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Molldrem S, Bagani S, Subrahmanyam V, Permar R, Matsiri O, Caiphus C, Kizito B, Modongo C, Shin SS. Botswana tuberculosis (TB) stakeholders broadly support scaling up next-generation whole genome sequencing: Ethical and practical considerations for Botswana and global health. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002479. [PMID: 37967081 PMCID: PMC10651001 DOI: 10.1371/journal.pgph.0002479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Global health agencies are increasingly promoting the scale-up of next-generation whole genome sequencing (NG-WGS) of pathogens into infectious disease control programs, including for tuberculosis (TB). However, little is known about how stakeholders in low-to-middle income countries (LMICs) understand the ethics, benefits, and risks of these proposals. We conducted a qualitative study in Greater Gaborone, Botswana to learn how TB stakeholders there viewed a potential scale-up of NG-WGS into Botswana's TB program. We conducted 30 interviews and four deliberative dialogues with TB stakeholders based in Greater Gaborone, the country's largest city and capital. We created and showed participants an animated video series about a fictional family that experienced TB diagnosis, treatment, contact tracing, and data uses that were informed by NG-WGS. We analyzed transcripts using reflexive thematic analysis. We found broad support for the scale-up of TB NG-WGS in Botswana, owing to perceived benefits. Support was qualified with statements about ensuring adequate planning, resource-allocation, community and stakeholder engagement, capacity-building, and assessing ethical norms around publishing data. Our results suggest that scaling up NG-WGS for TB in Botswana would be supported by stakeholders there, contingent upon the government and other entities adequately investing in the initiative. These findings are relevant to other LMICs considering scale-ups of NG-WGS and related technologies for infectious diseases and suggest the need for sustained research into the acceptability of pathogen sequencing in other contexts.
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Affiliation(s)
- Stephen Molldrem
- Institute for Bioethics and Health Humanities, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Vishnu Subrahmanyam
- Institute for Bioethics and Health Humanities, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rebecca Permar
- Program for Leadership and Character, Office of Academic Advising, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | | | | | | | | | - Sanghyuk S. Shin
- Sue & Bill Gross School of Nursing, University of California, Irvine, California, United States of America
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Micheni LN, Kassaza K, Kinyi H, Ntulume I, Bazira J. Detection of Mycobacterium tuberculosis multiple strains in sputum samples from patients with pulmonary tuberculosis in south western Uganda using MIRU-VNTR. Sci Rep 2022; 12:1656. [PMID: 35102181 PMCID: PMC8803872 DOI: 10.1038/s41598-022-05591-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Infections with multiple strains of Mycobacterium tuberculosis are now widely recognized as a common occurrence. Identification of patients infected with multiple strains provides both insight into the disease dynamics and the epidemiology of tuberculosis. Analysis of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeats (MIRU-VNTR) has been shown to be highly sensitive in detecting multiple M. tuberculosis strains even in sputum. The goal of this study was to identify cases of multiple M. tuberculosis strain infections among patients diagnosed with pulmonary tuberculosis in Southwestern Uganda and assessment of factors associated with multiple strain infections. DNA extracted directly from 78 sputum samples, each from an individual patient, was analyzed using the standard 24 loci MIRU-VNTR typing. Five (6.4%) of the 78 patients were infected with multiple strains of M. tuberculosis with all of them being the newly diagnosed cases while two-thirds of them were co-infected with HIV. Exact regression analysis projected that the natives were more likely to harbor multiple strains (OR; 0.981, 95% CI 0–7.926) as well as those with a high microbial load (OR; 0.390, 95% CI 0–3.8167). Despite these findings being not statistically significant due to the small sample size, this points to a critical component of disease dynamics that has clinical implications and emphasizes a need for a study using a larger cohort. It is also essential to study the potential factors associated with higher risk of exposure to newly diagnosed and HIV positive patients at the community level. In addition, our ability to detect multiple M. tuberculosis strains using the standard 24 loci MIRU-VNTR typing especially with allelic diversity in loci 2059 and 3171, which are excluded from the 15-locus MIRU-VNTR, lead us to recommend the use of this genotyping technique, especially in areas with tuberculosis endemicity similar to this study.
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Affiliation(s)
- Lisa Nkatha Micheni
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda. .,Department of Microbiology and Immunology, Kampala International University Western Campus, Box 71, Bushenyi, Uganda.
| | - Kennedy Kassaza
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda
| | - Hellen Kinyi
- Department of Biochemistry, School of Medicine, Kabale University, Box 317, Kabale, Uganda
| | - Ibrahim Ntulume
- Department of Microbiology and Immunology, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda.
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Asgharzadeh M, Taghinejad Z, Mahdavipoor B, Asgharzadeh V, Kafil HS, Rashedi J. Mixed tuberculosis infections in Northwest of Iran. LE INFEZIONI IN MEDICINA 2021; 29:583-588. [PMID: 35146368 PMCID: PMC8805470 DOI: 10.53854/liim-2904-12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 10/17/2021] [Indexed: 06/14/2023]
Abstract
Primary Mycobacterium tuberculosis (MTB) infection doesn't provide protection against secondary infection and patients can suffer from multiple strains of M. tuberculosis simultaneously. The aim of this study was to use molecular genotyping to identify cases of mixed infection in Northwest of Iran. One hundred and twenty-one positive culture isolates of M. tuberculosis were prepared from patients consecutively in Northwest of Iran from March 2017 to March 2018 and then microevolution and mix infection were assessed using the mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) method. MIRU-VNTR analysis revealed that nine samples (7.3%) had double alleles in at least one locus, as observed by five cases of microevolution, and four cases (3.3%) of mixed infection. According to this study, mixed infection in Northwest of Iran has significantly decreased compared to 13 years ago (7.1% decreased to 3.3%), and in order to eradicate tuberculosis it is necessary to identify all cases of mixed infection, at least in recurrent cases, in the future.
