These authors contributed equally to this work.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Emilia Cercenado
- Department of Medicine, Faculty of Medicine, Universidad Complutense de Madrid, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Department of Clinical Microbiology and Infectious Diseases, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Alix T Coste
- Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Infectious Diseases Service, University Hospital of Lausanne, Lausanne, Switzerland.,Institute of Microbiology, University Hospital of Lausanne, Lausanne, Switzerland.,These authors contributed equally to this work
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Mansoori N, Vaziri F, Amini S, Khanipour S, Pourazar Dizaji S, Douraghi M. Spoligotype and Drug Susceptibility Profiles of Mycobacterium tuberculosis Complex Isolates in Golestan Province, North Iran. Infect Drug Resist 2020; 13:2073-2081. [PMID: 32669860 PMCID: PMC7335844 DOI: 10.2147/idr.s255889] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 06/18/2020] [Indexed: 11/23/2022] Open
Abstract
Introduction Despite the moderate incidence of tuberculosis (TB) in many parts of Iran, Golestan province had a permanently higher TB incidence rate than the national average. Moreover, Golestan province receives immigrants, mainly from TB-endemic areas of Iran and neighbor countries. Here, we aimed to characterize the circulating Mycobacterium tuberculosis complex (MTBC) isolates in terms of the spoligotype and drug resistance patterns, across Golestan province. Materials and Methods A set of 166 MTBC isolates was collected during July 2014 to July 2015 and subjected to drug susceptibility testing for first- and second-line anti-TB drugs and spoligotyping. Results Of 166 MTBC isolates, 139 (83.7%) isolates were assigned to 28 spoligotype international types (SITs). The most frequent SITs were SIT127/Ural-2 (n=25, 15.1%), followed by SIT1/Beijing (n=21, 12.7%) and SIT3427/Ural-2 (n=18, 10.8%). The set of 18 isolates (10.8%) showed resistance to at least one drug, which mainly belonged to SIT1/Beijing (n=7, 38.9%), orphan patterns (n=4, 22.2%) and SIT357/CAS1-Delhi (n=3, 16.7%). In addition, four isolates (2.4%) were resistant to pyrazinamide. The analysis of mutation corresponded to resistance to rifampin and isoniazid showed that two isolates had Ser531Leu substitution in rpoB, four isolates had Ser315Thr substitution in katG and one isolate had [C(−15)T] in inhA locus. Conclusion High diversity in spoligotypes of the MTBC isolates and lack of dominant genotype might be due to residence of immigrants in this region and consequent reactivation of latent infection. In addition, due to the presence of extensively drug-resistant (XDR) isolates in Golestan province, it is important to conduct future studies to determine transmission pattern of drug-resistant isolates in this region.
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Affiliation(s)
- Noormohamad Mansoori
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Sirus Amini
- Regional Tuberculosis Reference Laboratory, Tehran University of Medical Sciences, Tehran, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Shahin Pourazar Dizaji
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Masoumeh Douraghi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran.,Food Microbiology Research Center, Tehran University of Medical Sciences, Tehran, Iran
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CapitalBio Mycobacterium real-time polymerase chain reaction detection test: Rapid diagnosis of Mycobacterium tuberculosis and nontuberculous mycobacterial infection. Int J Infect Dis 2020; 98:1-5. [PMID: 32553719 DOI: 10.1016/j.ijid.2020.06.042] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 06/10/2020] [Accepted: 06/11/2020] [Indexed: 12/18/2022] Open
Abstract
OBJECTIVES To evaluate the accuracy of the CapitalBio Mycobacterium real-time polymerase chain reaction (RT-PCR) detection test for pulmonary Mycobacterium tuberculosis (MTB) and nontuberculous mycobacterial (NTM) infection. METHODS This study analyzed 2,460 samples from patients with suspected pulmonary mycobacterial infection collected between 01 June 2018 and 31 July 2019. It aimed to determine the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) of the CapitalBio Mycobacterium detection test for MTB and NTM infections, and to evaluate its diagnostic accuracy compared with mycobacterial culture. RESULTS The sensitivity, specificity, PPV, NPV, and AUC of the CapitalBio Mycobacterium detection test for MTB was 83.0%, 79.9%, 80.8%, 82.2%, and 0.81, respectively. This was similar to the diagnostic accuracy of Xpert MTB/RIF for MTB and was significantly higher than that of smear. For pulmonary NTM infection, the sensitivity, specificity, PPV, NPV, and AUC of the test was 82.0%, 99.6%, 94.1%, 98.5%, and 0.91, respectively. The diagnostic accuracy of the CapitalBio Mycobacterium detection test was also significantly higher than that of smear for NTM. CONCLUSIONS The CapitalBio Mycobacterium detection test had good diagnostic accuracy for MTB and NTM infections. This is of great significance for the differential diagnosis of early pulmonary mycobacterial infection.
