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Chhotaray C, Tan Y, Mugweru J, Islam MM, Adnan Hameed HM, Wang S, Lu Z, Wang C, Li X, Tan S, Liu J, Zhang T. Advances in the development of molecular genetic tools for Mycobacterium tuberculosis. J Genet Genomics 2018; 45:S1673-8527(18)30114-0. [PMID: 29941353 DOI: 10.1016/j.jgg.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mycobacterium tuberculosis, a clinically relevant Gram-positive bacterium of great clinical relevance, is a lethal pathogen owing to its complex physiological characteristics and development of drug resistance. Several molecular genetic tools have been developed in the past few decades to study this microorganism. These tools have been instrumental in understanding how M. tuberculosis became a successful pathogen. Advanced molecular genetic tools have played a significant role in exploring the complex pathways involved in M. tuberculosis pathogenesis. Here, we review various molecular genetic tools used in the study of M. tuberculosis. Further, we discuss the applications of clustered regularly interspaced short palindromic repeat interference (CRISPRi), a novel technology recently applied in M. tuberculosis research to study target gene functions. Finally, prospective outcomes of the applications of molecular techniques in the field of M. tuberculosis genetic research are also discussed.
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Affiliation(s)
- Chiranjibi Chhotaray
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaoju Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Julius Mugweru
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Biological Sciences, University of Embu, P.O Box 6 -60100, Embu, Kenya
| | - Md Mahmudul Islam
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - H M Adnan Hameed
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhili Lu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Changwei Wang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xinjie Li
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Shouyong Tan
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China
| | - Jianxiong Liu
- State Key Laboratory of Respiratory Disease, Department of Clinical Laboratory, Guangzhou Chest Hospital, Guangzhou 510095, China.
| | - Tianyu Zhang
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Cannas A, Camassa S, Sali M, Butera O, Mazzarelli A, Sanguinetti M, Di Caro A, Delogu G, Girardi E. Genetic Diversity of Mycobacterium tuberculosis Isolates in the Metropolitan Area of Rome. Chemotherapy 2018; 63:148-154. [PMID: 29902788 DOI: 10.1159/000489860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/05/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND The presence in a geographic area of Mycobacterium tuberculosis (Mtb) strains belonging to different phylogeographic lineages and showing different drug susceptibility patterns may suggest recent transmission, with implications in terms of patient clinical management and disease control. The aim of this study was to carry out a preliminary epidemiological investigation of tuberculosis (TB) cases in Rome. METHODS A total of 232 Mtb isolates, collected from new or previously treated patients, admitted between 2008 and 2014 at 2 hospital settings in Rome with a diagnosis of TB, were analyzed by spoligotyping and analyzing 24 variable-number tandem repeats (VNTR) mycobacterial interspersed repetitive-unit (MIRU) loci. The SITVIT2 database and the MIRU-VNTRplus web applications were used to identify the strain genotypes and to generate phylogenetic trees. RESULTS Based on the position on the phylogenetic tree, 97.4% of the strains were associated with 1 of the 7 main lineages. The Euro-American lineage was the most commonly represented (81.9%) within both Italian and foreign-born populations, although all main lineages were present. The highest frequency of drug-resistant strains was found among the East-Asian lineage (Beijing genotype) isolated from foreign-born patients. CONCLUSIONS Dynamics of TB transmission in Rome indicate recent spread of Mtb strains belonging to phylogeographic lineages and clades usually found in countries and geographic areas with a high incidence of TB, similarly to what is observed in most metropolitan areas in Western Europe. Knowledge from molecular and classical epidemiology provides an important tool for disease control.