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Affiliation(s)
- Mohammad Asgharzadeh
- Biotechnology Research Center and Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Taghinejad
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behroz Mahdavipoor
- Department of Laboratory Sciences, Faculty of Paramedicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Vahid Asgharzadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jalil Rashedi
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Micheni LN, Kassaza K, Kinyi H, Ntulume I, Bazira J. Rifampicin and isoniazid drug resistance among patients diagnosed with pulmonary tuberculosis in southwestern Uganda. PLoS One 2021; 16:e0259221. [PMID: 34714879 PMCID: PMC8555815 DOI: 10.1371/journal.pone.0259221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/18/2021] [Indexed: 11/18/2022] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) has become a major threat to the control of tuberculosis globally. Uganda is among the countries with a relatively high prevalence of tuberculosis despite significant control efforts. In this study, the drug resistance of Mycobacterium tuberculosis to rifampicin (RIF) and isoniazid (INH) was investigated among patients diagnosed with pulmonary tuberculosis in Southwestern Uganda. A total of 283 sputum samples (266 from newly diagnosed and 17 from previously treated patients), collected between May 2018 and April 2019 at four different TB diagnostic centres, were assessed for RIF and INH resistance using high-resolution melt curve analysis. The overall prevalence of monoresistance to INH and RIF was 8.5% and 11% respectively, while the prevalence of MDR-TB was 6.7%. Bivariate analysis showed that patients aged 25 to 44 years were at a higher risk of developing MDR-TB (cOR 0.253). Furthermore, among the newly diagnosed patients, the prevalence of monoresistance to INH, RIF and MDR-TB was 8.6%, 10.2% and 6.4% respectively; while among the previously treated cases, these prevalence rates were 5.9%, 23.5% and 11.8%. These rates are higher than those reported previously indicating a rise in MTB drug resistance and may call for measures used to prevent a further rise in drug resistance. There is also a need to conduct frequent drug resistance surveys, to monitor and curtail the development and spread of drug-resistant TB.
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Affiliation(s)
- Lisa Nkatha Micheni
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
- Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Bushenyi, Uganda
| | - Kennedy Kassaza
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Hellen Kinyi
- Department of Biochemistry, School of Medicine, Kabale University, Kabale, Uganda
| | - Ibrahim Ntulume
- Department of Microbiology and Immunology, Faculty of Biomedical Sciences, Kampala International University Western Campus, Bushenyi, Uganda
| | - Joel Bazira
- Department of Microbiology, Faculty of Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
- * E-mail:
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Ushtanit A, Mikhailova Y, Lyubimova A, Makarova M, Safonova S, Filippov A, Borisov S, Zimenkov D. Genetic Profile of Linezolid-Resistant M. tuberculosis Clinical Strains from Moscow. Antibiotics (Basel) 2021; 10:antibiotics10101243. [PMID: 34680823 PMCID: PMC8532644 DOI: 10.3390/antibiotics10101243] [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: 09/09/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Linezolid, bedaquiline, and newer fluoroquinolones are currently placed as priority Group A drugs for the treatment of drug-resistant tuberculosis. The number of reported linezolid-resistant clinical strains is still low, and the correlation of molecular determinants with phenotype is not perfect. Methods: We determined the linezolid MICs for clinical isolates from the Moscow region and identified mutations in rplC and rrl genes. Results: All 16 linezolid-resistant isolates had previously reported mutations in the rplC or rrl loci, and 13 of them bore a RplC C154R substitution. Detection of this substitution in a heteroresistant state was not successful, probably, due to the more stable DNA secondary structure of the mutated fragment, which precludes its amplification in mixes with the wild-type DNA. Strains with an rplC mutation had higher linezolid MIC compared to isolates with rrl mutations. Conclusions: Linezolid resistance mostly emerged during treatment with the latest regimen. Three primary cases with linezolid resistance question the possible transmission of totally drug-resistant tuberculosis in the Moscow region, which demands further investigation.
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Affiliation(s)
- Anastasia Ushtanit
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
| | - Yulia Mikhailova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Alexandra Lyubimova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
| | - Marina Makarova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Svetlana Safonova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Alexey Filippov
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Sergey Borisov
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Danila Zimenkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
- Correspondence:
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Byrne AS, Goudreau A, Bissonnette N, Shamputa IC, Tahlan K. Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review. Front Genet 2020; 11:600692. [PMID: 33408740 PMCID: PMC7779811 DOI: 10.3389/fgene.2020.600692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.
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Affiliation(s)
| | - Alex Goudreau
- Science & Health Sciences Librarian, University of New Brunswick, Saint John, NB, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Isdore Chola Shamputa
- Department of Nursing & Health Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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Abstract
Tuberculosis (TB) is a major issue in global health and affects millions of people each year. Multidrug-resistant tuberculosis (MDR-TB) annually causes many deaths worldwide. Development of a way to diagnose and treat patients with MDR-TB can potentially reduce the incidence of the disease. The current study reviews the risk factors, pattern of progression, mechanism of resistance, and interaction between bacteria and the host immune system, which disrupts the immune response. It also targets the components of Mycobacterium tuberculosis (Mtb) and diagnosis and treatment options that could be available for clinical use in the near future. Mutations play an important role in development of MDR-TB and the selection of appropriate mutations can help to understand the type of resistance in patients to anti-TB drugs. In this way, they can be initially treated with proper and effective therapeutic choices, which can accelerate the course of treatment and improve patient health. Targeting the components and enzymes of Mtb is necessary for understanding bacterial survival and finding a way to destroy the pathogen and allow patients to recover faster and prevent the spread of disease, especially resistant strains.