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40
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Ansarin K, Sahebi L, Aftabi Y, Khalili M, Seyyedi M. Comparing IS6110-RFLP, PGRS-RFLP and IS6110-Mtb1/Mtb2 PCR methods for genotyping of Mycobacterium tuberculosis isolates. J Appl Microbiol 2020; 129:1062-1070. [PMID: 32330345 DOI: 10.1111/jam.14676] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 03/31/2020] [Accepted: 04/21/2020] [Indexed: 11/29/2022]
Abstract
AIMS Tuberculosis (TB) is still an important disease in the world, especially in developing countries. Applying efficient and suitable methods for genotyping Mycobacterium tuberculosis (MTB) isolates is a crucial step for identifying the MTB transmission mode and controlling its subsequent outcomes. Considering the complexity of IS6110-RFLP and PGRS-RFLP methods for MTB classification, suggesting other simple but reliable techniques could be helpful in the MTB studies, especially in low-income countries. METHODS AND RESULTS This study aimed to evaluate the capabilities of three methods for genotyping MTB isolates collected from Iran through comparing our previously published results for IS6110-RFLP and PGRS-RFLP methods and current results obtained from IS6110-Mtb1/Mtb2 PCR technique. A strong concordance was observed between the results of clustering by three techniques. Calculated Kendall's Tau concordance value for correlation of IS6110-RFLP and IS6110-Mtb1/Mtb2 PCR, for IS6110-RFLP and PGRS-RFLP, and for IS6110-Mtb1/Mtb2 PCR and PGRS-RFLP techniques was equal to 0·943, 0·898 and 0·85 respectively. CONCLUSIONS A strong correlation between IS6110-Mtb1/Mtb2 PCR, and IS6110-RFLP and PGRS-RFLP methods was observed and therefore IS6110-Mtb1/Mtb2 PCR discriminates MTBs capably. SIGNIFICANCE AND IMPACT OF THE STUDY The study showed that IS6110-Mtb1/Mtb2 PCR, which is a simple and economical MTB genotyping approach, could be a more appropriate method to be applied in the low-budget research programmes.
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Affiliation(s)
- Kh Ansarin
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - L Sahebi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Y Aftabi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - M Khalili
- Rahat Breathing and Sleep Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - M Seyyedi
- Tuberculosis and Lung Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Blanco-Conde S, González-Cortés C, López-Medrano R, Palacios-Gutiérrez JJ, Diez-Tascón C, Nebreda-Mayoral T, Sierra-García MJ, Rivero-Lezcano OM. A strategy based on Amplified Fragment Length Polymorphism (AFLP) for routine genotyping of nontuberculous mycobacteria at the clinical laboratory. Mol Biol Rep 2020; 47:3397-3405. [PMID: 32297290 DOI: 10.1007/s11033-020-05420-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 04/03/2020] [Indexed: 11/25/2022]
Abstract
The increasing worldwide incidence of mycobacteriosis and the need to achieve improved clinical management makes nontuberculous mycobacteria (NTM) genotyping a useful tool. However, because of technical difficulties, medium size microbiology laboratories do not attempt to compare the genetic patterns that each of their isolates present. We have aimed to optimize a genotyping method with a reduced hands-on experimental time and that requires few technical resources. A strategy based on the Amplified Fragment Length Polymorphism (AFLP) methodology was developed using two rare-cutters enzymes (SacI and BglII). One out of seven primers was sequentially used in each amplification reaction that was analyzed by agarose gel electrophoresis. This approach makes it possible the timely genotyping of a moderate number of strains and its characterization without the need of image analysis software. We have genotyped 28 Mycobacterium intracellulare and 4 M. abscessus. Clinical researchers are encouraged to routinely genotype their NTM isolates.
