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Tsenova L, Fallows D, Kolloli A, Singh P, O'Brien P, Kushner N, Kaplan G, Subbian S. Inoculum size and traits of the infecting clinical strain define the protection level against Mycobacterium tuberculosis infection in a rabbit model. Eur J Immunol 2020; 50:858-872. [PMID: 32130727 DOI: 10.1002/eji.201948448] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/27/2019] [Accepted: 03/03/2020] [Indexed: 12/28/2022]
Abstract
Host protective immunity against pathogenic Mycobacterium tuberculosis (Mtb) infection is variable and poorly understood. Both prior Mtb infection and BCG vaccination have been reported to confer some protection against subsequent infection and/or disease. However, the immune correlates of host protection with or without BCG vaccination remain poorly understood. Similarly, the host response to concomitant infection with mixed Mtb strains is unclear. In this study, we used the rabbit model to examine the host response to various infectious doses of virulent Mtb HN878 with and without prior BCG vaccination, as well as simultaneous infection with a mixture of two Mtb clinical isolates HN878 and CDC1551. We demonstrate that both the ability of host immunity to control pulmonary Mtb infection and the protective efficacy of BCG vaccination against the progression of Mtb infection to disease is dependent on the infectious inoculum. The host response to infection with mixed Mtb strains mirrors the differential responses seen during infection with each of the strains alone. The protective response mounted against a hyperimmunogenic Mtb strain has a limited impact on the control of disease caused by a hypervirulent strain. This preclinical study will aid in predicting the success of any vaccination strategy and in optimizing TB vaccines.
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Affiliation(s)
- Liana Tsenova
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Department of Biological Sciences, NYC College of Technology, Brooklyn, NY, USA
| | - Dorothy Fallows
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Celgene Corporation, Summit, NJ, USA
| | - Afsal Kolloli
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Pooja Singh
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Paul O'Brien
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Division of Cancer Biology, Department of Radiation Oncology, Rutgers University, Newark, NJ, USA
| | - Nicole Kushner
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Gilla Kaplan
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Selvakumar Subbian
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA
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52
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Anyansi C, Keo A, Walker BJ, Straub TJ, Manson AL, Earl AM, Abeel T. QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. BMC Genomics 2020; 21:80. [PMID: 31992201 PMCID: PMC6986090 DOI: 10.1186/s12864-020-6486-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/13/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains of M. tuberculosis within a sample. Although metagenomic tools exist to classify strains in a metagenomic sample, most tools have been developed for more divergent species, and therefore cannot provide the sensitivity required to disentangle strains within closely related bacterial species such as M. tuberculosis. Here we present QuantTB, a method to identify and quantify individual M. tuberculosis strains in whole genome sequencing data. QuantTB uses SNP markers to determine the combination of strains that best explain the allelic variation observed in a sample. QuantTB outputs a list of identified strains, their corresponding relative abundances, and a list of drugs for which resistance-conferring mutations (or heteroresistance) have been predicted within the sample. RESULTS We show that QuantTB has a high degree of resolution and is capable of differentiating communities differing by less than 25 SNPs and identifying strains down to 1× coverage. Using simulated data, we found QuantTB outperformed other metagenomic strain identification tools at detecting strains and quantifying strain multiplicity. In a real-world scenario, using a dataset of 50 paired clinical isolates from a study of patients with either reinfections or relapses, we found that QuantTB could detect mixed infections and reinfections at rates concordant with a manually curated approach. CONCLUSION QuantTB can determine infection multiplicity, identify hetero-resistance patterns, enable differentiation between relapse and re-infection, and clarify transmission events across seemingly unrelated patients - even in low-coverage (1×) samples. QuantTB outperforms existing tools and promises to serve as a valuable resource for both clinicians and researchers working with clinical TB samples.
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Affiliation(s)
- Christine Anyansi
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628XE, The Netherlands.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Arlin Keo
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628XE, The Netherlands
| | - Bruce J Walker
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,Applied Invention, LLC, 486 Green Street, Cambridge, MA, 02139, USA
| | - Timothy J Straub
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628XE, The Netherlands. .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
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53
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Application of MIRU-VNTR on smear slides: a shortcut for detection of polyclonal infections in tuberculosis patients. Mol Biol Rep 2020; 47:1681-1689. [PMID: 31939062 DOI: 10.1007/s11033-020-05257-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/08/2020] [Indexed: 01/20/2023]
Abstract
Mixed (polyclonal) infections are one of the main problems in tuberculosis (TB) management. The best available method for detecting polyclonal infections in TB is mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). According to multiple studies, MIRU-VNTR method can be applied to detect TB-related polyclonal infections in sputum samples or cultures. Setup of MIRU-VNTR on smear slides can be an efficient approach, regardless of the limitations of cultures and sputum samples in many laboratories. The present study aimed at investigating the diagnostic potential of MIRU-VNTR on smear slides in detecting mixed infections. Ziehl-Neelsen-stained microscopic slides were prepared from 14 clinical specimens. For amplifying 24 MIRU-VNTR loci, PCR assay was performed on the smear slides, clinical specimens, and cultures. Based on the 24-locus MIRU-VNTR analysis, polyclonal infections were reported in 42.85% of smear slides, while the corresponding rate was estimated at 57.1% (8/14) in the clinical samples. In the corresponding cultures, the rate of mixed infection was 7.14% (1/14). Use of smear slides can be a safe option for transferring clinical specimens between environmental and reference laboratories. Considering their significant impact on TB treatment, it is essential to diagnose mixed infections in low-resource countries with a high prevalence of mixed infections. The present findings show that direct MIRU-VNTR on smear slides can be conveniently used for the detection of mixed infections.
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54
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Gomez JL, Himes BE, Kaminski N. Molecular Diagnostics in Pulmonary Infections. PRECISION IN PULMONARY, CRITICAL CARE, AND SLEEP MEDICINE 2020. [PMCID: PMC7121992 DOI: 10.1007/978-3-030-31507-8_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Infection of the lung parenchyma, or pneumonia, accounts for over four million deaths per year worldwide (Ferkol and Schraufnagel, Ann Am Thorac Soc 11:404–406, 2014). The condition is common, but also over-diagnosed, in part due to relatively poor laboratory and radiographic diagnostics. Indeed, we continue to rely on antiquated tools such as sputum culture and chest X-ray – the former of which lacks speed and sensitivity, and the latter specificity (Albaum et al. Chest 110:343–50, 1996). The resulting presumptive diagnoses of pneumonia lead to excessive use of empiric broad spectrum antibiotics; indeed, by some estimates, 30–70% of antibiotic prescriptions for lower respiratory tract infection are inappropriate (Kraus, PLoS One 12(3): e0174584, 2017). This approach begets microbial resistance, exposes patients to medication side effects, and puts patients at risk of potentially life-threatening complications including Clostridium difficile colitis. To improve diagnostic certainty in patients with suspected pneumonia, we must begin to consider and implement emerging technologies for efficient and accurate characterization of host responses to infection and identification of pathogens. In this chapter, we will discuss precision diagnostics already in common practice and those poised to be, and how these tools may ultimately enable personalization in the diagnosis of pneumonia.
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Affiliation(s)
- Jose L. Gomez
- Assistant Professor Pulmonary, Critical Care and Sleep Medicine Section, Department of Medicine, Yale University School of Medicine, New Haven, CT USA
| | - Blanca E. Himes
- Assistant Professor of Informatics, Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA USA
| | - Naftali Kaminski
- Boehringer-Ingelheim Endowed, Professor of Internal Medicine, Chief of Pulmonary, Critical Care and Sleep Medicine, Yale University School of Medicine, New Haven, CT USA
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55
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Silva-Pereira TT, Ikuta CY, Zimpel CK, Camargo NCS, de Souza Filho AF, Ferreira Neto JS, Heinemann MB, Guimarães AMS. Genome sequencing of Mycobacterium pinnipedii strains: genetic characterization and evidence of superinfection in a South American sea lion (Otaria flavescens). BMC Genomics 2019; 20:1030. [PMID: 31888476 PMCID: PMC6937676 DOI: 10.1186/s12864-019-6407-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2019] [Accepted: 12/17/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Mycobacterium pinnipedii, a member of the Mycobacterium tuberculosis Complex (MTBC), is capable of infecting several host species, including humans. Recently, ancient DNA from this organism was recovered from pre-Columbian mummies of Peru, sparking debate over the origin and frequency of tuberculosis in the Americas prior to European colonization. RESULTS We present the first comparative genomic study of this bacterial species, starting from the genome sequencing of two M. pinnipedii isolates (MP1 and MP2) obtained from different organs of a stranded South American sea lion. Our results indicate that MP1 and MP2 differ by 113 SNPs (single nucleotide polymorphisms) and 46 indels, constituting the first report of a mixed-strain infection in a sea lion. SNP annotation analyses indicate that genes of the VapBC family, a toxin-antitoxin system, and genes related to cell wall remodeling are under evolutionary pressure for protein sequence change in these strains. OrthoMCL analysis with seven modern isolates of M. pinnipedii shows that these strains have highly similar proteomes. Gene variations were only marginally associated with hypothetical proteins and PE/PPE (proline-glutamate and proline-proline-glutamate, respectively) gene families. We also detected large deletions in ancient and modern M. pinnipedii strains, including a few occurring only in modern strains, indicating a process of genome reduction occurring over the past one thousand years. Our phylogenomic analyses suggest the existence of two modern clusters of M. pinnipedii associated with geographic location, and possibly host species, and one basal node associated with the ancient M. pinnipedii strains. Previously described MiD3 and MiD4 deletions may have occurred independently, twice, over the evolutionary course of the MTBC. CONCLUSION The presence of superinfection (i.e. mixed-strain infection) in this sea lion suggests that M. pinnipedii is highly endemic in this population. Mycobacterium pinnipedii proteomes of the studied isolates showed a high degree of conservation, despite being under genomic decay when compared to M. tuberculosis. This finding indicates that further genomes need to be sequenced and analyzed to increase the chances of finding variably present genes among strains or that M. pinnipedii genome remodeling occurred prior to bacterial speciation.
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Affiliation(s)
- Taiana T Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cristina K Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila C S Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Antônio F de Souza Filho
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José S Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Marcos B Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana M S Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil. .,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil.