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Affiliation(s)
- Majid Faridgohar
- Infectious Diseases Research Center, Kashan University of Medical Sciences, Kashan, Iran.,Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
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Abstract
PURPOSE OF REVIEW This review aims to describe the key principles in treatment of drug-resistant tuberculosis (TB) in people living with HIV, including early access to timely diagnostics, linkage into care, TB treatment strategies including the use of new and repurposed drugs, co-management of HIV disease, and treatment complications and programmatic support to optimize treatment outcomes. These are necessary strategies to decrease the likelihood of poor treatment outcomes including lower treatment completion rates and higher mortality. RECENT FINDINGS Diagnosis of drug-resistant TB is the gateway into care; yet understanding the utility and the limitations of genotypic methods in this population is necessary. The principles of TB treatment in HIV-infected individuals are similar to those without HIV co-infection, with few exceptions. However, adverse effects with potential significant morbidity may emerge during treatment, and timely antiretroviral therapy is essential to improve mortality in this patient population. Emerging data on the use of new and repurposed drugs and short course multidrug-resistant TB regimens and adherence strategies benefiting this population are reviewed. SUMMARY The clinical complexity of co-managing drug-resistant TB and HIV, and the higher rate of poor treatment outcomes in this population demand careful clinical management strategies, and multidisciplinary and comprehensive programmatic interventions to optimize treatment success in this vulnerable group.
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Early Detection of Emergent Extensively Drug-Resistant Tuberculosis by Flow Cytometry-Based Phenotyping and Whole-Genome Sequencing. Antimicrob Agents Chemother 2019; 63:AAC.01834-18. [PMID: 30670422 DOI: 10.1128/aac.01834-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022] Open
Abstract
A critical gap in tuberculosis (TB) treatment is detection of emergent drug resistance. We hypothesized that advanced phenotyping with whole-genome sequencing (WGS) will detect low-frequency Mycobacterium tuberculosis drug resistance. We assessed a reporter mycobacteriophage (Φ2GFP10) in vitro to detect drug-resistant subpopulations and predict M. tuberculosis bactericidal activity in this pilot study. Subsequently, we prospectively studied 20 TB patients with serial Φ2GFP10, Xpert MTB/RIF, and M. tuberculosis culture through end of treatment. WGS was performed, and single nucleotide polymorphisms (SNPs) were examined to detect mixed infection in selected M. tuberculosis isolates. Resistant M. tuberculosis isolates were detected at 1:100,000, and changes in cytometry-gated events were predictive of in vitro M. tuberculosis bactericidal activity using the Φ2GFP10 assay. Emergent drug resistance was detected in one patient by Φ2GFP10 at 3 weeks but not by conventional testing (M. tuberculosis culture and GeneXpert). WGS revealed a phylogeographically distinct extensively drug-resistant tuberculosis (XDR-TB) genome, identical to an XDR-TB isolate from the patient's spouse. Variant lineage-specific SNPs were present early, suggesting mixed infection as the etiology of emergent resistance with temporal trends providing evidence for selection during treatment. Φ2GFP10 can detect low-frequency drug-resistant M. tuberculosis and with WGS characterize emergent M. tuberculosis resistance. In areas of high TB transmission and drug resistance, rapid screening for heteroresistance should be considered.
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Karamagi E, Sensalire S, Muhire M, Kisamba H, Byabagambi J, Rahimzai M, Mugabe F, George U, Calnan J, Seyoum D, Birabwa E. Improving TB case notification in northern Uganda: evidence of a quality improvement-guided active case finding intervention. BMC Health Serv Res 2018; 18:954. [PMID: 30541533 PMCID: PMC6292080 DOI: 10.1186/s12913-018-3786-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/02/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Strategies to identify and treat undiagnosed prevalent cases that have not sought diagnostic services on their own, are necessary to treat TB in patients earlier and interrupt transmission. Late presentation for medical services of symptomatic patients require special efforts to detect early and notify TB in high risk populations. An intervention that combined quality improvement with facility-led active case finding (QI-ACF) was implemented in 10 districts of Northern Uganda with the highest TB burden to improve case notification among populations at highest risk of TB. METHODS Using QI-ACF intervention approach in 48 facilities, we; 1) targeted key vulnerable populations, 2) engaged district and facility teams in TB systems strengthening, 3) conducted systematic screening and diagnosis in vulnerable groups (people living with HIV, fishing communities, and prisoners), and 4) trained health workers on national x-ray diagnosis guidelines for smear-negative patients. Facility-led QI-ACF meant that health care providers identified the target population, mobilized and massively screened suspects, and addressed gaps in documentation. Chest X-ray diagnosis was promoted for smear-negative TB among those suspects whose sputum examination was negative. The effect of the intervention on case notification was then assessed separately over the post intervention period. RESULTS Over all TB case notification in the intervention districts increased from 171 to 223 per 100,000 population between the baseline months of October-December 2016 and end line month of April-June 2017. TB patient contacts had the majority of TB positive cases identified during active case finding (40, 6.1%). Fishing communities had the highest TB positivity rate at 6.8%. Prisoners accounted for the lowest number of TB positive cases at 34 (2.3%). CONCLUSION Targeting should be applied at all levels of TB intervention to improve yield: targeting districts and facilities with the lowest rates of case notification and targeting index patient contacts, HIV clients, and fishing communities. Screening tools are useful to guide health workers to identify presumptive cases. Efforts to improve availability of x-ray for TB diagnosis contributed to almost half of the new cases identified. Having all HIV patients who were eligible for viral load provide sputum for TB screening proved easy to implement.
