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Shankaregowda R, Allegretti YH, Sumana MN, Rao MR, Raphael E, Mahesh PA, Riley LW. Whole-Genome Sequencing of Mycobacterium tuberculosis Isolates from Diabetic and Non-Diabetic Patients with Pulmonary Tuberculosis. Microorganisms 2023; 11:1881. [PMID: 37630441 PMCID: PMC10457832 DOI: 10.3390/microorganisms11081881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/08/2023] [Accepted: 07/14/2023] [Indexed: 08/27/2023] Open
Abstract
The association of tuberculosis and type 2 diabetes mellitus has been a recognized re-emerging challenge in management of the convergence of the two epidemics. Though much of the literature has studied this association, there is less knowledge in the field of genetic diversities that might occur in strains infecting tuberculosis patients with and without diabetes. Our study focused on determining the extent of diversity of genotypes of Mycobacterium tuberculosis in both these categories of patients. We subjected 55 M. tuberculosis isolates from patients diagnosed with pulmonary TB with and without type 2 diabetes mellitus to whole-genome sequencing on Illumina Hi Seq platform. The most common lineage identified was lineage 1, the Indo-Oceanic lineage (n = 22%), followed by lineage 4, the Euro-American lineage (n = 18, 33%); lineage 3, the East-African Indian lineage (n = 13, 24%); and lineage 2, the East-Asian lineage (n = 1, 2%). There were no significant differences in the distribution of lineages in both diabetics and non-diabetics in the South Indian population, and further studies involving computational analysis and comparative transcriptomics are needed to provide deeper insights.
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Affiliation(s)
- Ranjitha Shankaregowda
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA 94720, USA; (R.S.); (L.W.R.)
- Department of Microbiology, JSS Medical College and Hospital, JSS AHER, Mysore 570015, India; (M.N.S.); (M.R.R.)
| | - Yuan Hu Allegretti
- School of Public Health, Division of Epidemiology, University of California, Berkeley, CA 94720, USA;
| | | | - Morubagal Raghavendra Rao
- Department of Microbiology, JSS Medical College and Hospital, JSS AHER, Mysore 570015, India; (M.N.S.); (M.R.R.)
| | - Eva Raphael
- Division of Epidemiology and Biostatistics, School of Medicine, University of California, San Fransico, CA 94143, USA;
| | - Padukudru Anand Mahesh
- Department of Respiratory Medicine, JSS Medical College and Hospital, JSS AHER, Mysore 570015, India
| | - Lee W. Riley
- School of Public Health, Division of Infectious Diseases and Vaccinology, University of California, Berkeley, CA 94720, USA; (R.S.); (L.W.R.)
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Iruedo JO, Pather MK. Time-to-Treatment Initiation in a Decentralised Community-Care Model of Drug-Resistant Tuberculosis Management in the OR Tambo District Municipality of South Africa. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:6423. [PMID: 37510655 PMCID: PMC10379855 DOI: 10.3390/ijerph20146423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023]
Abstract
BACKGROUND Drug-resistant tuberculosis (DR-TB) continues to challenge global efforts toward eradicating and having a tuberculosis-free world. Considering the high early mortality, especially among HIV-infected individuals, early diagnosis and prompt initiation of effective treatment are needed to significantly reduce mortality and halt transmission of DR-TB in the community. AIM This study aims to assess the effectiveness of a community DR-TB care model with the specific objective of determining the Time-to-treatment initiation of DR-TB among patients in the OR Tambo district municipality. METHODS A prospective cohort study of patients with DR-TB was conducted in the OR Tambo district municipality of Eastern Cape Province, South Africa. Patients were enrolled as they presented for treatment initiation at the decentralised facilities following a diagnosis of DR-TB and compared with a centralised site. RESULTS A total of 454 DR-TB patients from six facilities between 2018 and 2020 were included in the analysis. The mean age was 37.54 (SD = 14.94) years. There were slightly more males (56.2%) than females (43.8%). Most of the patients were aged 18-44 years (67.5%), without income (82.3%). Results showed that slightly over thirteen percent (13.4%) of patients initiated treatment the same day they were diagnosed with DR-TB, while 36.3% were on the time-to-treatment target of being initiated within 5 days. However, about a quarter (25.8%) of patients failed to initiate treatment two weeks after diagnosis. Time-to-treatment initiation (TTTI) varied according to the decentralised sites, with progressive improvement with each successive year between 2018 and 2021. No demographic factor was significantly associated with TTTI. CONCLUSION Despite rapid diagnosis, only 36% of patients were initiated on treatment promptly. Operational challenges remained, and services needed to be reorganised to maximise the exceptional potentials that a decentralised community DR-TB care model brings.