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56
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Pruvost O, Boyer K, Ravigné V, Richard D, Vernière C. Deciphering how plant pathogenic bacteria disperse and meet: Molecular epidemiology of Xanthomonas citri pv. citri at microgeographic scales in a tropical area of Asiatic citrus canker endemicity. Evol Appl 2019; 12:1523-1538. [PMID: 31462912 PMCID: PMC6708428 DOI: 10.1111/eva.12788] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/25/2019] [Accepted: 02/24/2019] [Indexed: 12/15/2022] Open
Abstract
Although some plant pathogenic bacteria represent a significant threat to agriculture, the determinants of their ecological success and evolutionary potential are still poorly understood. Refining our understanding of bacterial strain circulation at small spatial scales and the biological significance and evolutionary consequences of co-infections are key questions. The study of bacterial population biology can be challenging, because it requires high-resolution markers that can be genotyped with a high throughput. Here, we overcame this difficulty for Xanthomonas citri pv. citri, a genetically monomorphic bacterium causing Asiatic citrus canker (ACC). Using a genotyping method that did not require cultivating the bacterium or purifying DNA, we deciphered the pathogen's spatial genetic structure at several microgeographic scales, down to single lesion, in a situation of ACC endemicity. In a grove where copper was recurrently applied for ACC management, copper-susceptible and copper-resistant X. citri pv. citri coexisted and the bacterial population structured as three genetic clusters, suggesting a polyclonal contamination. The range of spatial dependency, estimated for the two largest clusters, was four times greater for the cluster predominantly composed of copper-resistant bacteria. Consistently, the evenness value calculated for this cluster was indicative of increased transmission. Linkage disequilibrium was high even at a tree scale, probably due to a combination of clonality and admixture. Approximately 1% of samples exhibited within-lesion multilocus polymorphism, explained at least in part by polyclonal infections. Canker lesions, which are of major biological significance as an inoculum source, may also represent a preferred niche for horizontal gene transfer. This study points out the potential of genotyping data for estimating the range of spatial dependency of plant bacterial pathogens, an important parameter for guiding disease management strategies.
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Affiliation(s)
| | | | | | - Damien Richard
- CIRADUMR PVBMTSaint Pierre, La RéunionFrance
- ANSESSaint Pierre, La RéunionFrance
- Université de la RéunionUMR PVBMTSaint Denis, La RéunionFrance
| | - Christian Vernière
- CIRADUMR PVBMTSaint Pierre, La RéunionFrance
- CIRADUMR BGPIMontpellierFrance
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57
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Schutz C, Ward A, Burton R, Nicol MP, Blumenthal L, Meintjes G, Kerkhoff AD. False rifampicin resistant results using Xpert MTB/RIF on urine samples in hospitalised HIV-infected patients. South Afr J HIV Med 2019; 20:978. [PMID: 31534789 PMCID: PMC6739559 DOI: 10.4102/sajhivmed.v20i1.978] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 05/24/2019] [Indexed: 11/01/2022] Open
Abstract
Background A small proportion of false rifampicin resistant results have previously been reported using GeneXpert MTB/RIF version G4 on sputum samples; however, this has not been investigated for urine samples in HIV-associated tuberculosis (TB). Objectives We sought to determine the proportion of false rifampicin resistant results using Xpert MTB/RIF version G4 on urine samples among HIV-infected inpatients investigated for TB. Methods Hospitalised HIV-infected patients undergoing systematic TB testing from two cohorts in Cape Town, South Africa, were enrolled. All patients with ≥1 urine Xpert result available were included. Rifampicin resistant urine Xpert results were classified into three mutually exclusive groups: (1) true rifampicin resistance, (2) false rifampicin resistance or (3) unknown after review of available microbiologic and clinical data. Results Overall, 1171 patients were included, from whom a total of 1704 urine Xpert results were available on unconcentrated and/or concentrated urine samples. There were 416 samples positive for TB (24.4% [95% CI 22.4-26.5]), of which 43/413 (10.4% [95% CI 7.6-13.8]) were rifampicin resistant (after excluding three results that were falsely positive due to contamination). Of 43 rifampicin resistant Xpert results (among 40 patients), 30 were classified as true resistance, 11 as false resistance and 2 could not be classified. Excluding unclassifiable results, 30/41 results were confirmed as true-positive urine Xpert rifampicin resistance (positive predictive value: 73.2% [95% CI 57.1-85.8]). Conclusion Urine Xpert testing showed a high proportion of false rifampicin resistance results. Urine Xpert rifampicin resistant results should be interpreted cautiously and confirmed when possible.
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Affiliation(s)
- Charlotte Schutz
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM) and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Amy Ward
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM) and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Rosie Burton
- GF Jooste Hospital; Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Division of Medical Microbiology, University of Cape Town and National Health Laboratory Services, Cape Town, South Africa
| | - Liz Blumenthal
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM) and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Graeme Meintjes
- Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM) and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Andrew D Kerkhoff
- Division of HIV, Infectious Diseases and Global Medicine at Zuckerberg San Francisco General Hospital and Trauma Center, Department of Medicine, University of California, San Francisco, United States
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58
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Novel clinical and dual infection by Histoplasma capsulatum genotypes in HIV patients from Northeastern, Brazil. Sci Rep 2019; 9:11789. [PMID: 31409874 PMCID: PMC6692370 DOI: 10.1038/s41598-019-48111-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
Histoplasmosis is a worldwide-distributed deep mycosis that affects healthy and immunocompromised hosts. Severe and disseminated disease is especially common in HIV-infected patients. At least 11 phylogenetic species are recognized and the majority of diversity is found in Latin America. The northeastern region of Brazil has one of the highest HIV/AIDS prevalence in Latin America and Ceará State has one of the highest death rates due to histoplasmosis in the world, where the mortality rate varies between 33-42%. The phylogenetic distribution and population genetic structure of 51 clinical isolates from Northeast Brazil was studied. For that morphological characteristics, exoantigens profile, and fungal mating types were evaluated. The genotypes were deduced by a MSLT in order to define local population structure of this fungal pathogen. In addition, the relationships of H. capsulatum genotypes with clinically relevant phenotypes and clinical aspects were investigated. The results suggest two cryptic species, herein named population Northeast BR1 and population Northeast BR2. These populations are recombining, exhibit a high level of haplotype diversity, and contain different ratios of mating types MAT1-1 and MAT1-2. However, differences in phenotypes or clinical aspects were not observed within these new cryptic species. A HIV patient can be co-infected by two or more genotypes from Northeast BR1 and/or Northeast BR2, which may have significant impact on disease progression due to the impaired immune response. We hypothesize that co-infections could be the result of multiple exposure events and may indicate higher risk of disseminated histoplasmosis, especially in HIV infected patients.
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van Leeuwen LM, Versteegen P, Zaharie SD, van Elsland SL, Jordaan A, Streicher EM, Warren RM, van der Kuip M, van Furth AM. Bacterial Genotyping of Central Nervous System Tuberculosis in South Africa: Heterogenic Mycobacterium tuberculosis Infection and Predominance of Lineage 4. J Clin Microbiol 2019; 57:e00415-19. [PMID: 31189579 PMCID: PMC6663911 DOI: 10.1128/jcm.00415-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/30/2019] [Indexed: 12/20/2022] Open
Abstract
Tuberculous meningitis (TBM), the most severe extrapulmonary manifestation of tuberculosis, is caused by the pathogen Mycobacterium tuberculosis The M. tuberculosis complex includes seven lineages, all described to harbor a unique geographical dissemination pattern and clinical presentation. In this study, we set out to determine whether a certain M. tuberculosis lineage demonstrated tropism to cause TBM in patients from Cape Town, South Africa. DNA was extracted from formalin-fixed paraffin-embedded central nervous system (CNS) tissue from a unique neuropathological cohort of 83 TBM patients, collected between 1975 and 2012. M. tuberculosis lineages 1, 2, 3, and 4 were determined using an allele-specific PCR and Sanger sequencing. Of the 83 patient specimens tested, bacterial characterization could be performed on 46 specimens (55%). M. tuberculosis lineage 4 was present in 26 patient specimens (56%), and non-lineage 4 was identified in 10 cases (22%). Moreover, genomic heterogeneity was detected in the CNS specimens of 7 adults and 3 children. We could show that infection of the CNS is not restricted to a single M. tuberculosis lineage and that even young children with rapid progression of disease can harbor more than one M. tuberculosis lineage in the CNS.
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Affiliation(s)
- L M van Leeuwen
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - P Versteegen
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - S D Zaharie
- Department of Anatomical Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - S L van Elsland
- Department of Paediatrics and Child Health, Tygerberg Hospital, Stellenbosch University, Cape Town, South Africa
| | - A Jordaan
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - E M Streicher
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - R M Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DST-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - M van der Kuip
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - A M van Furth
- Department of Pediatric Infectious Diseases and Immunology, Amsterdam Infection & Immunity Institute, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
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60
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Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019; 11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998, WGS has provided a more complete account of the genomic features that cause resistance in populations of M. tuberculosis, has helped to fill gaps in our knowledge of how both classical and new antitubercular drugs work, and has identified specific mutations that allow M. tuberculosis to escape the effects of these drugs. WGS studies have also revealed how resistance evolves both within an individual patient and within patient populations, including the important roles of de novo acquisition of resistance and clonal spread. These findings have informed decisions about which drug-resistance mutations should be included on extended diagnostic panels. From its origins as a basic science technique, WGS of M. tuberculosis is becoming part of the modern clinical microbiology laboratory, promising rapid and improved detection of drug resistance, and detailed and real-time epidemiology of TB outbreaks. We review the successes and highlight the challenges that remain in applying WGS to improve the control of drug-resistant TB through monitoring its evolution and spread, and to inform more rapid and effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, 21205, USA.
| | - Abigail L Manson
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, 2628, XE, Delft, The Netherlands
| | - Ashlee M Earl
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA.
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61
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Kargarpour Kamakoli M, Hadifar S, Khanipour S, Farmanfarmaei G, Fateh A, Siadat SD, Vaziri F. Comparison of MIRU-VNTR genotyping between old and fresh clinical samples in tuberculosis. Infect Dis (Lond) 2019; 51:659-667. [PMID: 31314640 DOI: 10.1080/23744235.2019.1638963] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Background: Twenty-four loci mycobacterial interspersed repetitive unit-variable number tandem repeat analysis (MIRU-VNTR) is extensively used for genotyping and detection of polyclonal infections in tuberculosis. The aim of the present study was to compare the direct and indirect MIRU-VNTR genotyping and detection of polyclonal infections between old and fresh clinical samples. Method: Two series of TB samples were collected for comparison. After genomic DNA extraction from clinical samples and their respective cultures, 24 loci MIRU-VNTR was performed. Results: In the 14 old samples, no mixed infections were observed, in clinical samples and their respective cultures. In nine fresh samples, 44.4% of mixed infection was observed in the clinical samples, but no mixed infections were observed in their respective cultures. Surprisingly, in the old samples, 92.86% of samples (13/14) had an allelic change between clinical samples and their respective cultures. On the other hand, in fresh samples, only one sample (1/9) had an allelic change between clinical samples and their respective cultures. Conclusions: We concluded that 24 loci MIRU-VNTR undoubtedly is successful in direct genotyping of clinical samples, especially for the fresh samples. However, selecting starting material, such as clinical sample or respective culture can be controversial for the old samples. Regarding polyclonal infections, the fresh samples gives us a better view to detect these infections, especially in the clinical sample.