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Affiliation(s)
- Esther Karamagi
- University Research Co., LLC, USAID Applying Science to Strengthen and Improve Systems (ASSIST) Project, USAID, Suite 611, Level 6, BMK House, Plot 45, Nyabong Road, P.O. Box 28745, Kampala, Uganda.
| | - Simon Sensalire
- University Research Co., LLC, USAID Applying Science to Strengthen and Improve Systems (ASSIST) Project, USAID, Suite 611, Level 6, BMK House, Plot 45, Nyabong Road, P.O. Box 28745, Kampala, Uganda
| | - Martin Muhire
- University Research Co., LLC, USAID Applying Science to Strengthen and Improve Systems (ASSIST) Project, USAID, Suite 611, Level 6, BMK House, Plot 45, Nyabong Road, P.O. Box 28745, Kampala, Uganda
| | - Herbert Kisamba
- University Research Co., LLC, USAID Applying Science to Strengthen and Improve Systems (ASSIST) Project, USAID, Suite 611, Level 6, BMK House, Plot 45, Nyabong Road, P.O. Box 28745, Kampala, Uganda
| | - John Byabagambi
- University Research Co., LLC, USAID Applying Science to Strengthen and Improve Systems (ASSIST) Project, USAID, Suite 611, Level 6, BMK House, Plot 45, Nyabong Road, P.O. Box 28745, Kampala, Uganda
| | - Mirwais Rahimzai
- University Research Co., LLC, USAID Applying Science to Strengthen and Improve Systems (ASSIST) Project, USAID, Suite 611, Level 6, BMK House, Plot 45, Nyabong Road, P.O. Box 28745, Kampala, Uganda
| | | | | | - Jacqueline Calnan
- United States Agency for International Development (USAID), Kampala, Uganda
| | - Dejene Seyoum
- United States Agency for International Development (USAID), Kampala, Uganda
| | - Estella Birabwa
- United States Agency for International Development (USAID), Kampala, Uganda
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Mycobacterium tuberculosis Next-Generation Whole Genome Sequencing: Opportunities and Challenges. Tuberc Res Treat 2018; 2018:1298542. [PMID: 30631597 PMCID: PMC6304523 DOI: 10.1155/2018/1298542] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/29/2018] [Accepted: 11/25/2018] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance is a threat to global tuberculosis (TB) control. Comprehensive and timely drug susceptibility determination is critical to inform appropriate treatment of drug-resistant tuberculosis (DR-TB). Phenotypic drug susceptibility testing (DST) is the gold standard for M. tuberculosis drug resistance determination. M. tuberculosis whole genome sequencing (WGS) has the potential to be a one-stop method for both comprehensive DST and epidemiological investigations. We discuss in this review the tremendous opportunities that next-generation WGS presents in terms of understanding the molecular epidemiology of tuberculosis and mechanisms of drug resistance. The potential clinical value and public health impact in the areas of DST for patient management and tracing of transmission chains for timely public health intervention are also discussed. We present the current challenges for the implementation of WGS in low and middle-income settings. WGS analysis has already been adapted routinely in laboratories to inform patient management and public health interventions in low burden high-income settings such as the United Kingdom. We predict that the technology will be adapted similarly in high burden settings where the impact on the epidemic will be greatest.
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Shin SS, Modongo C, Baik Y, Allender C, Lemmer D, Colman RE, Engelthaler DM, Warren RM, Zetola NM. Mixed Mycobacterium tuberculosis-Strain Infections Are Associated With Poor Treatment Outcomes Among Patients With Newly Diagnosed Tuberculosis, Independent of Pretreatment Heteroresistance. J Infect Dis 2018; 218:1974-1982. [PMID: 30085153 PMCID: PMC6217728 DOI: 10.1093/infdis/jiy480] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 08/02/2018] [Indexed: 11/14/2022] Open
Abstract
Background Heteroresistant Mycobacterium tuberculosis infections (defined as concomitant infection with drug-resistant and drug-susceptible strains) may explain the higher risk of poor tuberculosis treatment outcomes observed among patients with mixed-strain M. tuberculosis infections. We investigated the clinical effect of mixed-strain infections while controlling for pretreatment heteroresistance in a population-based sample of patients with tuberculosis starting first-line tuberculosis therapy in Botswana. Methods We performed 24-locus mycobacterial interspersed repetitive unit-variable number tandem-repeat analysis and targeted deep sequencing on baseline primary cultured isolates to detect mixed infections and heteroresistance, respectively. Drug-sensitive, micro-heteroresistant, macro-heteroresistant, and fixed-resistant infections were defined as infections in which the frequency of resistance was <0.1%, 0.1%-4%, 5%-94%, and ≥95%, respectively, in resistance-conferring domains of the inhA promoter, the katG gene, and the rpoB gene. Results Of the 260 patients with tuberculosis included in the study, 25 (9.6%) had mixed infections and 30 (11.5%) had poor treatment outcomes. Micro-heteroresistance, macro-heteroresistance, and fixed resistance were found among 11 (4.2%), 2 (0.8%), and 11 (4.2%), respectively, for isoniazid and 21 (8.1%), 0 (0%), and 10 (3.8%), respectively, for rifampicin. In multivariable analysis, mixed infections but not heteroresistant infections independently predicted poor treatment outcomes. Conclusions Among patients starting first-line tuberculosis therapy in Botswana, mixed infections were associated with poor tuberculosis treatment outcomes, independent of heteroresistance.