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Affiliation(s)
- Joshua Oise Iruedo
- Division Family Medicine and Primary Care, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch 7602, South Africa
| | - Michael K Pather
- Division Family Medicine and Primary Care, Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch 7602, South Africa
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Shen X, Yin L, Zhang A, Zhao R, Yin D, Wang J, Dai Y, Hou H, Pan X, Hu X, Zhang D, Liu Y. Prevalence and Characterization of Salmonella Isolated from Chickens in Anhui, China. Pathogens 2023; 12:pathogens12030465. [PMID: 36986387 PMCID: PMC10054756 DOI: 10.3390/pathogens12030465] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Revised: 03/09/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
Salmonella is one of the most important zoonotic pathogens that can cause both acute and chronic illnesses in poultry flocks, and can also be transmitted to humans from infected poultry. The purpose of this study was to investigate the prevalence, antimicrobial resistance, and molecular characteristics of Salmonella isolated from diseased and clinically healthy chickens in Anhui, China. In total, 108 Salmonella isolates (5.66%) were successfully recovered from chicken samples (n = 1908), including pathological tissue (57/408, 13.97%) and cloacal swabs (51/1500, 3.40%), and S. Enteritidis (43.52%), S. Typhimurium (23.15%), and S. Pullorum (10.19%) were the three most prevalent isolates. Salmonella isolates showed high rates of resistance to penicillin (61.11%), tetracyclines (47.22% to tetracycline and 45.37% to doxycycline), and sulfonamides (48.89%), and all isolates were susceptible to imipenem and polymyxin B. In total, 43.52% isolates were multidrug-resistant and had complex antimicrobial resistance patterns. The majority of isolates harbored cat1 (77.78%), blaTEM (61.11%), and blaCMY-2 (63.89%) genes, and the antimicrobial resistance genes in the isolates were significantly positively correlated with their corresponding resistance phenotype. Salmonella isolates carry high rates of virulence genes, with some of these reaching 100% (invA, mgtC, and stn). Fifty-seven isolates (52.78%) were biofilm-producing. The 108 isolates were classified into 12 sequence types (STs), whereby ST11 (43.51%) was the most prevalent, followed by ST19 (20.37%) and ST92 (13.89%). In conclusion, Salmonella infection in chicken flocks is still serious in Anhui Province, and not only causes disease in chickens but might also pose a threat to public health security.
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Affiliation(s)
- Xuehuai Shen
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Lei Yin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Anyun Zhang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, College of Life Sciences, Sichuan University, Chengdu 610017, China
| | - Ruihong Zhao
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Dongdong Yin
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Jieru Wang
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Yin Dai
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Hongyan Hou
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Xiaocheng Pan
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
- Correspondence: (X.P.); (Y.L.)
| | - Xiaomiao Hu
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Danjun Zhang
- Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Science, Hefei 230001, China
| | - Yongjie Liu
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence: (X.P.); (Y.L.)
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Xiao YX, Liu KH, Lin WH, Chan TH, Jou R. Whole-genome sequencing-based analyses of drug-resistant Mycobacterium tuberculosis from Taiwan. Sci Rep 2023; 13:2540. [PMID: 36781938 PMCID: PMC9925824 DOI: 10.1038/s41598-023-29652-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 02/08/2023] [Indexed: 02/15/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) posed challenges to global TB control. Whole-genome sequencing (WGS) is recommended for predicting drug resistance to guide DR-TB treatment and management. Nevertheless, data are lacking in Taiwan. Phenotypic drug susceptibility testing (DST) of 12 anti-TB drugs was performed for 200 Mycobacterium tuberculosis isolates. WGS was performed using the Illumina platform. Drug resistance profiles and lineages were predicted in silico using the Total Genotyping Solution for TB (TGS-TB). Using the phenotypic DST results as a reference, WGS-based prediction demonstrated high concordance rates of isoniazid (95.0%), rifampicin (RIF) (98.0%), pyrazinamide (98.5%) and fluoroquinolones (FQs) (99.5%) and 96.0% to 99.5% for second-line injectable drugs (SLIDs); whereas, lower concordance rates of ethambutol (87.5%), streptomycin (88.0%) and ethionamide (84.0%). Furthermore, minimum inhibitory concentrations confirmed that RIF rpoB S450L, FQs gyrA D94G and SLIDs rrs a1401g conferred high resistance levels. Besides, we identified lineage-associated mutations in lineage 1 (rpoB H445Y and fabG1 c-15t) and predominant lineage 2 (rpoB S450L and rpsL K43R). The WGS-based prediction of drug resistance is highly concordant with phenotypic DST results and can provide comprehensive genetic information to guide DR-TB precision therapies in Taiwan.