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Affiliation(s)
- Mansour Kargarpour Kamakoli
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Shima Hadifar
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Sharareh Khanipour
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Ghazaleh Farmanfarmaei
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Abolfazl Fateh
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Seyed Davar Siadat
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
| | - Farzam Vaziri
- a Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran , Tehran , Iran.,b Microbiology Research Center (MRC), Pasteur Institute of Iran , Tehran , Iran
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Konstantynovska O, Rekrotchuk M, Hrek I, Rohozhyn A, Rudova N, Poteiko P, Gerilovych A, Bortz E, Solodiankin O. Severe Clinical Outcomes of Tuberculosis in Kharkiv Region, Ukraine, Are Associated with Beijing Strains of Mycobacterium tuberculosis. Pathogens 2019; 8:pathogens8020075. [PMID: 31185670 PMCID: PMC6631893 DOI: 10.3390/pathogens8020075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022] Open
Abstract
Genotypic variation in Beijing lineages of Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has been associated with hyper virulence and the spread of extensively and multiple drug (X/MDR) resistant MTB strains in Eastern Europe, Central Asia, and East Asia. The clinical outcomes of 215 new cases of TB among the population of the Kharkiv region of Eastern Ukraine were analyzed to uncover factors associated with severe infection. Infecting MTB strains were profiled by 5 locus exact tandem repeats (ETRs) and 15 locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping. Among diverse MTB genotypes discovered in Ukraine, the Beijing genotype (MIRU-VNTR 42425) was significantly associated with risk factors for severe outcomes of disease in the study population, including TB/HIV co-infection and treatment failure. Strain replacement (superinfection) was observed in 10 patients, suggesting repeated exposure to novel MTB strains in hospital or community settings. Inclusion of MTB genotyping data may identify at-risk patients and improve treatment adherence to prevent X/MDR development for effective public health response against tuberculosis in Ukraine.
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Affiliation(s)
| | - Mariia Rekrotchuk
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Ivan Hrek
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Rohozhyn
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Nataliia Rudova
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Petro Poteiko
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Gerilovych
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.
| | - Oleksii Solodiankin
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
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63
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Khachatryan L, Kraakman MEM, Bernards AT, Laros JFJ. BacTag - a pipeline for fast and accurate gene and allele typing in bacterial sequencing data based on database preprocessing. BMC Genomics 2019; 20:338. [PMID: 31060512 PMCID: PMC6501397 DOI: 10.1186/s12864-019-5723-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 04/22/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Bacteria carry a wide array of genes, some of which have multiple alleles. These different alleles are often responsible for distinct types of virulence and can determine the classification at the subspecies levels (e.g., housekeeping genes for Multi Locus Sequence Typing, MLST). Therefore, it is important to rapidly detect not only the gene of interest, but also the relevant allele. Current sequencing-based methods are limited to mapping reads to each of the known allele reference, which is a time-consuming procedure. RESULTS To address this limitation, we developed BacTag - a pipeline that rapidly and accurately detects which genes are present in a sequencing dataset and reports the allele of each of the identified genes. We exploit the fact that different alleles of the same gene have a high similarity. Instead of mapping the reads to each of the allele reference sequences, we preprocess the database prior to the analysis, which makes the subsequent gene and allele identification efficient. During the preprocessing, we determine a representative reference sequence for each gene and store the differences between all alleles and this chosen reference. Throughout the analysis we estimate whether the gene is present in the sequencing data by mapping the reads to this reference sequence; if the gene is found, we compare the variants to those in the preprocessed database. This allows to detect which specific allele is present in the sequencing data. Our pipeline was successfully tested on artificial WGS E. coli, S. pseudintermedius, P. gingivalis, M. bovis, Borrelia spp. and Streptomyces spp. data and real WGS E. coli and K. pneumoniae data in order to report alleles of MLST house-keeping genes. CONCLUSIONS We developed a new pipeline for fast and accurate gene and allele recognition based on database preprocessing and parallel computing and performed better or comparable to the current popular tools. We believe that our approach can be useful for a wide range of projects, including bacterial subspecies classification, clinical diagnostics of bacterial infections, and epidemiological studies.
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Affiliation(s)
- Lusine Khachatryan
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Margriet E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexandra T Bernards
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen F J Laros
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.,GenomeScan, Leiden, The Netherlands
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64
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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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65
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Rao M, Ippolito G, Mfinanga S, Ntoumi F, Yeboah-Manu D, Vilaplana C, Zumla A, Maeurer M. Latent TB Infection (LTBI) - Mycobacterium tuberculosis pathogenesis and the dynamics of the granuloma battleground. Int J Infect Dis 2019; 80S:S58-S61. [PMID: 30822547 DOI: 10.1016/j.ijid.2019.02.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 02/22/2019] [Indexed: 11/17/2022] Open
Abstract
Latent tuberculosis infection (LTBI) is established in over 90% of persons infected with Mycobacterium tuberculosis (Mtb), from whom new active TB cases will arise. Understanding the spatio-temporal dynamics of host immune responses in LTBI granulomas is essential to designing effective post-exposure therapies that inhibit progression to TB. Information arising from cancer studies and other modalities - where local chronic inflammation leads to immunopathology - can help provide insights into the biological pathways at play in LTBI granulomas. Translational studies using patient material as well as LTBI+ donor-derived tissue samples are instrumental in understanding the various components of granuloma dynamics, immunological landscapes therein and how this could help to identify therapeutic targets. Deep sequencing technologies may aid to decipher the genetic changes in lung granuloma and blood samples from LTBI+ individuals associated with progression to active TB disease. This may lead to advancement of development of targeted Host-Directed Therapies (HDTs) and their evaluation as adjunct TB therapies for improving treatment outcomes for LTBI and pulmonary TB.
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Affiliation(s)
- Martin Rao
- Champalimaud Centre for the Unknown, Lisbon, Portugal.
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases, Lazzaro Spallanzani, Rome, Italy.
| | - Sayoki Mfinanga
- National Institute of Medical Research Muhimbili, Dar es Salaam, Tanzania.
| | - Francine Ntoumi
- University Marien NGouabi and Fondation Congolaise pour la Recherche Médicale (FCRM), Brazzaville, Congo; Institute for Tropical Medicine, University of Tübingen, Germany.
| | - Dorothy Yeboah-Manu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, Accra, Ghana.
| | - Cristina Vilaplana
- Experimental Tuberculosis Unit (UTE), Fundació Institut Germans Trias i Pujol (IGTP), Universitat Autònoma de Barcelona (UAB), Badalona, Catalonia, Spain.
| | - Alimuddin Zumla
- Division of Infection and Immunity, University College London and NIHR Biomedical Research Centre, UCL Hospitals NHS Foundation Trust, London, UK.
| | - Markus Maeurer
- Champalimaud Centre for the Unknown, Avenida Brasília, 1400-038 Lisbon, Portugal; Department of Haematology and Oncology, Krankenhaus Nordwest, Frankfurt, Germany.
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66
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Wood HN, Venken T, Willems H, Jacobs A, Reis AJ, Almeida da Silva PE, Homolka S, Niemann S, Rohde KH, Hooyberghs J. Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization. PLoS One 2019; 14:e0212064. [PMID: 30730960 PMCID: PMC6366778 DOI: 10.1371/journal.pone.0212064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 01/25/2019] [Indexed: 11/19/2022] Open
Abstract
In Mycobacterium tuberculosis (Mtb) the detection of single nucleotide polymorphisms (SNPs) is of high importance both for diagnostics, since drug resistance is primarily caused by the acquisition of SNPs in multiple drug targets, and for epidemiological studies in which strain typing is performed by SNP identification. To provide the necessary coverage of clinically relevant resistance profiles and strain types, nucleic acid-based measurement techniques must be able to detect a large number of potential SNPs. Since the Mtb problem is pressing in many resource-poor countries, requiring low-cost point-of-care biosensors, this is a non-trivial technological challenge. This paper presents a proof-of-concept in which we chose simple DNA-DNA hybridization as a sensing principle since this can be transferred to existing low-cost hardware platforms, and we pushed the multiplex boundaries of it. With a custom designed probe set and a physicochemical-driven data analysis it was possible to simultaneously detect the presence of SNPs associated with first- and second-line drug resistance and Mtb strain typing. We have demonstrated its use for the identification of drug resistance and strain type from a panel of phylogenetically diverse clinical strains. Furthermore, reliable detection of the presence of a minority population (<5%) of drug-resistant Mtb was possible.
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Affiliation(s)
- Hillary N. Wood
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
| | - Tom Venken
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Hanny Willems
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - An Jacobs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Ana Júlia Reis
- Laboratory of Tuberculosis, Faculty of Medicine, Universidade Federal do Rio Grande- FURG, Rio Grande so Sul, RS, Brazil
| | - Pedro Eduardo Almeida da Silva
- Laboratory of Tuberculosis, Faculty of Medicine, Universidade Federal do Rio Grande- FURG, Rio Grande so Sul, RS, Brazil
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Borstel, Germany
| | - Kyle H. Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, United States of America
- * E-mail:
| | - Jef Hooyberghs
- Flemish Institute for Technological Research, VITO, Mol, Belgium
- Theoretical Physics, Hasselt University, Diepenbeek, Belgium
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67
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Zürcher K, Ballif M, Fenner L, Borrell S, Keller PM, Gnokoro J, Marcy O, Yotebieng M, Diero L, Carter EJ, Rockwood N, Wilkinson RJ, Cox H, Ezati N, Abimiku AG, Collantes J, Avihingsanon A, Kawkitinarong K, Reinhard M, Hömke R, Huebner R, Gagneux S, Böttger EC, Egger M. Drug susceptibility testing and mortality in patients treated for tuberculosis in high-burden countries: a multicentre cohort study. THE LANCET. INFECTIOUS DISEASES 2019; 19:298-307. [PMID: 30744962 DOI: 10.1016/s1473-3099(18)30673-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 10/07/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Drug resistance is a challenge for the global control of tuberculosis. We examined mortality in patients with tuberculosis from high-burden countries, according to concordance or discordance of results from drug susceptibility testing done locally and in a reference laboratory. METHODS This multicentre cohort study was done in Côte d'Ivoire, Democratic Republic of the Congo, Kenya, Nigeria, South Africa, Peru, and Thailand. We collected Mycobacterium tuberculosis isolates and clinical data from adult patients aged 16 years or older. Patients were stratified by HIV status and tuberculosis drug resistance. Molecular or phenotypic drug susceptibility testing was done locally and at the Swiss National Center for Mycobacteria, Zurich, Switzerland. We examined mortality during treatment according to drug susceptibility test results and treatment adequacy in multivariable logistic regression models adjusting for sex, age, sputum microscopy, and HIV status. FINDINGS We obtained M tuberculosis isolates from 871 patients diagnosed between 2013 and 2016. After exclusion of 237 patients, 634 patients with tuberculosis were included in this analysis; the median age was 33·2 years (IQR 26·9-42·5), 239 (38%) were women, 272 (43%) were HIV-positive, and 69 (11%) patients died. Based on the reference laboratory drug susceptibility test, 394 (62%) strains were pan-susceptible, 45 (7%) monoresistant, 163 (26%) multidrug-resistant (MDR), and 30 (5%) had pre-extensively or extensively drug resistant (pre-XDR or XDR) tuberculosis. Results of reference and local laboratories were concordant for 513 (81%) of 634 patients and discordant for 121 (19%) of 634. Overall, sensitivity to detect any resistance was 90·8% (95% CI 86·5-94·2) and specificity 84·3% (80·3-87·7). Mortality ranged from 6% (20 of 336) in patients with pan-susceptible tuberculosis treated according to WHO guidelines to 57% (eight of 14) in patients with resistant strains who were under-treated. In logistic regression models, compared with concordant drug susceptibility test results, the adjusted odds ratio of death was 7·33 (95% CI 2·70-19·95) for patients with discordant results potentially leading to under-treatment. INTERPRETATION Inaccurate drug susceptibility testing by comparison with a reference standard leads to under-treatment of drug-resistant tuberculosis and increased mortality. Rapid molecular drug susceptibility test of first-line and second-line drugs at diagnosis is required to improve outcomes in patients with MDR tuberculosis and pre-XDR or XDR tuberculosis. FUNDING National Institutes of Allergy and Infectious Diseases, Swiss National Science Foundation, Swiss National Center for Mycobacteria.