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Affiliation(s)
- Sanghyuk S Shin
- Sue and Bill Gross School of Nursing, University of California, Irvine
| | - Chawangwa Modongo
- Botswana-Upenn Partnership, Gaborone, Botswana
- Department of Infectious Disease, Gaborone, Botswana
| | - Yeonsoo Baik
- Department of Epidemiology, Fielding School of Public Health, University of California, Los Angeles
| | | | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, Arizona
| | | | | | - Robin M Warren
- NRF/DST Centre of Excellence for Biomedical Tuberculosis Research
- South African Medical Research Council Centre for Tuberculosis Research, Stellenbosch University, Tygerberg, South Africa
- Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Nicola M Zetola
- Department of Radiation Oncology, University of Pennsylvania School of Medicine, Gaborone, Botswana
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Nathavitharana RR, Shi CX, Chindelevitch L, Calderon R, Zhang Z, Galea JT, Contreras C, Yataco R, Lecca L, Becerra MC, Murray MB, Cohen T. Polyclonal Pulmonary Tuberculosis Infections and Risk for Multidrug Resistance, Lima, Peru. Emerg Infect Dis 2018; 23:1887-1890. [PMID: 29048297 PMCID: PMC5652442 DOI: 10.3201/eid2311.170077] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Because within-host Mycobacterium tuberculosis diversity complicates diagnosis and treatment of tuberculosis (TB), we measured diversity prevalence and associated factors among 3,098 pulmonary TB patients in Lima, Peru. The 161 patients with polyclonal infection were more likely than the 115 with clonal or the 2,822 with simple infections to have multidrug-resistant TB.
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Tarashi S, Fateh A, Mirsaeidi M, Siadat SD, Vaziri F. Mixed infections in tuberculosis: The missing part in a puzzle. Tuberculosis (Edinb) 2017; 107:168-174. [PMID: 29050766 DOI: 10.1016/j.tube.2017.09.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/05/2017] [Accepted: 09/13/2017] [Indexed: 11/26/2022]
Abstract
The mixed strains infection phenomenon is a major problem posing serious challenges in control of tuberculosis (TB). In patients with mixed infection, several different strains of Mycobacterium tuberculosis can be isolated simultaneously. Although different genotyping methods and various molecular approaches can be employed for detection of mixed infection in clinical samples, the MIRU-VNTR technique is more sensitive with higher discriminative power than many widely used techniques. Furthermore, the recent introduction of whole genome sequencing (WGS) promises to reveal more details about mixed infection with high resolution. WGS has been used for detection of mixed infection with high sensitivity and discriminatory, but the technology is currently limited to developed countries. Mixed infection may involve strains with different susceptibility patterns, which may alter the treatment outcome. In this report, we review the current concepts of mixed strains infection and also infection involving strains with a different susceptibility pattern in TB. We evaluate the importance of identifying mixed infection for diagnosis as well as treatment and highlight the accuracy and clinical utility of direct genotyping of clinical specimens.
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Affiliation(s)
- Samira Tarashi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mehdi Mirsaeidi
- Division of Pulmonary and Critical Care, University of Miami, Miami, FL, USA
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, 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.
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15
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Kontsevaya I, Nikolayevskyy V, Kovalyov A, Ignatyeva O, Sadykhova A, Simak T, Tikhonova O, Dubrovskaya Y, Vasiliauskiene E, Davidaviciene E, Skenders G, Makurina O, Balabanova Y, Drobniewski F. Tuberculosis cases caused by heterogeneous infection in Eastern Europe and their influence on outcomes. INFECTION GENETICS AND EVOLUTION 2016; 48:76-82. [PMID: 27998730 DOI: 10.1016/j.meegid.2016.12.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 12/14/2016] [Accepted: 12/16/2016] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Mycobacterium tuberculosis superinfection is known to occur in areas with high rates of tuberculosis (TB) and has a significant impact on overall clinical TB management. AIM We aimed to estimate the superinfection rate in cohorts of drug sensitive and multi-drug resistant tuberculosis (MDR TB) patients from Eastern Europe and the potential role of a second MDR TB strain infecting a patient with active non-MDR TB in treatment outcome. METHODS The study population included 512 serial M. tuberculosis isolates obtained from 84 MDR- and 136 non-MDR TB patients recruited sequentially at sites in Lithuania, Latvia and Russia in 2011-2013. Strains were genotyped using standardized 24-loci Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeat (MIRU-VNTR) typing. RESULTS Changes in two or more MIRU-VNTR loci suggesting superinfection were detected in 13 patients (5.9%). We found 4 initially non-MDR TB patients superinfected with an MDR TB strain during treatment and 3 of them had an unsuccessful outcome. CONCLUSIONS An unsuccessful treatment outcome in patients initially diagnosed with drug sensitive TB might be explained by superinfection with an MDR TB strain. Bacteriological reversion could be indicative of superinfection with another strain. Archiving of all serial isolates and their genotyping in case of culture reversion could support therapeutic strategies in high MDR TB burden settings if resources are available.