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Affiliation(s)
- Yu-Xin Xiao
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Kuang-Hung Liu
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Wan-Hsuan Lin
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Tai-Hua Chan
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C
| | - Ruwen Jou
- Tuberculosis Research Center, Taiwan Centers for Disease Control, Ministry of Health and Welfare, No. 161, Kun-Yang Street, Taipei, 11561, Taiwan, R.O.C..
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan, R.O.C..
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Su F, Cao L, Ren X, Hu J, Tavengana G, Wu H, Zhou Y, Fu Y, Jiang M, Wen Y. The mutation rate of rpoB gene showed an upward trend with the increase of MIRU10, MIRU39 and QUB4156 repetitive number. BMC Genomics 2023; 24:26. [PMID: 36646991 PMCID: PMC9843906 DOI: 10.1186/s12864-023-09120-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) is a frequently used typing method for identifying the Beijing genotype of Mycobacterium tuberculosis (Mtb), which is easily transformed into rifampicin (RIF) resistance. The RIF resistance of Mtb is considered to be highly related with the mutation of rpoB gene. Therefore, this study aimed to analyze the relationship between the repetitive number of MIRU loci and the mutation of rpoB gene. METHODS An open-source whole-genome sequencing data of Mtb was used to detect the mutation of rpoB gene and the repetitive number of MIRU loci by bioinformatics methods. Cochran-Armitage analysis was performed to analyze the trend of the rpoB gene mutation rate and the repetitive number of MIRU loci. RESULTS Among 357 rifampicin-resistant tuberculosis (RR-TB), 304 strains with mutated rpoB genes were detected, and 6 of 67 rifampicin susceptible strains were detected mutations. The rpoB gene mutational rate showed an upward trend with the increase of MIRU10, MIRU39, QUB4156 and MIRU16 repetitive number, but only the repetitive number of MIRU10, MRIU39 and QUB4156 were risk factors for rpoB gene mutation. The Hunter-Gaston discriminatory index (HGDI) of MIRU10 (0.65) and QUB4156 (0.62) was high in the overall sample, while MIRU39 (0.39) and MIRU16 (0.43) showed a moderate discriminatory Power. CONCLUSION The mutation rate of rpoB gene increases with the addition of repetitive numbers of MIRU10, QUB4156 and MIRU39 loci.