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Affiliation(s)
- Kathrin Zürcher
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Marie Ballif
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Lukas Fenner
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Joachim Gnokoro
- Centre de Prise en Charge de Recherche et de Formation, Yopougon, Abidjan, Côte d'Ivoire
| | - Olivier Marcy
- Bordeaux Population Health Research Center, Inserm U1219, University of Bordeaux, Bordeaux, France
| | - Marcel Yotebieng
- Ohio State University, College of Public Health, Columbus, OH, USA
| | - Lameck Diero
- Department of Medicine, Moi University School of Medicine, and Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - E Jane Carter
- Department of Medicine, Moi University School of Medicine, and Moi Teaching and Referral Hospital, Eldoret, Kenya
| | - Neesha Rockwood
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa; Department of Medicine, Imperial College London, London, UK
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa; Department of Medicine, Imperial College London, London, UK; Francis Crick Institute, London, UK
| | - Helen Cox
- Division of Medical Microbiology and the Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicholas Ezati
- Institute of Human Virology, Abuja, Nigeria; National Tuberculosis and Leprosy Training Center, Saye, Zaria, Kaduna State, Nigeria
| | | | - Jimena Collantes
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Kamon Kawkitinarong
- HIV-NAT/Thai Red Cross AIDS Research Centre, Bangkok, Thailand; Tuberculosis Research Unit, Department of Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Rico Hömke
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Robin Huebner
- National Institutes of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine (ISPM), University of Bern, Bern, Switzerland; Centre for Infectious Disease Epidemiology & Research, School of Public Health & Family Medicine, University of Cape Town, Cape Town, South Africa.
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68
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Nelson KN, Shah NS, Mathema B, Ismail N, Brust JCM, Brown TS, Auld SC, Omar SV, Morris N, Campbell A, Allana S, Moodley P, Mlisana K, Gandhi NR. Spatial Patterns of Extensively Drug-Resistant Tuberculosis Transmission in KwaZulu-Natal, South Africa. J Infect Dis 2018; 218:1964-1973. [PMID: 29961879 PMCID: PMC6217717 DOI: 10.1093/infdis/jiy394] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 06/26/2018] [Indexed: 12/29/2022] Open
Abstract
Background Transmission is driving the global drug-resistant tuberculosis (TB) epidemic; nearly three-quarters of drug-resistant TB cases are attributable to transmission. Geographic patterns of disease incidence, combined with information on probable transmission links, can define the spatial scale of transmission and generate hypotheses about factors driving transmission patterns. Methods We combined whole-genome sequencing data with home Global Positioning System coordinates from 344 participants with extensively drug-resistant (XDR) TB in KwaZulu-Natal, South Africa, diagnosed from 2011 to 2014. We aimed to determine if genomically linked (difference of ≤5 single-nucleotide polymorphisms) cases lived close to one another, which would suggest a role for local community settings in transmission. Results One hundred eighty-two study participants were genomically linked, comprising 1084 case-pairs. The median distance between case-pairs' homes was 108 km (interquartile range, 64-162 km). Between-district, as compared to within-district, links accounted for the majority (912/1084 [84%]) of genomic links. Half (526 [49%]) of genomic links involved a case from Durban, the urban center of KwaZulu-Natal. Conclusions The high proportions of between-district links with Durban provide insight into possible drivers of province-wide XDR-TB transmission, including urban-rural migration. Further research should focus on characterizing the contribution of these drivers to overall XDR-TB transmission in KwaZulu-Natal to inform design of targeted strategies to curb the drug-resistant TB epidemic.
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Affiliation(s)
- Kristin N Nelson
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - N Sarita Shah
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York, New York
| | - Nazir Ismail
- National Institute for Communicable Diseases, Johannesburg
- University of Pretoria, South Africa
| | - James C M Brust
- Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York
| | - Tyler S Brown
- Infectious Diseases Division, Massachusetts General Hospital, Boston
| | - Sara C Auld
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Emory University School of Medicine, Atlanta, Georgia
| | | | - Natashia Morris
- Environment and Health Research Unit, South African Medical Research Council, Johannesburg
| | - Angie Campbell
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Salim Allana
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Pravi Moodley
- National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Neel R Gandhi
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Emory University School of Medicine, Atlanta, Georgia
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69
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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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Identifying Mixed Mycobacterium tuberculosis Infection and Laboratory Cross-Contamination during Mycobacterial Sequencing Programs. J Clin Microbiol 2018; 56:JCM.00923-18. [PMID: 30209183 PMCID: PMC6204665 DOI: 10.1128/jcm.00923-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 08/28/2018] [Indexed: 11/20/2022] Open
Abstract
The detection of laboratory cross-contamination and mixed tuberculosis infections is an important goal of clinical mycobacteriology laboratories. The objective of this study was to develop a method to detect mixtures of different Mycobacterium tuberculosis lineages in laboratories performing mycobacterial next-generation sequencing (NGS). The setting was the Public Health England National Mycobacteriology Laboratory Birmingham, which performs Illumina sequencing on DNA extracted from positive mycobacterial growth indicator tubes. We analyzed 4,156 samples yielding M. tuberculosis from 663 MiSeq runs, which were obtained during development and production use of a diagnostic process using NGS. The counts of the most common (major) variant and all other variants (nonmajor variants) were determined from reads mapping to positions defining M. tuberculosis lineages. Expected variation was estimated during process development. For each sample, we determined the nonmajor variant proportions at 55 sets of lineage-defining positions. The nonmajor variant proportion in the two most mixed lineage-defining sets (F2 metric) was compared with that of the 47 least-mixed lineage-defining sets (F47 metric). The following three patterns were observed: (i) not mixed by either metric; (ii) high F47 metric, suggesting mixtures of multiple lineages; and (iii) samples compatible with mixtures of two lineages, detected by differential F2 metric elevations relative to F47. Pattern ii was observed in batches, with similar patterns in the M. tuberculosis H37Rv control present in each run, and is likely to reflect cross-contamination. During production, the proportions of samples in the patterns were 97%, 2.8%, and 0.001%, respectively. The F2 and F47 metrics described could be used for laboratory process control in laboratories sequencing M. tuberculosis genomes.
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Cadena AM, Hopkins FF, Maiello P, Carey AF, Wong EA, Martin CJ, Gideon HP, DiFazio RM, Andersen P, Lin PL, Fortune SM, Flynn JL. Concurrent infection with Mycobacterium tuberculosis confers robust protection against secondary infection in macaques. PLoS Pathog 2018; 14:e1007305. [PMID: 30312351 PMCID: PMC6200282 DOI: 10.1371/journal.ppat.1007305] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 10/24/2018] [Accepted: 09/13/2018] [Indexed: 02/03/2023] Open
Abstract
For many pathogens, including most targets of effective vaccines, infection elicits an immune response that confers significant protection against reinfection. There has been significant debate as to whether natural Mycobacterium tuberculosis (Mtb) infection confers protection against reinfection. Here we experimentally assessed the protection conferred by concurrent Mtb infection in macaques, a robust experimental model of human tuberculosis (TB), using a combination of serial imaging and Mtb challenge strains differentiated by DNA identifiers. Strikingly, ongoing Mtb infection provided complete protection against establishment of secondary infection in over half of the macaques and allowed near sterilizing bacterial control for those in which a secondary infection was established. By contrast, boosted BCG vaccination reduced granuloma inflammation but had no impact on early granuloma bacterial burden. These findings are evidence of highly effective concomitant mycobacterial immunity in the lung, which may inform TB vaccine design and development.
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Affiliation(s)
- Anthony M. Cadena
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Forrest F. Hopkins
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Pauline Maiello
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Allison F. Carey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Eileen A. Wong
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Constance J. Martin
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Hannah P. Gideon
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Robert M. DiFazio
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | | | - Philana Ling Lin
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, United States of America
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, United States of America
| | - JoAnne L. Flynn
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
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Naidoo K, Dookie N, Naidoo K, Yende-Zuma N, Chimukangara B, Bhushan A, Govender D, Gengiah S, Padayatchi N. Recurrent tuberculosis among HIV-coinfected patients: a case series from KwaZulu-Natal. Infect Drug Resist 2018; 11:1413-1421. [PMID: 30233220 PMCID: PMC6130302 DOI: 10.2147/idr.s150644] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background Recurrent tuberculosis (TB) following TB treatment completion in HIV-infected individuals remains a major public health burden. We assessed the role of various risk factors in mediating the development of recurrent TB and subsequent resistance to antiretroviral therapy and anti-TB drugs. Patients and methods We analyzed secondary demographic, clinical, and laboratory data from medical records of five HIV-infected TB patients enrolled between 2009 and 2014 in a prospective observational study investigating TB recurrence. Paired clinical isolates of Myco-bacterium tuberculosis were typed by IS6110 restriction fragment length polymorphism analysis to determine the mechanism of TB recurrence. Plasma samples were genotyped to determine acquisition of HIV drug resistance mutations on antiretroviral treatment (ART). Results All five patients were HIV-coinfected, with a previous history of TB infection and prior exposure to anti-TB treatment, and residual lung damage, and demonstrated poor treatment adherence – significant risk factors linked to the development of recurrent TB disease. Furthermore, three of the five patients had multiple episodes of drug-susceptible TB infection with subsequent drug-resistant TB infection. Genotyping of the initial and recurrent M. tuberculosis isolates demonstrated three cases of recurrent TB because of relapse and two because of reinfection. All five patients had no mutations at ART initiation; however, by the end of the study follow-up, all patients developed dual class resistance. Conclusion This series demonstrates the complexity of recurrent TB in HIV coinfection. We highlight the challenges of managing coinfected patients and the increased propensity for the development of drug resistance. We report on the role of various risk factors mediating the development of resistance and subsequent clinical impact. This report underscores the need for structural clinical and adherence interventions for the management of complex treatment and dosing.