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Affiliation(s)
- Irina Kontsevaya
- Imperial College London, Du Cane Road, London W12 0NN, UK; N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation.
| | - Vladyslav Nikolayevskyy
- Imperial College London, Du Cane Road, London W12 0NN, UK; Public Health England National Mycobacterium Reference Laboratory, 2 Newark Street, London E1 2AT, UK; Queen Mary, University of London, Mile End Road, London E1 4NS, UK.
| | - Alexander Kovalyov
- N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation.
| | - Olga Ignatyeva
- N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation.
| | - Anna Sadykhova
- N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation.
| | - Tatiana Simak
- N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation.
| | - Olesya Tikhonova
- N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation.
| | - Yulia Dubrovskaya
- N.V. Postnikov Samara Region Clinical Tuberculosis Dispensary, 154 Novo-Sadovaya Street, Samara 443068, Russian Federation.
| | - Edita Vasiliauskiene
- Infectious Disease and TB Hospital, P. Sirvio str. 5, 10214 Vilnius, Lithuania; Vilnius University, Department of Physiology, Biochemistry and Laboratory Medicine, Faculty of Medicine, M. K. Ciurlionio str. 21, 03101 Vilnius, Lithuania.
| | - Edita Davidaviciene
- Infectious Disease and TB Hospital, P. Sirvio str. 5, 10214 Vilnius, Lithuania.
| | - Girts Skenders
- Tuberculosis and Lung Diseases Centre, Riga East University Hospital, 68 Lielvardes Street, LV-1006 Riga, Latvia.
| | - Olga Makurina
- Samara National Research University, 1 Akademika Pavlova Street, Samara 443011, Russian Federation.
| | - Yanina Balabanova
- Imperial College London, Du Cane Road, London W12 0NN, UK; Robert Koch Institute, Postfach 65 02 61, Berlin D-13302, Germany.
| | - Francis Drobniewski
- Imperial College London, Du Cane Road, London W12 0NN, UK; Queen Mary, University of London, Mile End Road, London E1 4NS, UK.
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16
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Ssengooba W, de Jong BC, Joloba ML, Cobelens FG, Meehan CJ. Whole genome sequencing reveals mycobacterial microevolution among concurrent isolates from sputum and blood in HIV infected TB patients. BMC Infect Dis 2016; 16:371. [PMID: 27495002 PMCID: PMC4974755 DOI: 10.1186/s12879-016-1737-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 07/28/2016] [Indexed: 03/14/2023] Open
Abstract
Background In the context of advanced immunosuppression, M. tuberculosis is known to cause detectable mycobacteremia. However, little is known about the intra-patient mycobacterial microevolution and the direction of seeding between the sputum and blood compartments. Methods From a diagnostic study of HIV-infected TB patients, 51 pairs of concurrent blood and sputum M. tuberculosis isolates from the same patient were available. In a previous analysis, we identified a subset with genotypic concordance, based on spoligotyping and 24 locus MIRU-VNTR. These paired isolates with identical genotypes were analyzed by whole genome sequencing and phylogenetic analysis. Results Of the 25 concordant pairs (49 % of the 51 paired isolates), 15 (60 %) remained viable for extraction of high quality DNA for whole genome sequencing. Two patient pairs were excluded due to poor quality sequence reads. The median CD4 cell count was 32 (IQR; 16–101)/mm3 and ten (77 %) patients were on ART. No drug resistance mutations were identified in any of the sequences analyzed. Three (23.1 %) of 13 patients had SNPs separating paired isolates from blood and sputum compartments, indicating evidence of microevolution. Using a phylogenetic approach to identify the ancestral compartment, in two (15 %) patients the blood isolate was ancestral to the sputum isolate, in one (8 %) it was the opposite, and ten (77 %) of the pairs were identical. Conclusions Among HIV-infected patients with poor cellular immunity, infection with multiple strains of M. tuberculosis was found in half of the patients. In those patients with identical strains, whole genome sequencing indicated that M. tuberculosis intra-patient microevolution does occur in a few patients, yet did not reveal a consistent direction of spread between sputum and blood. This suggests that these compartments are highly connected and potentially seed each other repeatedly. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1737-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda. .,Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium. .,Department of Global Health and Amsterdam, Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.