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Affiliation(s)
- Angela Cannas
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Serena Camassa
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Gemelli, Rome, Italy
| | - Michela Sali
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Gemelli, Rome, Italy
| | - Ornella Butera
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Antonio Mazzarelli
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Gemelli, Rome, Italy
| | - Antonino Di Caro
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Giovanni Delogu
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Gemelli, Rome, Italy
| | - Enrico Girardi
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
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Dekhil N, Skhairia MA, Mhenni B, Ben Fradj S, Warren R, Mardassi H. Automated IS6110-based fingerprinting of Mycobacterium tuberculosis: Reaching unprecedented discriminatory power and versatility. PLoS One 2018; 13:e0197913. [PMID: 29856789 PMCID: PMC5983439 DOI: 10.1371/journal.pone.0197913] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/10/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Several technical hurdles and limitations have restricted the use of IS6110 restriction fragment length polymorphism (IS6110 RFLP), the most effective typing method for detecting recent tuberculosis (TB) transmission events. This has prompted us to conceive an alternative modality, IS6110-5'3'FP, a plasmid-based cloning approach coupled to a single PCR amplification of differentially labeled 5' and 3' IS6110 polymorphic ends and their automated fractionation on a capillary sequencer. The potential of IS6110-5'3'FP to be used as an alternative to IS6110 RFLP has been previously demonstrated, yet further technical improvements are still required for optimal discriminatory power and versatility. OBJECTIVES Here we introduced critical amendments to the original IS6110-5'3'FP protocol and compared its performance to that of 24-loci multiple interspersed repetitive unit-variable number tandem repeats (MIRU-VNTR), the current standard method for TB transmission analyses. METHODS IS6110-5'3'FP protocol modifications involved: (i) the generation of smaller-sized polymorphic fragments for efficient cloning and PCR amplification, (ii) omission of the plasmid amplification step in E. coli for shorter turnaround times, (iii) the use of more stable fluorophores for increased sensitivity, (iv) automated subtraction of background fluorescent signals, and (v) the automated conversion of fluorescent peaks into binary data. RESULTS In doing so, the overall turnaround time of IS6110-5'3'FP was reduced to 4 hours. The new protocol allowed detecting almost all 5' and 3' IS6110 polymorphic fragments of any given strain, including IS6110 high-copy number Beijing strains. IS6110-5'3'FP proved much more discriminative than 24-loci MIRU-VNTR, particularly with strains of the M. tuberculosis lineage 4. CONCLUSIONS The IS6110-5'3'FP protocol described herein reached the optimal discriminatory potential of IS6110 fingerprinting and proved more accurate than 24-loci MIRU-VNTR in estimating recent TB transmission. The method, which is highly cost-effective, was rendered versatile enough to prompt its evaluation as an automatized solution for a TB integrated molecular surveillance.
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Affiliation(s)
- Naira Dekhil
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Mohamed Amine Skhairia
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Besma Mhenni
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Saloua Ben Fradj
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Rob Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Helmi Mardassi
- Unit of Typing & Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
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Ibrahim M, Yar AM, Zaman G, Yan C, Khurshid M, Bokhari H. Genome sequence and analysis of Mycobacterium tuberculosis strain SWLPK. J Glob Antimicrob Resist 2018; 13:211-213. [DOI: 10.1016/j.jgar.2018.04.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 04/17/2018] [Accepted: 04/26/2018] [Indexed: 10/16/2022] Open
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The Epidemiological Significance and Temporal Stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats-Based Method Applied to Mycobacterium tuberculosis in China. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2018; 15:ijerph15040782. [PMID: 29673235 PMCID: PMC5923824 DOI: 10.3390/ijerph15040782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/11/2018] [Accepted: 04/11/2018] [Indexed: 11/17/2022]
Abstract
This study aimed to validate the epidemiological significance and temporal stability of Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) typing in a genetically and geographically diverse set of clinical isolates from patients diagnosed with pulmonary tuberculosis in China. Between 2010 and 2013, a total of 982 Mycobacterium tuberculosis isolates were collected from four population-based investigations in China. Apart from the currently applied 24-locus MIRU-VNTR, six additional hypervariable loci were analyzed in order to validate the MIRU-VNTR combinations in terms of their epidemiological links, clustering time span, and paired geographic distance. In vitro temporal stability was analyzed for both individual MIRU-VNTR loci, and for several combinations of loci. In the present study, four MIRU-VNTR combinations, including the hypervariable loci 3820, 3232, 2163a, and 4120, were evaluated. All of these combinations obtained a Hunter-Gaston discriminatory index (HGDI) value over 0.9900 with a reduced clustering proportion (from 32.0% to 25.6%). By comparing epidemiological links, clustering time span, and paired geographic distance, we found that the performances of the four MIRU-VNTR combinations were comparable to the insertion sequence 6110 restriction fragment length polymorphism (IS6110-RFLP), and significantly better than that of 24-locus MIRU-VNTR genotyping alone. The proportion of temporally stable loci ranged from 90.5% to 92.5% within the combined MIRU-VNTR genotyping, which is higher than IS6110-RFLP (85.4%). By adding four hypervariable loci to the standard 24-locus MIRU-VNTR genotyping, we obtained a high discriminatory power, stability and epidemiological significance. This algorithm could therefore be used to improve tuberculosis transmission surveillance and outbreak investigation in China.