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Affiliation(s)
- Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa, .,South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa,
| | - Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa, .,KwaZulu Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa
| | - Kasavan Naidoo
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa,
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa,
| | - Benjamin Chimukangara
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa, .,KwaZulu Natal Research Innovation and Sequencing Platform (KRISP), University of KwaZulu-Natal, Durban, South Africa.,Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
| | - Ambika Bhushan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa,
| | - Dhineshree Govender
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa,
| | - Santhanalakshmi Gengiah
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa,
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa, .,South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa,
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Sobkowiak B, Glynn JR, Houben RMGJ, Mallard K, Phelan JE, Guerra-Assunção JA, Banda L, Mzembe T, Viveiros M, McNerney R, Parkhill J, Crampin AC, Clark TG. Identifying mixed Mycobacterium tuberculosis infections from whole genome sequence data. BMC Genomics 2018; 19:613. [PMID: 30107785 PMCID: PMC6092779 DOI: 10.1186/s12864-018-4988-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 07/31/2018] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Mixed, polyclonal Mycobacterium tuberculosis infection occurs in natural populations. Developing an effective method for detecting such cases is important in measuring the success of treatment and reconstruction of transmission between patients. Using whole genome sequence (WGS) data, we assess two methods for detecting mixed infection: (i) a combination of the number of heterozygous sites and the proportion of heterozygous sites to total SNPs, and (ii) Bayesian model-based clustering of allele frequencies from sequencing reads at heterozygous sites. RESULTS In silico and in vitro artificially mixed and known pure M. tuberculosis samples were analysed to determine the specificity and sensitivity of each method. We found that both approaches were effective in distinguishing between pure strains and mixed infection where there was relatively high (> 10%) proportion of a minor strain in the mixture. A large dataset of clinical isolates (n = 1963) from the Karonga Prevention Study in Northern Malawi was tested to examine correlations with patient characteristics and outcomes with mixed infection. The frequency of mixed infection in the population was found to be around 10%, with an association with year of diagnosis, but no association with age, sex, HIV status or previous tuberculosis. CONCLUSIONS Mixed Mycobacterium tuberculosis infection was identified in silico using whole genome sequence data. The methods presented here can be applied to population-wide analyses of tuberculosis to estimate the frequency of mixed infection, and to identify individual cases of mixed infections. These cases are important when considering the evolution and transmission of the disease, and in patient treatment.
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Affiliation(s)
- Benjamin Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Rein M. G. J. Houben
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- TB Modelling Group, TB Centre, London School of Hygiene and Tropical Medicine, London, UK
| | - Kim Mallard
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - José Afonso Guerra-Assunção
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Bill Lyons Informatics Centre, University College London, London, UK
| | | | | | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Amelia C. Crampin
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
- Karonga Prevention Study, Chilumba, Malawi
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
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Genetic diversity of Mycobacterium tuberculosis complex isolates circulating in an area with high tuberculosis incidence: Using 24-locus MIRU-VNTR method. Tuberculosis (Edinb) 2018; 112:89-97. [PMID: 30205974 DOI: 10.1016/j.tube.2018.08.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 07/15/2018] [Accepted: 08/02/2018] [Indexed: 01/24/2023]
Abstract
We aimed to determine the genetic diversity, phylogenetic relationship and transmission dynamics of Mycobacterium tuberculosis complex (MTBC) genotypes in an area with high tuberculosis (TB) incidence. A set of 164 MTBC isolates from new TB patients of Golestan province, Iran, were subjected to genotyping using the standard 24-locus MIRU-VNTR method. Recent TB transmission was evaluated and phylogenetic relationships were analysed by minimum spanning tree and cluster-graph methods. Among the 164 isolates, 132 distinct patterns were detected. The 48 clustered isolates (29.3%) were distributed into 16 clusters ranging in size from 2 to 12 isolates. The most frequent genotype was Central Asian Strain/Delhi (CAS/Delhi) (n = 67, 40.8%), followed by NEW-1 (n = 53, 32.3%) and Beijing (n = 19, 11.6%) genotypes. Thirty five (72.9%) of NEW-1 isolates were recovered from immigrant patients and 84.2% (n = 16) of Beijing genotypes recovered from native cases. Statistically significant association was found between clustering and smoking (p = 0.047), drug addiction (p = 0.01) and prison history (p = 0.003). The estimated proportion of recent transmission was 19.5%. Presence of highly diverse MTBC isolates circulating in this province without a dominant genotype might be a consequence of importation of various genotypes in this area.
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75
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Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing. J Clin Microbiol 2018; 56:JCM.00666-18. [PMID: 29848567 PMCID: PMC6062781 DOI: 10.1128/jcm.00666-18] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
The current methods available to diagnose antimicrobial-resistant Mycobacterium tuberculosis infections require a positive culture or only test a limited number of resistance-associated mutations. A rapid accurate identification of antimicrobial resistance enables the prompt initiation of effective treatment. Here, we determine the utility of whole-genome sequencing (WGS) of M. tuberculosis directly from routinely obtained diagnostic sputum samples to provide a comprehensive resistance profile compared to that from mycobacterial growth indicator tube (MGIT) WGS. We sequenced M. tuberculosis from 43 sputum samples by targeted DNA enrichment using the Agilent SureSelectXT kit, and 43 MGIT positive samples from each participant. Thirty two (74%) sputum samples and 43 (100%) MGIT samples generated whole genomes. The times to antimicrobial resistance profiles and concordance were compared with Xpert MTB/RIF and phenotypic resistance testing from cultures of the same samples. Antibiotic susceptibility could be predicted from WGS of sputum within 5 days of sample receipt and up to 24 days earlier than WGS from MGIT culture and up to 31 days earlier than phenotypic testing. Direct sputum results could be reduced to 3 days with faster hybridization and if only regions encoding drug resistance are sequenced. We show that direct sputum sequencing has the potential to provide comprehensive resistance detection significantly faster than MGIT whole-genome sequencing or phenotypic testing of resistance from cultures in a clinical setting. This improved turnaround time enables prompt appropriate treatment with associated patient and health service benefits. Improvements in sample preparation are necessary to ensure comparable sensitivities and complete resistance profile predictions in all cases.
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76
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Challenge in direct Spoligotyping of Mycobacterium tuberculosis: a problematic issue in the region with high prevalence of polyclonal infections. BMC Res Notes 2018; 11:486. [PMID: 30016972 PMCID: PMC6050728 DOI: 10.1186/s13104-018-3579-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/06/2018] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Based on our recent studies the prevalence of polyclonal infection in tuberculosis clinical specimens is more than 50% in Tehran, Iran. With this background, Spoligotyping was performed on clinical specimens and their respective cultures, and we examined whether mixed infections interfere with the results or not. RESULTS Based on the Spoligotyping pattern, among the fourteen patients, 57.1% had different genotypes in clinical samples and their respective cultures. These discrepant patterns were suggestive of polyclonal infections in clinical samples with possible overlapping Spoligotype patterns. We propose that in societies with high mixed infections (e.g. Iran), direct Spoligotyping on clinical samples can be controversial.
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77
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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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78
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Auld SC, Shah NS, Cohen T, Martinson NA, Gandhi NR. Where is tuberculosis transmission happening? Insights from the literature, new tools to study transmission and implications for the elimination of tuberculosis. Respirology 2018; 23:10.1111/resp.13333. [PMID: 29869818 PMCID: PMC6281783 DOI: 10.1111/resp.13333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/14/2018] [Accepted: 05/20/2018] [Indexed: 12/12/2022]
Abstract
More than 10 million new cases of tuberculosis (TB) are diagnosed worldwide each year. The majority of these cases occur in low- and middle-income countries where the TB epidemic is predominantly driven by transmission. Efforts to 'end TB' will depend upon our ability to halt ongoing transmission. However, recent studies of new approaches to interrupt transmission have demonstrated inconsistent effects on reducing population-level TB incidence. TB transmission occurs across a wide range of settings, that include households and hospitals, but also community-based settings. While home-based contact investigations and infection control programmes in hospitals and clinics have a successful track record as TB control activities, there is a gap in our knowledge of where, and between whom, community-based transmission of TB occurs. Novel tools, including molecular epidemiology, geospatial analyses and ventilation studies, provide hope for improving our understanding of transmission in countries where the burden of TB is greatest. By integrating these diverse and innovative tools, we can enhance our ability to identify transmission events by documenting the opportunity for transmission-through either an epidemiologic or geospatial connection-alongside genomic evidence for transmission, based upon genetically similar TB strains. A greater understanding of locations and patterns of transmission will translate into meaningful improvements in our current TB control activities by informing targeted, evidence-based public health interventions.
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Affiliation(s)
- Sara C Auld
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - N Sarita Shah
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Center for TB Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neel R Gandhi
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
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79
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Schneider KA. Large and finite sample properties of a maximum-likelihood estimator for multiplicity of infection. PLoS One 2018; 13:e0194148. [PMID: 29630605 PMCID: PMC5890990 DOI: 10.1371/journal.pone.0194148] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 02/26/2018] [Indexed: 12/30/2022] Open
Abstract
Reliable measures of transmission intensities can be incorporated into metrics for monitoring disease-control interventions. Genetic (molecular) measures like multiplicity of infection (MOI) have several advantages compared with traditional measures, e.g., R0. Here, we investigate the properties of a maximum-likelihood approach to estimate MOI and pathogen-lineage frequencies. By verifying regulatory conditions, we prove asymptotical unbiasedness, consistency and efficiency of the estimator. Finite sample properties concerning bias and variance are evaluated over a comprehensive parameter range by a systematic simulation study. Moreover, the estimator's sensitivity to model violations is studied. The estimator performs well for realistic sample sizes and parameter ranges. In particular, the lineage-frequency estimates are almost unbiased independently of sample size. The MOI estimate's bias vanishes with increasing sample size, but might be substantial if sample size is too small. The estimator's variance matrix agrees well with the Cramér-Rao lower bound, even for small sample size. The numerical and analytical results of this study can be used for study design. This is exemplified by a malaria data set from Venezuela. It is shown how the results can be used to determine the necessary sample size to achieve certain performance goals. An implementation of the likelihood method and a simulation algorithm for study design, implemented as an R script, is available as S1 File alongside a documentation (S2 File) and example data (S3 File).
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80
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Feijao P, Yao HT, Fornika D, Gardy J, Hsiao W, Chauve C, Chindelevitch L. MentaLiST - A fast MLST caller for large MLST schemes. Microb Genom 2018; 4. [PMID: 29319471 PMCID: PMC5857373 DOI: 10.1099/mgen.0.000146] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.