| | - Bouke C de Jong
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases, New York University, New York, NY, USA
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Frank G Cobelens
- Department of Global Health and Amsterdam, Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands.,KNCV Tuberculosis Foundation, The Hague, Netherlands
| | - Conor J Meehan
- Unit of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
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Pérez-Lago L, Lirola MM, Navarro Y, Herranz M, Ruiz-Serrano MJ, Bouza E, García-de-Viedma D. Co-infection with Drug-Susceptible and Reactivated Latent Multidrug-Resistant Mycobacterium tuberculosis. Emerg Infect Dis 2016; 21:2098-100. [PMID: 26488258 PMCID: PMC4622252 DOI: 10.3201/eid2111.150683] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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18
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Yuan XL, Wen Q, Ni MD, Wang LK. Immune formulation-assisted conventional therapy on anti-infective effectiveness of multidrug-resistant Mycobacterium tuberculosis infection mice. ASIAN PAC J TROP MED 2016; 9:293-7. [PMID: 26972405 DOI: 10.1016/j.apjtm.2016.01.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 12/20/2015] [Accepted: 12/30/2015] [Indexed: 10/22/2022] Open
Abstract
OBJECTIVE To study the effect of immune formulation-assisted conventional therapy on anti-infective ability of multidrug-resistant Mycobacterium tuberculosis infection mice. METHODS BALB/c mice were used as experimental animals, multidrug-resistant M. tuberculosis infection models were built, randomly divided into model group, moxifloxacin group, thymopentin group and combined treatment group and given corresponding drug intervention, and then colony numbers in the spleen and lung, T lymphocyte subset contents and programmed death-1 (PD-1) expression levels in peripheral blood were detected. RESULTS Colony numbers in lung and spleen of moxifloxacin group and thymopentin group were significantly lower than those of model group and colony numbers in lung and spleen of combined treatment group were significantly lower than those of moxifloxacin group and thymopentin group; contents of CD3(+)CD4(+)T cells, Th1 and Th17 in peripheral blood of moxifloxacin group and thymopentin group were higher than those of model group, and contents of CD3(+)CD8(+)T cells, Th2 and Treg were lower than those of model group; contents of CD3(+)CD4(+)T cells, Th1 and Th17 in peripheral blood of combined treatment group were higher than those of moxifloxacin group and thymopentin group, and contents of CD3(+)CD8(+)T cells, Th2 and Treg were lower than those of moxifloxacin group and thymopentin group; PD-1 expression levels on T lymphocyte, B lymphocyte and monocyte surface in peripheral blood of moxifloxacin group and thymopentin group were lower than those of model group, and PD-1 expression levels on T lymphocyte, B lymphocyte and monocyte surface in peripheral blood of combined treatment group were lower than those of moxifloxacin group and thymopentin group. CONCLUSIONS Immune formulation thymopentin can enhance the anti-infective ability of multidrug-resistant M. tuberculosis infection mice, decrease bacterial load in lung and spleen, and enhance immune function.
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Affiliation(s)
- Xiu-Li Yuan
- Internal Medicine Department No. 3, Eastern Medical District of Linyi People's Hospital, Linyi City, Shandong Province, 276034, People's Republic of China
| | - Qiang Wen
- Internal Medicine Department No. 3, Eastern Medical District of Linyi People's Hospital, Linyi City, Shandong Province, 276034, People's Republic of China
| | - Ming-De Ni
- Internal Medicine Department No. 3, Eastern Medical District of Linyi People's Hospital, Linyi City, Shandong Province, 276034, People's Republic of China
| | - Li-Kun Wang
- Infection Department, Eastern Medical District of Linyi People's Hospital, Linyi City, Shandong Province, 276034, People's Republic of China.
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Cohen T, Chindelevitch L, Misra R, Kempner ME, Galea J, Moodley P, Wilson D. Within-Host Heterogeneity of Mycobacterium tuberculosis Infection Is Associated With Poor Early Treatment Response: A Prospective Cohort Study. J Infect Dis 2016; 213:1796-9. [PMID: 26768249 DOI: 10.1093/infdis/jiw014] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 01/06/2016] [Indexed: 11/12/2022] Open
Abstract
The clinical management of tuberculosis is a major challenge in southern Africa. The prevalence of within-host genetically heterogeneous Mycobacterium tuberculosis infection and its effect on treatment response are not well understood. We enrolled 500 patients with tuberculosis in KwaZulu-Natal and followed them through 2 months of treatment. Using mycobacterial interspersed repetitive units-variable number of tandem repeats genotyping to identify mycobacterial heterogeneity, we report the prevalence and evaluate the association of heterogeneity with treatment response. Upon initiation of treatment, 21.1% of participants harbored a heterogeneous M. tuberculosis infection; such heterogeneity was independently associated with a nearly 2-fold higher odds of persistent culture positivity after 2 months of treatment (adjusted odds ratio, 1.90; 95% confidence interval, 1.03-3.50).
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Affiliation(s)
- Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Leonid Chindelevitch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Reshma Misra
- Infection Prevention and Control, University of KwaZulu-Natal, Durban
| | | | | | - Prashini Moodley
- Infection Prevention and Control, University of KwaZulu-Natal, Durban
| | - Douglas Wilson
- Department of Internal Medicine, Edendale Hospital, University of KwaZulu-Natal, Pietermaritzburg, South Africa
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20
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Boisson-Dupuis S, Bustamante J, El-Baghdadi J, Camcioglu Y, Parvaneh N, El Azbaoui S, Agader A, Hassani A, El Hafidi N, Mrani NA, Jouhadi Z, Ailal F, Najib J, Reisli I, Zamani A, Yosunkaya S, Gulle-Girit S, Yildiran A, Cipe FE, Torun SH, Metin A, Atikan BY, Hatipoglu N, Aydogmus C, Kilic SS, Dogu F, Karaca N, Aksu G, Kutukculer N, Keser-Emiroglu M, Somer A, Tanir G, Aytekin C, Adimi P, Mahdaviani SA, Mamishi S, Bousfiha A, Sanal O, Mansouri D, Casanova JL, Abel L. Inherited and acquired immunodeficiencies underlying tuberculosis in childhood. Immunol Rev 2015; 264:103-20. [PMID: 25703555 DOI: 10.1111/imr.12272] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M.tb) and a few related mycobacteria, is a devastating disease, killing more than a million individuals per year worldwide. However, its pathogenesis remains largely elusive, as only a small proportion of infected individuals develop clinical disease either during primary infection or during reactivation from latency or secondary infection. Subacute, hematogenous, and extrapulmonary disease tends to be more frequent in infants, children, and teenagers than in adults. Life-threatening primary TB of childhood can result from known acquired or inherited immunodeficiencies, although the vast majority of cases remain unexplained. We review here the conditions conferring a predisposition to childhood clinical diseases caused by mycobacteria, including not only M.tb but also weakly virulent mycobacteria, such as BCG vaccines and environmental mycobacteria. Infections with weakly virulent mycobacteria are much rarer than TB, but the inherited and acquired immunodeficiencies underlying these infections are much better known. Their study has also provided genetic and immunological insights into childhood TB, as illustrated by the discovery of single-gene inborn errors of IFN-γ immunity underlying severe cases of TB. Novel findings are expected from ongoing and future human genetic studies of childhood TB in countries that combine a high proportion of consanguineous marriages, a high incidence of TB, and an excellent clinical care, such as Iran, Morocco, and Turkey.