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156
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Genetic profiling of Mycobacterium bovis strains from slaughtered cattle in Eritrea. PLoS Negl Trop Dis 2018; 12:e0006406. [PMID: 29664901 PMCID: PMC5922621 DOI: 10.1371/journal.pntd.0006406] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 04/27/2018] [Accepted: 03/23/2018] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium bovis (M.bovis) is the main causative agent for bovine tuberculosis (BTB) and can also be the cause of zoonotic tuberculosis in humans. In view of its zoonotic nature, slaughterhouse surveillance, potentially resulting in total or partial condemnation of the carcasses and organs, is conducted routinely. Spoligotyping, VNTR profiling, and whole genome sequencing (WGS) of M. bovis isolated from tissues with tuberculosis-like lesions collected from 14 cattle at Eritrea’s largest slaughterhouse in the capital Asmara, were conducted.The 14 M. bovis isolates were classified into three different spoligotype patterns (SB0120, SB0134 and SB0948) and six VNTR profiles. WGS results matched those of the conventional genotyping methods and further discriminated the six VNTR profiles into 14 strains. Furthermore, phylogenetic analysis of the M. bovis isolates suggests two independent introductions of BTB into Eritrea possibly evolving from a common ancestral strain in Europe.This molecular study revealed the most important strains of M. bovis in Eritrea and their (dis)similarities with the strains generally present in East Africa and Europe, as well as potential routes of introduction of M. bovis. Though the sample size is small, the current study provides important information as well as platform for future in-depth molecular studies on isolates from both the dairy and the traditional livestock sectors in Eritrea and the region. This study provides information onthe origin of some of the M. bovis strains in Eritrea, its genetic diversity, evolution and patterns of spread between dairy herds. Such information is essential in the development and implementation of future BTB control strategy for Eritrea. The livestock sector plays a major role in poverty and hunger reduction in the vast majority of Africa, as a source of food, cash income, manure, draught power, transportation, savings, insurance and social status. However, for livestock to play this vital role, the impact of diseases of economic and zoonotic importance need to be reduced. Bovine tuberculosis, mainly caused by Mycobacterium bovis, is such an infectious disease. Slaughterhouse (gross pathology) surveillance, followed by bacterial culture and genotyping, are options to identify the disease-causing agents, their distribution, and enabling trace back of the sources of infections, in order to prevent their re-introduction and spread. Unfortunately, genotyping is by far not generally introduced in the continent. In the present study, tissues with tuberculosis-like lesions were collected from the Asmara municipal slaughterhouse, the largest slaughterhouse in Eritrea, and bacterial culture, classical Mycobacterium tuberculosis complex typing (Spoligotyping and VNTR profiling), as well as whole genome sequencing (WGS) were used to gain insight into the spatial and temporal distribution, genetic diversity and evolution of M. bovis strains circulating in Eritrean dairy cattle. The results revealed (dis)similarities of the Eritrean M. bovis strains with the strains generally present in Africa and Europe, potential routes of introduction to Eritrea and genetic diversity of the M. bovis strains. Future in-depth molecular studies including more samples from dairy cattle as well as cattle and goats from the traditional livestock sector are recommended.