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Affiliation(s)
- Pedro Feijao
- 1School of Computing Science, Simon Fraser University, Vancouver, Canada
| | - Hua-Ting Yao
- 2École Polytechnique, Université Paris-Saclay, Palaiseau, France
| | - Dan Fornika
- 3BC Centre for Disease Control, Vancouver, Canada
| | - Jennifer Gardy
- 4School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - William Hsiao
- 5Department of Pathology and Laboratory Medicine, University of British Columbia and BC Centre for Disease Control, Vancouver, Canada
| | - Cedric Chauve
- 6Department of Mathematics, Simon Fraser University, Vancouver, Canada
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81
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Leung CC, Chee CBE, Zhang Y. Tuberculosis updates 2018: Innovations and developments to end TB. Respirology 2017; 23:356-358. [PMID: 29266552 DOI: 10.1111/resp.13244] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/05/2017] [Indexed: 11/30/2022]
Affiliation(s)
- Chi Chiu Leung
- Tuberculosis and Chest Service, Department of Health, Hong Kong, China
| | - Cynthia B E Chee
- TB Control Unit, Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Cayci YT, Bilgin K, Coban AY, Birinci A, Durupınar B. An evaluation of false-positive rifampicin resistance on the Xpert MTB/RIF. Mem Inst Oswaldo Cruz 2017; 112:756-759. [PMID: 29091135 PMCID: PMC5661898 DOI: 10.1590/0074-02760170051] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 07/07/2017] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis (MTB) is one of the most significant causes of mortality and morbidity. Early diagnose is important especially in multiple drug resistant tuberculosis to avoid transmission. Traditional techniques requires at least one to three weeks for diagnosis of tuberculosis. Diagnostic delays with multiple drug resistant tuberculosis are associated with worse clinical outcomes and increased transmission The Xpert MTB/RIF assay is one of the new diagnostic device for the diagnosis of tuberculosis and rapid detection of rifampicin resistance. OBJECTIVE We assessed the performance of Xpert MTB/RIF assay for detecting rifampicin resistance using phenotypic drug susceptibility tests as automated BD MGIT 960. METHODS Total of 2136 specimens were included in the study. Xpert MTB/RIF testing was performed on samples, using version 4 cartridges, according to the manufacturer's recommendations. The MTBC culture and first-line phenotypic DST were performed in automated BD MGIT 960 (Becton & Dickinson, USA) according to the recommendations of the manufacturer. Agar proportion was used in the case of inconsistency for rifampicin resistance. FINDINGS Thirty-four samples (19 respiratory and 15 nonrespiratory samples) were determined as positive for M. tuberculosis complex by Xpert MTB/RIF (Cepheid GeneXpert® System, USA). Xpert MTB/RIF assay detected 4/34 (11.7%) specimens as rifampicin resistant. One of the rifampicin resistant isolates was determined susceptible in MGIT 960 automated system. This isolate was also tested with agar proportion method and found susceptible to rifampicin. MAIN CONCLUSION The Xpert MTB/RIF assay can be used as first-line assay for the detection of M. tuberculosis. However, microbiologists must be aware of the limitations of the assay.
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Affiliation(s)
- Yeliz Tanriverdi Cayci
- Ondokuz Mayis University, Medical Faculty, Department of Medical Microbiology, Samsun, Turkey
| | - Kemal Bilgin
- Ondokuz Mayis University, Vocational School of Health Services, Department of Medical Services and Techniques, Samsun, Turkey
| | - Ahmet Yilmaz Coban
- Ondokuz Mayis University, Medical Faculty, Department of Medical Microbiology, Samsun, Turkey
| | - Asuman Birinci
- Ondokuz Mayis University, Medical Faculty, Department of Medical Microbiology, Samsun, Turkey
| | - Belma Durupınar
- Ondokuz Mayis University, Medical Faculty, Department of Medical Microbiology, Samsun, Turkey
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83
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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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84
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Nsofor CA, Jiang Q, Wu J, Gan M, Liu Q, Zuo T, Zhu G, Gao Q. Transmission is a Noticeable Cause of Resistance Among Treated Tuberculosis Patients in Shanghai, China. Sci Rep 2017; 7:7691. [PMID: 28794425 PMCID: PMC5550506 DOI: 10.1038/s41598-017-08061-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/06/2017] [Indexed: 02/07/2023] Open
Abstract
It is generally believed that drug resistance among treated tuberculosis (TB) patients is as a result of acquired drug resistance due to inappropriate treatment. Previous studies have shown that primary drug resistance caused by transmission also plays a role among treated cases. Differentiating the two types of drug resistance will help in developing appropriate strategies for control of drug resistant tuberculosis. In this study, we tested the hypothesis that drug resistance among treated TB patients is mainly caused by primary resistance rather than acquired resistance. Defining resistance profiles by molecular drug susceptibility test, we used Unit Variable Number Tandem Repeats (VNTR) to genotype and Whole Genome Sequencing (WGS) to confirm the accordance of the first and last Mycobacterium tuberculosis isolates from treated pulmonary TB patients in Shanghai from 2009–2015. Among 81 patients with increasing drug resistance, out of 390 patients enrolled, paired isolates from 59.3% (48/81) had different VNTR patterns indicating primary drug resistance. Our results have demonstrated that primary resistance due to exogenous reinfection is the major cause of drug resistance among treated TB patients in Shanghai; thus, strategies aimed at preventing and interrupting transmission are urgently needed to effectively reduce the epidemic of drug resistant tuberculosis.
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Affiliation(s)
- Chijioke A Nsofor
- School of Basic Medicine, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Fudan University, Shanghai, China
| | - Qi Jiang
- School of Basic Medicine, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Fudan University, Shanghai, China
| | - Jie Wu
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Mingyu Gan
- School of Basic Medicine, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Fudan University, Shanghai, China
| | - Qingyun Liu
- School of Basic Medicine, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Fudan University, Shanghai, China
| | - Tianyu Zuo
- School of Basic Medicine, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Fudan University, Shanghai, China
| | - Guofeng Zhu
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China.
| | - Qian Gao
- School of Basic Medicine, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Fudan University, Shanghai, China.
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85
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Chisholm RH, Tanaka MM. The emergence of latent infection in the early evolution of Mycobacterium tuberculosis. Proc Biol Sci 2017; 283:rspb.2016.0499. [PMID: 27194699 DOI: 10.1098/rspb.2016.0499] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium tuberculosis has an unusual natural history in that the vast majority of its human hosts enter a latent state that is both non-infectious and devoid of any symptoms of disease. From the pathogen perspective, it seems counterproductive to relinquish reproductive opportunities to achieve a détente with the host immune response. However, a small fraction of latent infections reactivate to the disease state. Thus, latency has been argued to provide a safe harbour for future infections which optimizes the persistence of M. tuberculosis in human populations. Yet, if a pathogen begins interactions with humans as an active disease without latency, how could it begin to evolve latency properties without incurring an immediate reproductive disadvantage? We address this question with a mathematical model. Results suggest that the emergence of tuberculosis latency may have been enabled by a mechanism akin to cryptic genetic variation in that detrimental latency properties were hidden from natural selection until their expression became evolutionarily favoured.
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Affiliation(s)
- Rebecca H Chisholm
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia Evolution and Ecology Research Centre, University of New South Wales, Sydney 2052, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia Evolution and Ecology Research Centre, University of New South Wales, Sydney 2052, Australia
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86
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Egbe NF, Muwonge A, Ndip L, Kelly RF, Sander M, Tanya V, Ngwa VN, Handel IG, Novak A, Ngandalo R, Mazeri S, Morgan KL, Asuquo A, de C Bronsvoort BM. Molecular epidemiology of Mycobacterium bovis in Cameroon. Sci Rep 2017; 7:4652. [PMID: 28680043 PMCID: PMC5498612 DOI: 10.1038/s41598-017-04230-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/11/2017] [Indexed: 11/28/2022] Open
Abstract
We describe the largest molecular epidemiological study of Bovine Tuberculosis (bTB) in a sub-Saharan African country with higher spatial resolution providing new insights into bTB. Four hundred and ninety-nine samples were collected for culture from 201 and 179 cattle with and without bTB-like lesions respectively out of 2,346 cattle slaughtered at Bamenda, Ngaoundere, Garoua and Maroua abattoirs between 2012–2013. Two hundred and fifty-five M. bovis were isolated, identified and genotyped using deletion analysis, Hain® Genotype MTBC, spoligotyping and MIRU-VNTR. African 1 was the dominant M. bovis clonal complex, with 97 unique genotypes including 19 novel spoligotypes representing the highest M. bovis genetic diversity observed in Africa to date. SB0944 and SB0953 dominated (63%) the observed spoligotypes. A third of animals with multiple lesions had multiple strain infections. Higher diversity but little evidence of recent transmission of M. bovis was more common in Adamawa compared to the North-West Region. The Adamawa was characterised by a high frequency of singletons possibly due to constant additions from an active livestock movement network compared to the North-West Region where a local expansion was more evident. The latter combined with population-based inferences suggest an unstable and stable bTB-endemic status in the North-West and Adamawa Regions respectively.
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Affiliation(s)
- N F Egbe
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Microbiology and Parasitology Unit, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | - A Muwonge
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - L Ndip
- Laboratory for Emerging Infectious Diseases, University of Buea, Buea, Cameroon.,Department of Biomedical Sciences, Faculty of Health Sciences, University of Buea, Buea, Cameroon
| | - R F Kelly
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Farm Animal Clinical Sciences, School of Veterinary Medicine, University of Glasgow, Glasgow, G61 1QH, UK
| | - M Sander
- Tuberculosis Reference Laboratory, Bamenda, P.O. Box 586, Cameroon
| | - V Tanya
- Cameroon Academy of Sciences, P.O. Box 1457, Yaoundé, Cameroon
| | - V Ngu Ngwa
- School of Veterinary Medicine and Sciences, University of Ngaoundere, B.P. 454, Ngaoundere, Cameroon
| | - I G Handel
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - A Novak
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - R Ngandalo
- Laboratoire de Recherches Vétérinaires et Zootechniques de Farcha, N'Djaména, Chad
| | - S Mazeri
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - K L Morgan
- Institute of Ageing and Chronic Disease, University of Liverpool, Leahurst Campus, Neston, Wirral, CH64 7TE, UK
| | - A Asuquo
- Microbiology and Parasitology Unit, Faculty of Allied Medical Sciences, University of Calabar, Calabar, Nigeria
| | - B M de C Bronsvoort
- Division of Genetics and Genomics, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.,Centre for Tropical Livestock Genetics and Health, The Roslin Institute and the Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
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87
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Chao WC, Chuang PC, Wu DH, Wu CL, Liu PY, Shieh CC, Jou R. Using genotyping to delineate tuberculosis transmission in long-term care facilities: single facility 4-year experience. BMC Infect Dis 2017; 17:421. [PMID: 28610564 PMCID: PMC5470217 DOI: 10.1186/s12879-017-2526-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 06/05/2017] [Indexed: 11/13/2022] Open
Abstract
Background Residents in long-term care facilities (LTCFs) are vulnerable to tuberculosis (TB) transmission; however, to delineate possible routes of TB transmission in LTCFs is difficult. This study aimed to address the use of regular genotyping surveillance to delineate TB transmission in LTCFs. Methods All of Mycobacterium tuberculosis isolates in the reported 620-bed LTCF between July 2011 and August 2015 were genotyped, and we retrospectively compared epidemiological data and genotyping results. Results A total of 42 subjects were diagnosed with culture-positive pulmonary TB infection during the 4-year period. Their median age was 76.5 years, and 64.3% (27/42) of them were male. Genotyping identified 5 clustered TB infections involving 76.2% (32/42) of all TB subjects. In a multivariate logistic regression model adjusted for age, sex, chronic obstructive pulmonary disease, and body mass index, subjects with clustered TB infection were less likely to be Activities of Daily Living (ADL)-dependence (adjOR 0.073, 95% CI 0.007–0.758) when compared with subjects having individual TB infections. Prolonged surveillance is essential given that the median interval to diagnose secondary subjects was 673 days. Finally, only 63.0% (17/27) of the 27 secondary TB subjects in this study had contact history with index subject in the same ward. Conclusions In conclusion, possible routes of TB transmission in a complex TB outbreak at LTCFs might be delineated by routine genotyping surveillance and regular health check-up. Electronic supplementary material The online version of this article (doi:10.1186/s12879-017-2526-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wen-Cheng Chao
- Department of Medical Research, Taichung Veterans General Hospital, Taichung, Taiwan.,Institute of Clinical Medicine, National Cheng Kung University Medical College, Tainan, Taiwan
| | - Pei-Chun Chuang
- Reference Laboratory of Mycobacteriology, Tuberculosis Research Center, Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei City, 10050, Taiwan
| | - Don-Han Wu
- Department of Internal Medicine, Taichung Veterans General Hospital Chiayi branch, Chiayi, Taiwan
| | - Chieh-Liang Wu
- Department of Internal Medicine, Taichung Veterans General Hospital, Taichung, Taiwan.,Center for Quality Management, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Po-Yu Liu
- Center for Quality Management, Taichung Veterans General Hospital, Taichung, Taiwan
| | - Chi-Chang Shieh
- Institute of Clinical Medicine, National Cheng Kung University Medical College, Tainan, Taiwan
| | - Ruwen Jou
- Reference Laboratory of Mycobacteriology, Tuberculosis Research Center, Centers for Disease Control, No.6, Linsen S. Rd., Jhongjheng District, Taipei City, 10050, Taiwan. .,Institute of Microbiology and Immunology, National Yang-Ming University, Taipei, Taiwan.