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Affiliation(s)
- Sara Blanco-Conde
- Servicio de Análisis Clínicos, Hospital de Palamós, Edificio Fleming, Carrer Hospital 36, 17230, Girona, Spain
| | | | - Ramiro López-Medrano
- Servicio de Microbiología Clínica, Hospital Universitario de León, Altos de Nava, s/n, 24080, León, Spain
| | - Juan José Palacios-Gutiérrez
- Unidad de Referencia Regional de Micobacterias, Servicio de Microbiología, Hospital Universitario Central de Asturias, Avda. Roma s/n, 33011, Oviedo, Asturias, Spain
| | - Cristina Diez-Tascón
- Servicio de Anatomía Patológica, Hospital Universitario de León, Altos de Nava, s/n, 24080, León, Spain
| | - Teresa Nebreda-Mayoral
- Servicio de Microbiología, Hospital Clínico Universitario de Valladolid, C/ Ramon y Cajal 3, 47005, Valladolid, Spain
| | | | - Octavio Miguel Rivero-Lezcano
- Unidad de Investigación, Hospital Universitario de León, Altos de Nava, s/n, 24080, León, Spain.
- Institute of Biomedical Research of Salamanca (IBSAL), Salamanca, Spain.
- Institute of Biomedicine, University of León, León, Spain.
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Brumfield KD, Hasan NA, Leddy MB, Cotruvo JA, Rashed SM, Colwell RR, Huq A. A comparative analysis of drinking water employing metagenomics. PLoS One 2020; 15:e0231210. [PMID: 32271799 PMCID: PMC7145143 DOI: 10.1371/journal.pone.0231210] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 03/18/2020] [Indexed: 12/13/2022] Open
Abstract
The microbiological content of drinking water traditionally is determined by employing culture-dependent methods that are unable to detect all microorganisms, especially those that are not culturable. High-throughput sequencing now makes it possible to determine the microbiome of drinking water. Thus, the natural microbiota of water and water distribution systems can now be determined more accurately and analyzed in significantly greater detail, providing comprehensive understanding of the microbial community of drinking water applicable to public health. In this study, shotgun metagenomic analysis was performed to determine the microbiological content of drinking water and to provide a preliminary assessment of tap, drinking fountain, sparkling natural mineral, and non-mineral bottled water. Predominant bacterial species detected were members of the phyla Actinobacteria and Proteobacteria, notably the genera Alishewanella, Salmonella, and Propionibacterium in non-carbonated non-mineral bottled water, Methyloversatilis and Methylibium in sparkling natural mineral water, and Mycobacterium and Afipia in tap and drinking fountain water. Fecal indicator bacteria, i.e., Escherichia coli or enterococci, were not detected in any samples examined in this study. Bacteriophages and DNA encoding a few virulence-associated factors were detected but determined to be present only at low abundance. Antibiotic resistance markers were detected only at abundance values below our threshold of confidence. DNA of opportunistic plant and animal pathogens was identified in some samples and these included bacteria (Mycobacterium spp.), protozoa (Acanthamoeba mauritaniensis and Acanthamoeba palestinensis), and fungi (Melampsora pinitorqua and Chryosporium queenslandicum). Archaeal DNA (Candidatus Nitrosoarchaeum) was detected only in sparkling natural mineral water. This preliminary study reports the complete microbiome (bacteria, viruses, fungi, and protists) of selected types of drinking water employing whole-genome high-throughput sequencing and bioinformatics. Investigation into activity and function of the organisms detected is in progress.