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157
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Diel R, Niemann S, Nienhaus A. Risk of tuberculosis transmission among healthcare workers. ERJ Open Res 2018; 4:00161-2017. [PMID: 29637080 PMCID: PMC5890027 DOI: 10.1183/23120541.00161-2017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/16/2018] [Indexed: 11/10/2022] Open
Abstract
Data from a prospective molecular-epidemiological study (1997–2015) of patients with culture-confirmed tuberculosis in Hamburg, Germany, were evaluated to assess the occupational risk of Mycobacterium tuberculosis complex transmission in a low-incidence setting. Isolates of M. tuberculosis complex were genotyped using IS6110 restriction fragment length polymorphism analysis. Results of structured questionnaires, geographical mapping and additional patient interviews were used for confirming epidemiological links. Out of the 2393 cases, 918 (38.4%) were classified into 224 clusters comprising 2–70 patients per cluster. Among the 918 cluster members, epidemiological links could be confirmed in 340 (37.0%) patients. In total, 55 (2.3%) patients were healthcare workers; 26 healthcare workers remained unclustered, but 29 healthcare workers belonged to cluster groups. Conventional contact tracing performed before genotyping to identify sources of the reported index cases detected only 73 (3.1%) patients. Logistic regression analysis confirmed work in the healthcare sector as strongest predictor for clustering of patients with verified epidemiological links (odds ratio (OR) 3.1, 95% CI 1.6–5.9), followed by alcoholism (OR 2.3, 95% CI 1.7–3.2) and sputum smear positivity (OR 1.8, 95% CI 1.4–2.3). Immigrants were more likely to be cluster nonmembers (OR 0.3, 95% CI 0.3–0.5). Recent transmission in Hamburg within the 19-year study period was found to be strongly associated with working in a healthcare facility. Although clusters also include many “imported” strains from abroad or regional highly prevalent M. tuberculosis strains with no evident epidemiological connection, routine molecular-epidemiological survey is indispensable to optimising and controlling the effectiveness of TB control strategies in German healthcare settings. Tuberculosis transmission among healthcare workershttp://ow.ly/aGn030iGLvF
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Affiliation(s)
- Roland Diel
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Kiel, Germany.,LungClinic Grosshansdorf, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology Group, Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Borstel, Germany
| | - Albert Nienhaus
- Institute for Health Service Research in Dermatology and Nursing, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Institution for Statutory Accident Insurance and Prevention in the Health and Welfare Services (BGW), Hamburg, Germany
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158
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Jajou R, de Neeling A, van Hunen R, de Vries G, Schimmel H, Mulder A, Anthony R, van der Hoek W, van Soolingen D. Epidemiological links between tuberculosis cases identified twice as efficiently by whole genome sequencing than conventional molecular typing: A population-based study. PLoS One 2018; 13:e0195413. [PMID: 29617456 PMCID: PMC5884559 DOI: 10.1371/journal.pone.0195413] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 03/21/2018] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Patients with Mycobacterium tuberculosis isolates sharing identical DNA fingerprint patterns can be epidemiologically linked. However, municipal health services in the Netherlands are able to confirm an epidemiological link in only around 23% of the patients with isolates clustered by the conventional variable number of tandem repeat (VNTR) genotyping. This research aims to investigate whether whole genome sequencing (WGS) is a more reliable predictor of epidemiological links between tuberculosis patients than VNTR genotyping. METHODS VNTR genotyping and WGS were performed in parallel on all Mycobacterium tuberculosis complex isolates received at the Netherlands National Institute for Public Health and the Environment in 2016. Isolates were clustered by VNTR when they shared identical 24-loci VNTR patterns; isolates were assigned to a WGS cluster when the pair-wise genetic distance was ≤ 12 single nucleotide polymorphisms (SNPs). Cluster investigation was performed by municipal health services on all isolates clustered by VNTR in 2016. The proportion of epidemiological links identified among patients clustered by either method was calculated. RESULTS In total, 535 isolates were genotyped, of which 25% (134/535) were clustered by VNTR and 14% (76/535) by WGS; the concordance between both typing methods was 86%. The proportion of epidemiological links among WGS clustered cases (57%) was twice as common than among VNTR clustered cases (31%). CONCLUSION When WGS was applied, the number of clustered isolates was halved, while all epidemiologically linked cases remained clustered. WGS is therefore a more reliable tool to predict epidemiological links between tuberculosis cases than VNTR genotyping and will allow more efficient transmission tracing, as epidemiological investigations based on false clustering can be avoided.