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88
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McIvor A, Koornhof H, Kana BD. Relapse, re-infection and mixed infections in tuberculosis disease. Pathog Dis 2017; 75:3003284. [PMID: 28334088 DOI: 10.1093/femspd/ftx020] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/16/2017] [Indexed: 01/19/2023] Open
Abstract
Tuberculosis (TB) disease can be characterized by genotypic and phenotypic complexity in Mycobacterium tuberculosis bacilli within a single patient. This microbiological heterogeneity has become an area of intense study due its perceived importance in drug tolerance, drug resistance and as a surrogate measure of transmission rates. This review presents a descriptive analysis of research describing the prevalence of mixed-strain TB infections in geographically distinct locations. Despite significant variation in disease burden and a rampant human immunodeficiency virus (HIV)-TB co-epidemic, there was no difference in the prevalence range of mixed infections reported in African countries when compared to the rest of the world. The occurrence of recurrent TB was associated with a higher prevalence of mixed-strain infections, but this difference was not reported as statistically significant. These interpretations were limited by differences in the design and overall size of the studies assessed. Factors such as sputum quality, culture media, number of repeated culture steps, molecular typing methods and HIV-infection status can affect the detection of mixed-strain infection. It is recommended that future clinical studies should focus on settings with varying TB burdens, with a common sample processing protocol to gain further insight into these phenomena and develop novel transmission blocking strategies.
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Affiliation(s)
- Amanda McIvor
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa
| | - Hendrik Koornhof
- Centre for Tuberculosis, National Institute for Communicable Diseases and National Health Laboratory Service, Johannesburg, 2000, South Africa
| | - Bavesh Davandra Kana
- DST/NRF Centre of Excellence for Biomedical TB Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg 2000, South Africa.,CAPRISA, Centre for the AIDS Programme of Research in South Africa, Durban, 4001, South Africa
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89
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Pfeiffer W, Braun J, Burchell J, Witte CL, Rideout BA. Whole-genome analysis of mycobacteria from birds at the San Diego Zoo. PLoS One 2017; 12:e0173464. [PMID: 28267758 PMCID: PMC5340394 DOI: 10.1371/journal.pone.0173464] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/22/2017] [Indexed: 11/25/2022] Open
Abstract
Methods Mycobacteria isolated from more than 100 birds diagnosed with avian mycobacteriosis at the San Diego Zoo and its Safari Park were cultured postmortem and had their whole genomes sequenced. Computational workflows were developed and applied to identify the mycobacterial species in each DNA sample, to find single-nucleotide polymorphisms (SNPs) between samples of the same species, to further differentiate SNPs between as many as three different genotypes within a single sample, and to identify which samples are closely clustered genomically. Results Nine species of mycobacteria were found in 123 samples from 105 birds. The most common species were Mycobacterium avium and Mycobacterium genavense, which were in 49 and 48 birds, respectively. Most birds contained only a single mycobacterial species, but two birds contained a mixture of two species. The M. avium samples represent diverse strains of M. avium avium and M. avium hominissuis, with many pairs of samples differing by hundreds or thousands of SNPs across their common genome. By contrast, the M. genavense samples are much closer genomically; samples from 46 of 48 birds differ from each other by less than 110 SNPs. Some birds contained two, three, or even four genotypes of the same bacterial species. Such infections were found in 4 of 49 birds (8%) with M. avium and in 11 of 48 birds (23%) with M. genavense. Most were mixed infections, in which the bird was infected by multiple mycobacterial strains, but three infections with two genotypes differing by ≤ 10 SNPs were likely the result of within-host evolution. The samples from 31 birds with M. avium can be grouped into nine clusters within which any sample is ≤ 12 SNPs from at least one other sample in the cluster. Similarly, the samples from 40 birds with M. genavense can be grouped into ten such clusters. Information about these genomic clusters is being used in an ongoing, companion study of mycobacterial transmission to help inform management of bird collections.
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Affiliation(s)
- Wayne Pfeiffer
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Josephine Braun
- Wildlife Disease Laboratories, San Diego Zoo Global, San Diego, California, United States of America
| | - Jennifer Burchell
- Wildlife Disease Laboratories, San Diego Zoo Global, San Diego, California, United States of America
| | - Carmel L. Witte
- Wildlife Disease Laboratories, San Diego Zoo Global, San Diego, California, United States of America
| | - Bruce A. Rideout
- Wildlife Disease Laboratories, San Diego Zoo Global, San Diego, California, United States of America
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90
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Bengtson HN, Homolka S, Niemann S, Reis AJ, da Silva PE, Gerasimova YV, Kolpashchikov DM, Rohde KH. Multiplex detection of extensively drug resistant tuberculosis using binary deoxyribozyme sensors. Biosens Bioelectron 2017; 94:176-183. [PMID: 28284077 DOI: 10.1016/j.bios.2017.02.051] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 02/21/2017] [Accepted: 02/28/2017] [Indexed: 02/07/2023]
Abstract
Current diagnostic tools for Mycobacterium tuberculosis (Mtb) have many disadvantages including low sensitivity, slow turnaround times, or high cost. Accurate, easy to use, and inexpensive point of care molecular diagnostic tests are urgently needed for the analysis of multidrug resistant (MDR) and extensively drug resistant (XDR) Mtb strains that emerge globally as a public health threat. In this study, we established proof-of-concept for a novel diagnostic platform (TB-DzT) for Mtb detection and the identification of drug resistant mutants using binary deoxyribozyme sensors (BiDz). TB-DzT combines a multiplex PCR with single nucleotide polymorphism (SNP) detection using highly selective BiDz sensors targeting loci associated with species typing and resistance to rifampin, isoniazid and fluoroquinolone antibiotics. Using the TB-DzT assay, we demonstrated accurate detection of Mtb and 5 mutations associated with resistance to three anti-TB drugs in clinical isolates. The assay also enables detection of a minority population of drug resistant Mtb, a clinically relevant scenario referred to as heteroresistance. Additionally, we show that TB-DzT can detect the presence of unknown mutations at target loci using combinatorial BiDz sensors. This diagnostic platform provides the foundation for the development of cost-effective, accurate and sensitive alternatives for molecular diagnostics of MDR- and XDR-TB.
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Affiliation(s)
- Hillary N Bengtson
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA
| | - Susanne Homolka
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Borstel, Germany
| | - Ana Júlia Reis
- Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | | | - Yulia V Gerasimova
- Department of Chemistry, College of Sciences, University of Central Florida, Orlando, FL, USA
| | - Dmitry M Kolpashchikov
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA; Department of Chemistry, College of Sciences, University of Central Florida, Orlando, FL, USA
| | - Kyle H Rohde
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL, USA.
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91
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Shen X, Yang C, Wu J, Lin S, Gao X, Wu Z, Tian J, Gan M, Luo T, Wang L, Yu C, Mei J, Pan Q, DeRiemer K, Yuan Z, Gao Q. Recurrent tuberculosis in an urban area in China: Relapse or exogenous reinfection? Tuberculosis (Edinb) 2017; 103:97-104. [PMID: 28237039 PMCID: PMC5638046 DOI: 10.1016/j.tube.2017.01.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/26/2017] [Accepted: 01/29/2017] [Indexed: 12/12/2022]
Abstract
Recurrent tuberculosis is an important indicator of the effectiveness of tuberculosis control and can occur by relapse or exogenous reinfection. We conducted a retrospective cohort study on all bacteriologically confirmed tuberculosis cases that were successfully treated between 2000 and 2012 in Shanghai, an urban area with a high number but a low prevalence rate of tuberculosis cases and a low prevalence of HIV infection. Genotyping the Mycobacterium tuberculosis from clinical isolates was used to distinguish between relapse and reinfection. In total, 5.3% (710/13,417) of successfully treated cases had a recurrence, a rate of 7.55 (95% CI 7.01-8.13) episodes per 1000 person-years, more than 18 times the rate of tuberculosis in the general population. Patients who were male, age 30-59, retreatment cases, had cavitation, diabetes, drug-resistant or multidrug-resistant tuberculosis in their initial episode of tuberculosis, were at high risk for a recurrence. Among 141 recurrent cases that had paired isolates, 59 (41.8%) had different genotypes, indicating reinfection with a different strain. Patients who completed treatment were still at high risk of another episode of tuberculosis and exogenous reinfection contributed a significant proportion of the recurrent tuberculosis cases. Targeted control strategies are needed to prevent new tuberculosis infections in this setting.
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Affiliation(s)
- Xin Shen
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China; The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science, Fudan University, Shanghai, 200032, China
| | - Chongguang Yang
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science, Fudan University, Shanghai, 200032, China; Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, 60 College Street, New Haven, CT, 06510, USA
| | - Jie Wu
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China
| | - Senlin Lin
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China
| | - Xu Gao
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science, Fudan University, Shanghai, 200032, China
| | - Zheyuan Wu
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China
| | - Jiyun Tian
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science, Fudan University, Shanghai, 200032, China
| | - Mingyu Gan
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science, Fudan University, Shanghai, 200032, China
| | - Tao Luo
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science, Fudan University, Shanghai, 200032, China
| | - Lili Wang
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China
| | - Chenlei Yu
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China
| | - Jian Mei
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China
| | - Qichao Pan
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China
| | - Kathryn DeRiemer
- School of Medicine, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA.
| | - ZhengAn Yuan
- Department of Tuberculosis Control, Shanghai Municipal Center for Disease Control and Prevention, 1380 West Zhong Shan Road, Shanghai, 200336, China.
| | - Qian Gao
- The Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Science, Fudan University, Shanghai, 200032, China.