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Affiliation(s)
- Stéphanie Boisson-Dupuis
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY, USA; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, Institut National de la Santé et de la Recherche Médicale, INSERM-U1163, Paris, France; Paris Descartes University, Imagine Institute, Paris, France
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21
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Ssengooba W, Cobelens FG, Nakiyingi L, Mboowa G, Armstrong DT, Manabe YC, Joloba ML, de Jong BC. High Genotypic Discordance of Concurrent Mycobacterium tuberculosis Isolates from Sputum and Blood of HIV-Infected Individuals. PLoS One 2015; 10:e0132581. [PMID: 26176604 PMCID: PMC4503667 DOI: 10.1371/journal.pone.0132581] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/16/2015] [Indexed: 11/19/2022] Open
Abstract
Background Among HIV-infected individuals with CD4 less than 200 cells/mm3, tuberculosis often has an atypical presentation, is more likely to be disseminated and is diagnostically challenging. We sought to understand the genotypic discordance of concurrent sputum and blood M. tuberculosis (MTB) isolates from HIV-infected individuals. Methods From a prospective diagnostic accuracy study with 182 HIV-infected culture-positive TB adults, isolates were obtained from 51 of 66 participants who were MTB culture-positive by both sputum and blood. Isolates were subjected to susceptibility testing to 1st line drugs, spoligotyping and 24 locus- MIRU-VNTR. Results The median age of the participants was 31 (IQR; 27–38) years and 51% were male. The median CD4 count was 29 (IQR; 10–84) cells/mm3 with 20% taking ART; 8.0% were previously treated for TB, and 63% were AFB smear-negative. The isolates belonged to two of the main global MTB-lineages; East-African-Indian (L3) 17 (16.7%) and Euro-American (L4) 85 (83.3%). We identified 26 (51.0%) participants with discordant MTB-genotypes between sputum and blood, including two patients with evidence of mixed infection in either compartment. Having discordant MTB-genotypes was not predicted by the MTB-lineage in either blood or sputum, CD4 cell count, or any other clinical characteristic. Conclusions There is a high genotypic discordance among M. tuberculosis concurrently isolated from sputum and blood of HIV-infected individuals. These findings suggest that infection with more than one strain of M. tuberculosis occurs in at least half of patients with advanced HIV infection.
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Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- Unit of Mycobacteriology Institute of Tropical Medicine, Antwerp, Belgium
| | - Frank G. Cobelens
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, Netherlands
- KNCV Tuberculosis Foundation, The Hague, Netherlands
| | - Lydia Nakiyingi
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
| | - Gerald Mboowa
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
| | - Derek T. Armstrong
- Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Yukari C. Manabe
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
- Johns Hopkins University School of Medicine, Baltimore, MD, United States of America
| | - Moses L. Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda
- Infectious Diseases Institute, College of Health Sciences Makerere University, Kampala, Uganda
| | - Bouke C. de Jong
- Unit of Mycobacteriology Institute of Tropical Medicine, Antwerp, Belgium
- Division of Infectious Diseases, New York University, New York, NY, United States of America
- * E-mail:
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22
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Mixed Infections and Rifampin Heteroresistance among Mycobacterium tuberculosis Clinical Isolates. J Clin Microbiol 2015; 53:2138-47. [PMID: 25903578 DOI: 10.1128/jcm.03507-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/16/2015] [Indexed: 11/20/2022] Open
Abstract
Mixed infections and heteroresistance of Mycobacterium tuberculosis contribute to the difficulty of diagnosis, treatment, and control of tuberculosis. However, there is still no proper solution for these issues. This study aimed to investigate the potential relationship between mixed infections and heteroresistance and to determine the high-risk groups related to these factors. A total of 499 resistant and susceptible isolates were subjected to spoligotyping and 24-locus variable-number tandem repeat methods to analyze their genotypic lineages and the occurrence of mixed infections. Two hundred ninety-two randomly selected isolates were sequenced on their rpoB gene to examine mutations and heteroresistance. The results showed that 12 patients had mixed infections, and the corresponding isolates belonged to Manu2 (n = 8), Beijing (n = 2), T (n = 1), and unknown (n = 1) lineages. Manu2 was found to be significantly associated with mixed infections (odds ratio, 47.72; confidence interval, 9.68 to 235.23; P < 0.01). Four isolates (1.37%) were confirmed to be heteroresistant, which was caused by mixed infections in three (75%) isolates; these belonged to Manu2. Additionally, 3.8% of the rifampin-resistant isolates showing no mutation in the rpoB gene were significantly associated with mixed infections (χ(2), 56.78; P < 0.01). This study revealed for the first time that Manu2 was the predominant group in the cases of mixed infections, and this might be the main reason for heteroresistance and a possible mechanism for isolates without any mutation in the rpoB gene to become rifampin resistant. Further studies should focus on this lineage to clarify its relevance to mixed infections.
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