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Affiliation(s)
- Fan Su
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Lei Cao
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Xia Ren
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Jian Hu
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Grace Tavengana
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Huan Wu
- grid.443626.10000 0004 1798 4069School of Laboratory Medicine, Wannan Medical College, Wuhu, Anhui Province China
| | - Yumei Zhou
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Yuhan Fu
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
| | - Mingfei Jiang
- grid.443626.10000 0004 1798 4069School of Clinical Medicine, Wannan Medical College, Wuhu, Anhui Province China
| | - Yufeng Wen
- grid.443626.10000 0004 1798 4069School of Public Health, Wannan Medical College, Wuhu, Anhui Province China
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Guo S, Chongsuvivatwong V, Lei S. Comparison on Major Gene Mutations Related to Rifampicin and Isoniazid Resistance between Beijing and Non-Beijing Strains of Mycobacterium tuberculosis: A Systematic Review and Bayesian Meta-Analysis. Genes (Basel) 2022; 13:genes13101849. [PMID: 36292734 PMCID: PMC9601453 DOI: 10.3390/genes13101849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: The Beijing strain of Mycobacterium tuberculosis (MTB) is controversially presented as the predominant genotype and is more drug resistant to rifampicin and isoniazid compared to the non-Beijing strain. We aimed to compare the major gene mutations related to rifampicin and isoniazid drug resistance between Beijing and non-Beijing genotypes, and to extract the best evidence using the evidence-based methods for improving the service of TB control programs based on genetics of MTB. Method: Literature was searched in Google Scholar, PubMed and CNKI Database. Data analysis was conducted in R software. The conventional and Bayesian random-effects models were employed for meta-analysis, combining the examinations of publication bias and sensitivity. Results: Of the 8785 strains in the pooled studies, 5225 were identified as Beijing strains and 3560 as non-Beijing strains. The maximum and minimum strain sizes were 876 and 55, respectively. The mutations prevalence of rpoB, katG, inhA and oxyR-ahpC in Beijing strains was 52.40% (2738/5225), 57.88% (2781/4805), 12.75% (454/3562) and 6.26% (108/1724), respectively, and that in non-Beijing strains was 26.12% (930/3560), 28.65% (834/2911), 10.67% (157/1472) and 7.21% (33/458), separately. The pooled posterior value of OR for the mutations of rpoB was 2.72 ((95% confidence interval (CI): 1.90, 3.94) times higher in Beijing than in non-Beijing strains. That value for katG was 3.22 (95% CI: 2.12, 4.90) times. The estimate for inhA was 1.41 (95% CI: 0.97, 2.08) times higher in the non-Beijing than in Beijing strains. That for oxyR-ahpC was 1.46 (95% CI: 0.87, 2.48) times. The principal patterns of the variants for the mutations of the four genes were rpoB S531L, katG S315T, inhA-15C > T and oxyR-ahpC intergenic region. Conclusion: The mutations in rpoB and katG genes in Beijing are significantly more common than that in non-Beijing strains of MTB. We do not have sufficient evidence to support that the prevalence of mutations of inhA and oxyR-ahpC is higher in non-Beijing than in Beijing strains, which provides a reference basis for clinical medication selection.
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Affiliation(s)
- Shengqiong Guo
- Guizhou Provincial Center for Disease Prevention and Control, Guiyang 550004, China
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
- Correspondence:
| | | | - Shiguang Lei
- Guizhou Provincial Center for Disease Prevention and Control, Guiyang 550004, China
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Panova AE, Vinokurov AS, Shemetova AA, Burmistrova IA, Shulgina MV, Samoilova AG, Vasilyeva IA, Vakhrusheva DV, Umpeleva TV, Eremeeva NI, Lavrenchuk LS, Golubeva LA, Danilova TI, Vasilyeva TB, Ugol'kova VA, Sosova NV, Lekhlyaider MV, Gorshkova IA, Romanova TA. Molecular characteristics of Mycobacterium tuberculosis drug-resistant isolates from HIV- and HIV+ tuberculosis patients in Russia. BMC Microbiol 2022; 22:138. [PMID: 35590243 PMCID: PMC9118847 DOI: 10.1186/s12866-022-02553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background High burden of drug-resistant (DR) tuberculosis (TB) is a significant threat to national TB control programs all over the world and in the Russian Federation. Different Mycobacterium tuberculosis (MTB) genotypes are hypothesized to have specific characteristics affecting TB control programs. For example, Beijing strains are supposed to have higher mutation rates compared to strains of other genotypes and subsequently higher capability to develop drug-resistance. Results Clinical MTB isolates from HIV- and HIV+ patients from four regions of Russia were analyzed for genotypes and mutations conferring resistance to Isoniazid, Rifampicin, Ethambutol, aminoglycosides, and fluoroquinolones. Analysis of genotypes and polymorphism of genomic loci according to the HIV status of the patients – sources of MTB isolates were performed. Studied MTB isolates from HIV- TB patients belonged to 15 genotypes and from HIV + TB patients – to 6 genotypes. Beijing clinical isolates dominated in HIV- (64,7%) and HIV+ (74,4%) groups. Other isolates were of LAM (including LAM1 and LAM9), Ural, and 4 minor groups of genotypes (including 5 subclones T). The spectrum of genotypes in the HIV- group was broader than in the HIV+ group. PR of B0/W148 Beijing was significantly lower than of other Beijing genotypes in susceptible and MDR-XDR isolates. Rates of isolates belonging to non-Beijing genotypes were higher than Beijing in susceptible isolates from HIV- patients. Conclusions Beijing genotype isolates prevailed in clinical isolates of all drug susceptibility profiles both from HIV- and HIV+ patients, although B0/W148 Beijing genotype did not dominate in this study. Genome loci and mutations polymorphisms were more pronounced in clinical isolates from HIV- patients, than from HIV+.