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Affiliation(s)
- Rana Jajou
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Albert de Neeling
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Rianne van Hunen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - Gerard de Vries
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - Henrieke Schimmel
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Arnout Mulder
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Richard Anthony
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Wim van der Hoek
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
- Radboud University Medical Centre, Department of Medical Microbiology, Nijmegen, The Netherlands
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159
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Coll P, García de Viedma D. Molecular epidemiology of tuberculosis. Enferm Infecc Microbiol Clin 2018; 36:233-240. [PMID: 29463429 DOI: 10.1016/j.eimc.2018.01.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Accepted: 01/13/2018] [Indexed: 01/05/2023]
Abstract
The application of genotyping tools allowed us to discriminate between the Mycobacterium tuberculosis isolates obtained in the laboratory. The differentiation between single strains opened the door to molecular epidemiology studies, which had helped us to progress in our knowledge of how this pathogen is transmitted in the progressively more complex socio-epidemiological scenario. The genetic stability of this microorganism led to develop specific methodologies, which are thoroughly revised in this chapter. In addition to their application in epidemiology, we review, how they can offer a response to different diagnostic and clinical challenges. Finally, we focus on describing the novel genomic revolution we are experiencing in the analysis of tuberculosis, the methodology in which it is based and the novel possibilities it offers, including new routes of integrating both the molecular and genomic languages in innovative post-genomic proposals, better suited to our real-life context.
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Affiliation(s)
- Pere Coll
- Servicio Microbiología, Hospital de Sant Pau, Barcelona, España; Departament de Genètica i Microbiologia, UniversitatAutònoma de Barcelona, , Bellaterra, España; Institut de Recerca, Hospital de Sant Pau, Barcelona, España.
| | - Darío García de Viedma
- Servicio Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, España; Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, España; CIBER Enfermedades respiratorias, CIBERES, Madrid, España.
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160
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Abstract
Preharvest food safety research and activities have advanced over time with the recognition of the importance and complicated nature of the preharvest phase of food production. In developed nations, implementation of preharvest food safety procedures along with strict monitoring and containment at various postharvest stages such as slaughter, processing, storage, and distribution have remarkably reduced the burden of foodborne pathogens in humans. Early detection and adequate surveillance of pathogens at the preharvest stage is of the utmost importance to ensure a safe meat supply. There is an urgent need to develop rapid, cost-effective, and point-of-care diagnostics which could be used at the preharvest stage and would complement postmortem and other quality checks performed at the postharvest stage. With newer methods and technologies, more efforts need to be directed toward developing rapid, sensitive, and specific methods for detection or screening of foodborne pathogens at the preharvest stage. In this review, we will discuss the molecular methods available for detection and molecular typing of bacterial foodborne pathogens at the farm. Such methods include conventional techniques such as endpoint PCR, real-time PCR, DNA microarray, and more advanced techniques such as matrix-assisted layer desorption ionization-time of flight mass spectrometry and whole-genome sequencing.