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Affiliation(s)
- Kyle D. Brumfield
- Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States of America
| | - Nur A. Hasan
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States of America
- CosmosID Inc., Rockville, MD, United States of America
| | - Menu B. Leddy
- Essential Environmental and Engineering Systems, Huntington Beach, CA, United States of America
| | - Joseph A. Cotruvo
- Joseph Cotruvo and Associates LLC, Washington, DC, United States of America
| | - Shah M. Rashed
- Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America
- CosmosID Inc., Rockville, MD, United States of America
| | - Rita R. Colwell
- Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America
- University of Maryland Institute for Advanced Computer Studies, University of Maryland, College Park, MD, United States of America
- CosmosID Inc., Rockville, MD, United States of America
| | - Anwar Huq
- Maryland Pathogen Research Institute, University of Maryland, MD, College Park, United States of America
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Hajiaheman Y, Yang Y, Shayilanbieke N, Jin G. Mycobacterium culturing and drug resistance of osteoarticular tuberculosis in Xinjiang, China. Medicine (Baltimore) 2020; 99:e19697. [PMID: 32311949 PMCID: PMC7220655 DOI: 10.1097/md.0000000000019697] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
This study aims to elucidate the strains and drug resistance of mycobacterium isolated from osteoarticular tuberculosis (OATB) patients and provide a reference for the diagnosis and treatment of OATB.Sixty-nine clinically diagnosed and surgically treated OATB patients were collected in time period of January 2017 to December 2018 at the First Affiliated Hospital of Xinjiang Medical University. The BACTEC MGIT 960 system was used for mycobacteria culturing, strain identification, and drug susceptibility testing, and the mycobacteria culture positive rate, species distribution, and drug resistance were analyzed.Within 4 weeks, 24 (34.78%) isolates of mycobacteria culture were positive; 40 (57.97%) isolates were positive, when culturing time was expanded to 8 weeks, and the difference was statistically significant (P < .05). Among the 40 isolates, 24 (60%) were identified as mycobacterium tuberculosis (MTB), 10 (25%) were Mycobacterium bovis, and 6 (15%) were non-tuberculous mycobacteria (NTM). Among total 69 isolates, 40 were enrolled in drug sensitivity test, and 15 (37.5%) isolates were confirmed drug resistant strains, in which 5 isolates were MTB, 4 isolates were M. bovis, and 6 isolates of NTM.The pathogen of clinically diagnosed OATB was mainly MTB. However, M. bovis and NTM also accounted for a considerable proportion, and their drug resistance rate was higher. Extending the culturing time appropriately could improve the culture positive rate. NTM was a drug resistant strain, and mycobacteria culturing, strain identification, and drug resistance analysis should be carried out to serve as a guide for individual treatment.
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Elsafi SSMS, Nour BM, Abakar AD, Omer IH, Almugadam BS. Vitamin D level and it is association with the severity of pulmonary tuberculosis in patients attended to Kosti Teaching Hospital, Sudan. AIMS Microbiol 2020; 6:65-74. [PMID: 32226915 PMCID: PMC7099198 DOI: 10.3934/microbiol.2020004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/09/2020] [Indexed: 01/08/2023] Open
Abstract
Globally, tuberculosis is one of the major causes of morbidity and mortality in many countries. Previous studies suggest that the incidence and severity of tuberculosis are associated with low levels of vitamin D (Vit D). Therefore, this study aimed to determine the occurrence and associated factors of vitamin D3 deficiency in pulmonary tuberculosis patients at White Nile State, Sudan. 101 individuals of diagnosed pulmonary tuberculosis patients (71 males and 30 females) and 100 non-TB controls (58 males and 42 females) were included in this study. Sputum samples were obtained from TB patients and subjected to examination for acid-fast bacilli (AFB) using Ziehl-Neelsen (ZN) stain and Gene Xpert analysis. Blood samples were collected from both groups and Serum 25(OH)-vitamin D3 was determined by an Enzyme-Linked Immunosorbent Assay. HIV infection in Tuberculosis (TB) group was also investigated using the immunochromatographic test. In our study, the majority of TB patients were suffered from TB relapse (36.6%); non-HIV infected individuals (99.1%) or showed a positive result for AFB (61.4%) in Gene Xpert analysis. Moreover, there is a significant difference in microscopy findings and bacillary levels of AFB, and Rifampicin (RIF) susceptibility pattern of M. tuberculosis strain among sputum samples of TB patients, P-values less 0.0001. Furthermore, we found that TB patients were suffered from vitamin D deficiency. In particular, the mean of vitamin D level was significantly much lower in TB patients (26.7 ± 1.6) compared to non-TB controls (117.3 ± 3.2), P-value equal 0.0001. Likewise, it's much lower in females, individuals of 21-40 years old, and patients with high bacillary levels or those infected by Rifampicin resistance strain. Accordingly, our study was highlighted the TB and Vit D deficiency relationship and showed the need for further studies to a better understanding of the impact of TB on Vit D level and investigate whether vitamin D supplementation can have a role in the prevention and treatment of tuberculosis.