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Affiliation(s)
- Anna E Panova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Anatoliy S Vinokurov
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Anastasiya A Shemetova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Irina A Burmistrova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Marina V Shulgina
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation.
| | - Anastasiya G Samoilova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Irina A Vasilyeva
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Diana V Vakhrusheva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Tatiana V Umpeleva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Nataliya I Eremeeva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Leonid S Lavrenchuk
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Lyudmila A Golubeva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Tatiana I Danilova
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Tatiana B Vasilyeva
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Vera A Ugol'kova
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Nataliya V Sosova
- Regional TB dispensary of Stavropolskiy kray, Stavropol, Russian Federation
| | - Marina V Lekhlyaider
- Regional TB dispensary of Chelyabinskaya oblast, Chelyabinsk, Russian Federation
| | - Irina A Gorshkova
- Regional TB dispensary of Chelyabinskaya oblast, Chelyabinsk, Russian Federation
| | - Tatiana A Romanova
- Regional TB dispensary of Kemerovskaya oblast, Kemerovo, Russian Federation
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022. [DOI: https://doi.org/10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022. [DOI: https:/doi.org/10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Mudliar SKR, Kulsum U, Rufai SB, Umpo M, Nyori M, Singh S. Snapshot of Mycobacterium tuberculosis Phylogenetics from an Indian State of Arunachal Pradesh Bordering China. Genes (Basel) 2022; 13:genes13020263. [PMID: 35205308 PMCID: PMC8872330 DOI: 10.3390/genes13020263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 02/07/2023] Open
Abstract
Uncontrolled transmission of Mycobacterium tuberculosis (M. tuberculosis, MTB) drug resistant strains is a challenge to control efforts of the global tuberculosis program. Due to increasing multi-drug resistant (MDR) cases in Arunachal Pradesh, a northeastern state of India, the tracking and tracing of these resistant MTB strains is crucial for infection control and spread of drug resistance. This study aims to correlate the phenotypic DST, genomic DST (gDST) and phylogenetic analysis of MDR-MTB strains in the region. Of the total 200 samples 22 (11%) patients suspected of MDR-TB and 160 (80%) previously treated MDR-TB cases, 125 (62.5%) were identified as MTB. MGIT-960 SIRE DST detected 71/125 (56.8%) isolates as MDR/RR-MTB of which 22 (30.9%) were detected resistant to second-line drugs. Whole-genome sequencing of 65 isolates and their gDST found Ser315Thr mutation in katG (35/45; 77.8%) and Ser531Leu mutation in rpoB (21/41; 51.2%) associated with drug resistance. SNP barcoding categorized the dataset with Lineage2 (41; 63.1%) being predominant followed by Lineage3 (10; 15.4%), Lineage1 (8; 12.3%) and Lineage4 (6; 9.2%) respectively. Phylogenetic assignment by cgMLST gave insights of two Beijing sub-lineages viz; 2.2.1 (SNP difference < 19) and 2.2.1.2 (SNP difference < 9) associated with recent ongoing transmission in Arunachal Pradesh. This study provides insights in identifying two virulent Beijing sub-lineages (sub-lineage 2.2.1 and 2.2.1.2) with ongoing transmission of TB drug resistance in Arunachal Pradesh.
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Affiliation(s)
- Shiv kumar Rashmi Mudliar
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
| | - Umay Kulsum
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
| | - Syed Beenish Rufai
- Infectious Diseases and Immunity in Global Health Program, Research Institute of the McGill University Health Center, Montreal, QC H4A 3J1, Canada;
- McGill International TB Center, Montreal, QC H4A 3J1, Canada
| | - Mika Umpo
- Tomo Riba Institute of Health & Medical Sciences, Naharlagun 791110, Arunachal Pradesh, India;
| | - Moi Nyori
- State TB Cell, Naharlagun 791110, Arunachal Pradesh, India;
| | - Sarman Singh
- Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, Madhya Pradesh, India; (S.k.R.M.); (U.K.)
- Correspondence: ; Tel.: +91-9810813435
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