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161
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Chamie G, Kato-Maeda M, Emperador DM, Wandera B, Mugagga O, Crandall J, Janes M, Marquez C, Kamya MR, Charlebois ED, Havlir DV. Spatial overlap links seemingly unconnected genotype-matched TB cases in rural Uganda. PLoS One 2018; 13:e0192666. [PMID: 29438413 PMCID: PMC5811029 DOI: 10.1371/journal.pone.0192666] [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: 10/26/2017] [Accepted: 01/26/2018] [Indexed: 11/25/2022] Open
Abstract
Introduction Incomplete understanding of TB transmission dynamics in high HIV prevalence settings remains an obstacle for prevention. Understanding where transmission occurs could provide a platform for case finding and interrupting transmission. Methods From 2012–2015, we sought to recruit all adults starting TB treatment in a Ugandan community. Participants underwent household (HH) contact investigation, and provided names of social contacts, sites of work, healthcare and socializing, and two sputum samples. Mycobacterium tuberculosis culture-positive specimens underwent 24-loci MIRU-VNTR and spoligotyping. We sought to identify epidemiologic links between genotype-matched cases by analyzing social networks and mapping locations where cases reported spending ≥12 hours over the one-month pre-treatment. Sites of spatial overlap (≤100m) between genotype-matched cases were considered potential transmission sites. We analyzed social networks stratified by genotype clustering status, with cases linked by shared locations, and compared network density by location type between clustered vs. non-clustered cases. Results Of 173 adults with TB, 131 (76%) were enrolled, 108 provided sputum, and 84/131 (78%) were MTB culture-positive: 52% (66/131) tested HIV-positive. Of 118 adult HH contacts, 105 (89%) were screened and 3 (2.5%) diagnosed with active TB. Overall, 33 TB cases (39%) belonged to 15 distinct MTB genotype-matched clusters. Within each cluster, no cases shared a HH or reported shared non-HH contacts. In 6/15 (40%) clusters, potential epidemiologic links were identified by spatial overlap at specific locations: 5/6 involved health care settings. Genotype-clustered TB social networks had significantly greater network density based on shared clinics (p<0.001) and decreased density based on shared marketplaces (p<0.001), compared to non-clustered networks. Conclusions In this molecular epidemiologic study, links between MTB genotype-matched cases were only identifiable via shared locations, healthcare locations in particular, rather than named contacts. This suggests most transmission is occurring between casual contacts, and emphasizes the need for improved infection control in healthcare settings in rural Africa.
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Affiliation(s)
- Gabriel Chamie
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
- * E-mail:
| | - Midori Kato-Maeda
- Curry International Tuberculosis Center, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, United States of America
| | - Devy M. Emperador
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
| | - Bonnie Wandera
- Makerere University-University of California, San Francisco (MU-UCSF) Research Collaboration, Kampala, Uganda
| | - Olive Mugagga
- Makerere University-University of California, San Francisco (MU-UCSF) Research Collaboration, Kampala, Uganda
| | - John Crandall
- California Department of Public Health, Richmond, California, United States of America
| | - Michael Janes
- Curry International Tuberculosis Center, Division of Pulmonary and Critical Care Medicine, University of California, San Francisco, United States of America
| | - Carina Marquez
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
| | - Moses R. Kamya
- Department of Medicine, School of Medicine, Makerere University College of Health Sciences, Kampala, Uganda
| | - Edwin D. Charlebois
- Center for AIDS Prevention Studies, Department of Medicine, University of California, San Francisco, United States of America
| | - Diane V. Havlir
- Division of HIV, Infectious Diseases and Global Medicine, University of California, San Francisco, California, United States of America
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Malm S, Linguissi LSG, Tekwu EM, Vouvoungui JC, Kohl TA, Beckert P, Sidibe A, Rüsch-Gerdes S, Madzou-Laboum IK, Kwedi S, Penlap Beng V, Frank M, Ntoumi F, Niemann S. New Mycobacterium tuberculosis Complex Sublineage, Brazzaville, Congo. Emerg Infect Dis 2018; 23:423-429. [PMID: 28221129 PMCID: PMC5382753 DOI: 10.3201/eid2303.160679] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Tuberculosis is a leading cause of illness and death in Congo. No data are available about the population structure and transmission dynamics of the Mycobacterium tuberculosis complex strains prevalent in this central Africa country. On the basis of single-nucleotide polymorphisms detected by whole-genome sequencing, we phylogenetically characterized 74 MTBC isolates from Brazzaville, the capital of Congo. The diversity of the study population was high; most strains belonged to the Euro-American lineage, which split into Latin American Mediterranean, Uganda I, Uganda II, Haarlem, X type, and a new dominant sublineage named Congo type (n = 26). Thirty strains were grouped in 5 clusters (each within 12 single-nucleotide polymorphisms), from which 23 belonged to the Congo type. High cluster rates and low genomic diversity indicate recent emergence and transmission of the Congo type, a new Euro-American sublineage of MTBC.