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Affiliation(s)
| | - Bakri Mohammed Nour
- Department of Medical Parasitology, Faculty of Medical Laboratory Sciences, University of Gezira, Wad Medani, Sudan
| | - Adam Dawoud Abakar
- Department of Medical Parasitology, Faculty of Medical Laboratory Sciences, University of Gezira, Wad Medani, Sudan.,Department of Parasitology, Blue Nile National Institute for Communicable Diseases, University of Gezira, Sudan
| | - Izzedeen Haroun Omer
- Department of Medicine, Faculty of Medicine, University of El Imam El Mahdi, Kosti, Sudan
| | - Babiker Saad Almugadam
- Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of El Imam El Mahdi, Kosti, Sudan
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PPE51 Is Involved in the Uptake of Disaccharides by Mycobacterium tuberculosis. Cells 2020; 9:cells9030603. [PMID: 32138343 PMCID: PMC7140425 DOI: 10.3390/cells9030603] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/20/2020] [Accepted: 02/28/2020] [Indexed: 01/09/2023] Open
Abstract
We have recently found that selected thio-disaccharides possess bactericidal effects against Mycobacterium tuberculosis but not against Escherichia coli or Staphylococcus aureus. Here, we selected spontaneous mutants displaying resistance against the investigated thio-glycoside. According to next-generation sequencing, four of six analyzed mutants which were resistant to high concentrations of the tested chemical carried nonsynonymous mutations in the gene encoding the PPE51 protein. The complementation of these mutants with an intact ppe51 gene returned their sensitivity to the wild-type level. The uptake of tritiated thio-glycoside was significantly more abundant in wild-type Mycobacterium tuberculosis compared to the strain carrying the mutated ppe51 gene. The ppe51 mutations or CRISPR-Cas9-mediated downregulation of PPE51 expression affected the growth of mutant strains on minimal media supplemented with disaccharides (maltose or lactose) but not with glycerol or glucose as the sole carbon and energy source. Taking the above into account, we postulate that PPE51 participates in the uptake of disaccharides by tubercle bacilli.
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46
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Luciano SA, Roess A. Human zoonotic tuberculosis and livestock exposure in low- and middle-income countries: A systematic review identifying challenges in laboratory diagnosis. Zoonoses Public Health 2020; 67:97-111. [PMID: 31919980 PMCID: PMC7027859 DOI: 10.1111/zph.12684] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 09/18/2019] [Accepted: 12/11/2019] [Indexed: 11/30/2022]
Abstract
BACKGROUND Zoonotic tuberculosis (zTB) accounts for 1.4% of the global tuberculosis burden, with the largest disease burden in low- and middle-income countries (LMICs). These populations have increased exposure to zTB due to livestock rearing practices and raw dairy consumption. This qualitative systematic literature review evaluates the quality of the literature that examines the association between human zTB in LMICs and frequent exposure to livestock and livestock products and summarizes current gaps in laboratory detection methods. METHODS The Navigation Guide, a systematic review framework utilized to assess environmental health exposures, was used to conduct this literature review. Peer-reviewed research articles were selected and evaluated for risk of bias and quality of evidence. Only studies conducted in LMICs that mentioned livestock or livestock product exposure and had a confirmed diagnosis were eligible. RESULTS Fifteen studies met the inclusion criteria. Reported prevalence of human zTB ranged from 0% to 28%, with cattle and raw dairy the primary exposures. All confirmed zTB cases were Mycobacterium bovis. Eight of the 15 studies included livestock sampling, predominantly cattle and reported prevalence of zTB between 0% and 23%. Laboratory methods used included nearly a dozen different culture methods and a variety of molecular methods, some of which are not appropriate for zTB. CONCLUSIONS This review revealed the need for appropriate and standardized laboratory diagnostic methods, and large prospective studies of at-risk populations to determine exposures that lead to an increased risk of tuberculosis conversion/infection to better understand the true burden of disease. Standardized, easy to implement laboratory diagnostics is an imperative focus for this scientific field to better identify the burden of zTB. Future studies pairing livestock and human subjects will allow better characterization of the high zTB transmission areas for targeted control and prevention programmes.