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92
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Evaluation of the impact of polyclonal infection and heteroresistance on treatment of tuberculosis patients. Sci Rep 2017; 7:41410. [PMID: 28120910 PMCID: PMC5264600 DOI: 10.1038/srep41410] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 12/20/2016] [Indexed: 11/29/2022] Open
Abstract
Mixed strain infections of Mycobacterium tuberculosis make diagnosis, treatment, and control of tuberculosis (TB) more difficult. This study was aimed to evaluate the relationship between mixed infections, antibiotic resistance patterns and treatment of TB patients. In this study, among 2850 suspected TB clinical samples, a total of ninety-six clinical samples from 66 TB confirmed patients were subjected to the 24-locus variable-number tandem repeat method to evaluate the prevalence of mixed infections. For all studied strains, 288 colonies (three individual clones for each sample) were isolated from different colonies and separately analyzed by the Drug Susceptibility Test (DST). For all patients, follow up was done after 6 months of treatment. Based on direct 24 loci MIRU-VNTR, in the 66 TB patients, 53% (35/66) showed mixed infection. In the mixed samples, 45.71% (16/35) showed different antibiotic resistant patterns. Among the mixed infection patients, eight (22.9%; 8/35) showed treatment failure after six- month therapy. Six of these non-treated patients (75%; 6/8) had different antibiotic resistant patterns. We conclude that mixed infections, have a negative impact on treatment of TB patients especially when co-infecting M. tuberculosis strains display heteroresistance.
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93
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Farmanfarmaei G, Kargarpour Kamakoli M, Sadegh HR, Masoumi M, Abdolrahimi F, Fateh A, Ebrahimzadeh N, Javadi G, Rahimi Jamnani F, Vaziri F, Siadat SD. Bias in detection of Mycobacterium tuberculosis polyclonal infection: Use clinical samples or cultures? Mol Cell Probes 2017; 33:1-3. [PMID: 28130122 DOI: 10.1016/j.mcp.2017.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 12/23/2016] [Accepted: 01/23/2017] [Indexed: 01/03/2023]
Abstract
The application of MIRU-VNTR has unveiled that infection by Mycobacterium tuberculosis can be polyclonal. Our comparative study demonstrated that based on the studied samples (clinical specimen or culture) detection of polyclonal M. tuberculosis infection can be significantly different.
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Affiliation(s)
- Ghazaleh Farmanfarmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Hamid Reza Sadegh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farid Abdolrahimi
- Department of Mycobacteriology and Pulmonary Research, 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
| | - Nayereh Ebrahimzadeh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Gholamreza Javadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- 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.
| | - 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
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94
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Sadegh H, Kargarpour Kamakoli M, Farmanfarmaei G, Masoumi M, Abdolrahimi F, Fateh A, Ebrahimzadeh N, Rahimi Jamnani F, Vaziri F, Siadat SD. Pros and cons of direct genotyping on tuberculosis clinical samples. Microb Pathog 2016; 103:135-138. [PMID: 28034830 DOI: 10.1016/j.micpath.2016.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 12/16/2016] [Accepted: 12/16/2016] [Indexed: 11/28/2022]
Abstract
OBJECTIVE Prompt genotyping of Mycobacterium tuberculosis (M. tuberculosis) is crucial for improving molecular epidemiological investigation of tuberculosis (TB). METHODS We performed a retrospective study to evaluate the use of 24 loci MIRU-VNTR (mycobacterial interspersed repetitive unit-variable number of tandem-repeat) directly on 135 clinical samples from 84 TB patients. RESULTS There was a direct correlation between genotyping on clinical samples by MIRU-VNTR and bacterial load (P = 0.001). VNTR loci were amplified successfully for 41.5% of the clinical samples (19-24 loci), 32.6% (13-18 loci), 23.7% (7-12 loci) and 2.2% (1-6 loci). Loci of 2401, 577, 2996 and 154 had the highest power to show the mixed strains infection in clinical samples. CONCLUSIONS Direct MIRU-VNTR is partially successful in complete genotyping of M. tuberculosis strains. On the other hand, detection of polyclonal infection is undoubtedly reliable based on the direct MIRU-VNTR.
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Affiliation(s)
- Hamidreza Sadegh
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Ghazaleh Farmanfarmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Farid Abdolrahimi
- Department of Mycobacteriology and Pulmonary Research, 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
| | - Nayereh Ebrahimzadeh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Rahimi Jamnani
- 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.
| | - 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
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95
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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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96
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Ayabina D, Hendon-Dunn C, Bacon J, Colijn C. Diverse drug-resistant subpopulations of Mycobacterium tuberculosis are sustained in continuous culture. J R Soc Interface 2016; 13:rsif.2016.0745. [PMID: 27807274 PMCID: PMC5134024 DOI: 10.1098/rsif.2016.0745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/11/2016] [Indexed: 01/09/2023] Open
Abstract
Drug resistance to tuberculosis (TB) has become more widespread over the past decade. As such, understanding the emergence and fitness of antibiotic-resistant subpopulations is crucial for the development of new interventions. Here we use a simple mathematical model to explain the differences in the response to isoniazid (INH) of Mycobacterium tuberculosis cells cultured under two growth rates in a chemostat. We obtain posterior distributions of model parameters consistent with data using a Markov chain Monte Carlo (MCMC) method. We explore the dynamics of diverse INH-resistant subpopulations consistent with these data in a multi-population model. We find that the simple model captures the qualitative behaviour of the cultures under both dilution rates and also present testable predictions about how diversity is maintained in such cultures.
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Affiliation(s)
- Diepreye Ayabina
- Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Charlotte Hendon-Dunn
- Public Health England, National Infection Service, Porton Down, Salisbury SP4 0JG, UK
| | - Joanna Bacon
- Public Health England, National Infection Service, Porton Down, Salisbury SP4 0JG, UK
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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97
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Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis. Nat Med 2016; 22:1470-1474. [PMID: 27798613 DOI: 10.1038/nm.4205] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/14/2016] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we report genomic analysis of 2,693 samples collected post mortem from lung and extrapulmonary biopsies of 44 subjects in KwaZulu-Natal, South Africa, who received minimal antitubercular treatment and most of whom were HIV seropositive. We found that purifying selection occurred within individual patients, without the need for patient-to-patient transmission. Despite negative selection, mycobacteria diversified within individuals to form sublineages that co-existed for years. These sublineages, as well as distinct strains from mixed infections, were differentially distributed throughout the lung, suggesting temporary barriers to pathogen migration. As a consequence, samples taken from the upper airway often captured only a fraction of the population diversity, challenging current methods of outbreak tracing and resistance diagnostics. Phylogenetic analysis indicated that dissemination from the lungs to extrapulmonary sites was as frequent as between lung sites, supporting the idea of similar migration routes within and between organs, at least in subjects with HIV. Genomic diversity therefore provides a record of pathogen diversification and repeated dissemination across the body.
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98
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Shin SS, Modongo C, Zetola NM. The impact of mixed infections on the interpretation of molecular epidemiology studies of tuberculosis. Int J Tuberc Lung Dis 2016; 20:423-4. [PMID: 27046727 DOI: 10.5588/ijtld.15.1024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Sanghyuk S Shin
- Department of Epidemiology, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Nicola M Zetola
- Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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99
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Vectors as Epidemiological Sentinels: Patterns of Within-Tick Borrelia burgdorferi Diversity. PLoS Pathog 2016; 12:e1005759. [PMID: 27414806 PMCID: PMC4944968 DOI: 10.1371/journal.ppat.1005759] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 06/18/2016] [Indexed: 01/13/2023] Open
Abstract
Hosts including humans, other vertebrates, and arthropods, are frequently infected with heterogeneous populations of pathogens. Within-host pathogen diversity has major implications for human health, epidemiology, and pathogen evolution. However, pathogen diversity within-hosts is difficult to characterize and little is known about the levels and sources of within-host diversity maintained in natural populations of disease vectors. Here, we examine genomic variation of the Lyme disease bacteria, Borrelia burgdorferi (Bb), in 98 individual field-collected tick vectors as a model for study of within-host processes. Deep population sequencing reveals extensive and previously undocumented levels of Bb variation: the majority (~70%) of ticks harbor mixed strain infections, which we define as levels Bb diversity pre-existing in a diverse inoculum. Within-tick diversity is thus a sample of the variation present within vertebrate hosts. Within individual ticks, we detect signatures of positive selection. Genes most commonly under positive selection across ticks include those involved in dissemination in vertebrate hosts and evasion of the vertebrate immune complement. By focusing on tick-borne Bb, we show that vectors can serve as epidemiological and evolutionary sentinels: within-vector pathogen diversity can be a useful and unbiased way to survey circulating pathogen diversity and identify evolutionary processes occurring in natural transmission cycles. Lyme disease, caused by a bacteria carried by deer ticks, is the most common vector-borne disease in North America and over 30,000 cases are reported each year in the United States. Ticks may be infected with multiple strains of the Lyme disease bacteria, which differ in transmissibility and the harm they pose to humans. In this study, we collected 98 infected deer ticks from across the United States and southern Canada. We used genetic techniques to investigate the diversity of the Lyme disease bacteria infecting each individual tick. We find that 70% of ticks are infected with multiple strains of the Lyme disease bacteria, indicating that humans may be exposed to and infected with multiple bacterial strains from a single tick bite. We also find evidence that the Lyme disease bacteria is evolving in response to the immune defenses of its natural hosts (including rodents and birds). Our study shows that individual ticks and other disease vectors can be studied as epidemiological sentinels, which reveal the extensive diversity of pathogens circulating in natural disease cycles and how they are evolving.
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100
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Gan M, Liu Q, Yang C, Gao Q, Luo T. Deep Whole-Genome Sequencing to Detect Mixed Infection of Mycobacterium tuberculosis. PLoS One 2016; 11:e0159029. [PMID: 27391214 PMCID: PMC4938208 DOI: 10.1371/journal.pone.0159029] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/24/2016] [Indexed: 11/18/2022] Open
Abstract
Mixed infection by multiple Mycobacterium tuberculosis (MTB) strains is associated with poor treatment outcome of tuberculosis (TB). Traditional genotyping methods have been used to detect mixed infections of MTB, however, their sensitivity and resolution are limited. Deep whole-genome sequencing (WGS) has been proved highly sensitive and discriminative for studying population heterogeneity of MTB. Here, we developed a phylogenetic-based method to detect MTB mixed infections using WGS data. We collected published WGS data of 782 global MTB strains from public database. We called homogeneous and heterogeneous single nucleotide variations (SNVs) of individual strains by mapping short reads to the ancestral MTB reference genome. We constructed a phylogenomic database based on 68,639 homogeneous SNVs of 652 MTB strains. Mixed infections were determined if multiple evolutionary paths were identified by mapping the SNVs of individual samples to the phylogenomic database. By simulation, our method could specifically detect mixed infections when the sequencing depth of minor strains was as low as 1× coverage, and when the genomic distance of two mixed strains was as small as 16 SNVs. By applying our methods to all 782 samples, we detected 47 mixed infections and 45 of them were caused by locally endemic strains. The results indicate that our method is highly sensitive and discriminative for identifying mixed infections from deep WGS data of MTB isolates.
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Affiliation(s)
- Mingyu Gan
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qingyun Liu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Chongguang Yang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institutes of Biomedical Sciences and Institute of Medical Microbiology, School of Basic Medical Sciences, Fudan University, Shanghai, China
- * E-mail: (QG); (TL)
| | - Tao Luo
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, Sichuan, China
- * E-mail: (QG); (TL)
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