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Affiliation(s)
- Sarah Anne Luciano
- Department of Environmental and Occupational HealthThe George Washington UniversityWashingtonDistrict of Columbia
| | - Amira Roess
- Department of Global and Community HealthGeorge Mason UniversityFairfaxVirginia
- Department of Global HealthThe George Washington UniversityWashingtonDistrict of Columbia
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Xiao G, He X, Zhang S, Liu Y, Liang Z, Liu H, Zhang J, Ou M, Cai S, Lai W, Zhang T, Ren L, Zhang G. Cas12a/Guide RNA-Based Platform for Rapid and Accurate Identification of Major Mycobacterium Species. J Clin Microbiol 2020; 58:e01368-19. [PMID: 31723010 PMCID: PMC6989083 DOI: 10.1128/jcm.01368-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 11/04/2019] [Indexed: 12/26/2022] Open
Abstract
Mycobacterium tuberculosis infection and nontuberculous mycobacteria (NTM) infections exhibit similar clinical symptoms; however, the therapies for these two types of infections are different. Therefore, the rapid and accurate identification of M. tuberculosis and NTM species is very important for the control of tuberculosis and NTM infections. In the present study, a Cas12a/guide RNA (gRNA)-based platform was developed to identify M. tuberculosis and most NTM species. By designing species-specific gRNA probes targeting the rpoB sequence, a Cas12a/gRNA-based platform successfully identified M. tuberculosis and six major NTM species (Mycobacterium abscessus, Mycobacterium intracellulare, Mycobacterium avium, Mycobacterium kansasii, Mycobacterium gordonae, and Mycobacterium fortuitum) without cross-reactivity. In a blind assessment, a total of 72 out of 73 clinical Mycobacterium isolates were correctly identified, which is consistent with previous rpoB sequencing results. These results suggest that the Cas12a/gRNA-based platform is a promising tool for the rapid, accurate, and cost-effective identification of both M. tuberculosis and NTM species.
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Affiliation(s)
- Guohui Xiao
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Xing He
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Su Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Yaya Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Zhihang Liang
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan, China
| | - Houming Liu
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Juanjuan Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Min Ou
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Shuhao Cai
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Wenjie Lai
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health (GIBH), Chinese Academy of Sciences (CAS), Guangzhou, China
| | - Lili Ren
- Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Guangdong Key Laboratory of Emerging Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, China
- School of Basic Medical Sciences, Guangdong Medical University, Dongguan, China
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Education and training in microbial forensics. MICROBIAL FORENSICS 2020. [PMCID: PMC7153755 DOI: 10.1016/b978-0-12-815379-6.00032-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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49
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Skuce R, Breadon E, Allen A, Milne G, McCormick C, Hughes C, Rutherford D, Smith G, Thompson S, Graham J, Harwood R, Byrne A. Longitudinal dynamics of herd-level Mycobacterium bovis MLVA type surveillance in cattle in Northern Ireland 2003-2016. INFECTION GENETICS AND EVOLUTION 2019; 79:104131. [PMID: 31786341 DOI: 10.1016/j.meegid.2019.104131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/27/2019] [Indexed: 02/02/2023]
Abstract
Investigating genetically-structured diversity in pathogen populations over time is important to better understand disease maintenance and spread. Herd-level surveillance of Mycobacterium bovis genotypes (multi-locus VNTR analysis types, MLVA types) from all culture-confirmed bovine tuberculosis (TB) herd cases was undertaken in Northern Ireland (NI), generating an unparalleled, longitudinal, population-level 14-year survey for this pathogen. Across this population, 295 genetically-distinct M. bovis MLVA types were identified in the 19,717 M. bovis isolates surveyed. Of these, the most frequent was MLVA type 002 (23.0%); 151 MLVA types were represented more than once, in groups ranging from 2 to 4438 isolates. Only 23 MLVA types were isolated in all 14 years. Investigating inter-annual frequency of M. bovis MLVA types, examples of statistically-significant expansions (MLVA types 002, 004, 006, 009 and 027), contractions (MLVA types 001, 007 and 011) and maintenance (MLVA types 003 and 005) were disclosed, during a period of fluctuating bovine TB herd-level incidence at the NI scale. The fixed period frequency distribution of MLVA types remained highly right-skewed. Novel VNTR copy number variant MLVA types (N = 242; an average of 17 per annum) were identified throughout the survey. The MLVA type distribution in the landscape was not random; MLVA types showed statistically-significant geographical localization and strong spatial associations with Divisional Veterinary Office (DVO) regions. There was also evidence of differential risk of particular MLVA types across breeds (Holstein/Friesian vs. other), age-class, and sex and some evidence of an association between the number of animals testing positive for bovine TB during the disclosing test and particular MLVA types, although there was substantial variation.
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Affiliation(s)
- R Skuce
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK.
| | - E Breadon
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - A Allen
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - G Milne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - C McCormick
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - C Hughes
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - D Rutherford
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic (⁎)current address
| | - G Smith
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - S Thompson
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - J Graham
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - R Harwood
- Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - A Byrne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK; One-Health Unit, Surveillance, Animal By-Products and TSEs (SAT), Division Department of Agriculture, Food and Marine (DAFM), Agriculture House, Dublin 2, Ireland
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Reis AJ, Diniz JLCG, Silva ABS, Silveira J, Basso R, Vieira R, von Groll A, Ramis IB, da Silva PEA. Laboratory tools for tuberculosis control in a setting with a high burden of HIV/AIDS. J Med Microbiol 2019; 68:1622-1628. [PMID: 31596198 DOI: 10.1099/jmm.0.001089] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Nosocomial transmission of Mycobacterium tuberculosis is an important health issue and the detection of tuberculosis (TB) cases is the main tool for controlling this disease.Aim. We aimed to assess the possible occurrence of nosocomial transmission of M. tuberculosis in a reference hospital for HIV/AIDS patients and evaluate both the performance of the Xpert MTB/RIF (Xpert) platform and drug resistance profiles.Methodology. We evaluated the performance of the Xpert platform. Samples that tested positive on the BACTEC MGIT 320 (MGIT320) platform were submitted for genotyping and drug susceptibility testing.Results. In this study, pulmonary and extrapulmonary samples from 407 patients were evaluated, and among these, 15.5 % were diagnosed with TB by the MGIT320 platform, with a TB/HIV coinfection rate of 52.4 %. The Xpert platform gave positive results for TB for 11 samples with negative results on the MGIT320 platform. In the genotyping results, 53.3 % of the strains clustered; of these strains, half were in two of the four clusters formed, and the patients had visited the hospital on the same day. Drug resistance was observed in 11.7 % of the strains.Conclusion. Putative nosocomial transmission of M. tuberculosis was detected, showing that genotyping is a powerful approach for understanding the dynamics of M. tuberculosis transmission, especially in a high-burden TB and HIV landscape.
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Affiliation(s)
- Ana J Reis
- Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Jaciara L C G Diniz
- Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Ana B S Silva
- Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Jussara Silveira
- Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Rossana Basso
- Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Roseli Vieira
- Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Andrea von Groll
- Rede TB (TB Research Network in Brazil), Rio de Janeiro, RJ, Brazil.,Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Ivy B Ramis
- Rede TB (TB Research Network in Brazil), Rio de Janeiro, RJ, Brazil.,Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
| | - Pedro E A da Silva
- Rede TB (TB Research Network in Brazil), Rio de Janeiro, RJ, Brazil.,Faculty of Medicine, Federal University of Rio Grande (FURG), Rio Grande, Rio Grande do Sul, Brazil
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