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163
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Campbell F, Strang C, Ferguson N, Cori A, Jombart T. When are pathogen genome sequences informative of transmission events? PLoS Pathog 2018; 14:e1006885. [PMID: 29420641 PMCID: PMC5821398 DOI: 10.1371/journal.ppat.1006885] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 02/21/2018] [Accepted: 01/18/2018] [Indexed: 01/19/2023] Open
Abstract
Recent years have seen the development of numerous methodologies for reconstructing transmission trees in infectious disease outbreaks from densely sampled whole genome sequence data. However, a fundamental and as of yet poorly addressed limitation of such approaches is the requirement for genetic diversity to arise on epidemiological timescales. Specifically, the position of infected individuals in a transmission tree can only be resolved by genetic data if mutations have accumulated between the sampled pathogen genomes. To quantify and compare the useful genetic diversity expected from genetic data in different pathogen outbreaks, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating whole genome sequences sampled from transmission pairs. Using parameter values obtained by literature review, we simulate outbreak scenarios alongside sequence evolution using two models described in the literature to describe transmission divergence of ten major outbreak-causing pathogens. We find that while mean values vary significantly between the pathogens considered, their transmission divergence is generally very low, with many outbreaks characterised by large numbers of genetically identical transmission pairs. We describe the impact of transmission divergence on our ability to reconstruct outbreaks using two outbreak reconstruction tools, the R packages outbreaker and phybreak, and demonstrate that, in agreement with previous observations, genetic sequence data of rapidly evolving pathogens such as RNA viruses can provide valuable information on individual transmission events. Conversely, sequence data of pathogens with lower mean transmission divergence, including Streptococcus pneumoniae, Shigella sonnei and Clostridium difficile, provide little to no information about individual transmission events. Our results highlight the informational limitations of genetic sequence data in certain outbreak scenarios, and demonstrate the need to expand the toolkit of outbreak reconstruction tools to integrate other types of epidemiological data. The increasing availability of genetic sequence data has sparked an interest in using pathogen whole genome sequences to reconstruct the history of individual transmission events in an infectious disease outbreak. However, such methodologies rely on pathogen genomes mutating rapidly enough to discriminate between infected individuals, an assumption that remains to be investigated. To determine pathogen outbreaks for which genetic data is expected to be informative of transmission events, we introduce here the concept of ‘transmission divergence’, defined as the number of mutations separating pathogen genome sequences sampled from transmission pairs. We characterise transmission divergence of ten major outbreak causing pathogens using simulations and find significant variation between diseases, with viral outbreaks generally exhibiting higher transmission divergence than bacterial ones. We reconstruct these outbreaks using the R-packages outbreaker and phybreak and find that genetic sequence data, though useful for rapidly evolving pathogens, provides little to no information about outbreaks with low transmission divergence, such as Streptococcus pneumoniae and Shigella sonnei. Our results demonstrate the need to incorporate other sources of outbreak data, such as contact tracing data and spatial location data, into outbreak reconstruction tools.
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Affiliation(s)
- Finlay Campbell
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
| | - Camilla Strang
- Centre for Preventive Medicine, Department of Epidemiology and Disease Surveillance, Animal Health Trust, Suffolk, United Kingdom
| | - Neil Ferguson
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
| | - Anne Cori
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
| | - Thibaut Jombart
- MRC Centre for Outbreak Analysis and Modelling, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, United Kingdom
- * E-mail: (FC); (TJ); (AC)
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164
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Saltykova A, Wuyts V, Mattheus W, Bertrand S, Roosens NHC, Marchal K, De Keersmaecker SCJ. Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:. PLoS One 2018; 13:e0192504. [PMID: 29408896 PMCID: PMC5800660 DOI: 10.1371/journal.pone.0192504] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/24/2018] [Indexed: 12/05/2022] Open
Abstract
Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp. enterica serovar Typhimurium and serovar 1,4,[5],12:i:- isolates including five isolates from a confirmed outbreak and three isolates obtained from the same patient at different time points. The analysis was carried out using the original (high-coverage) and a down-sampled (low-coverage) datasets and two different reference genomes. All three tested workflows, namely CSI Phylogeny-based workflow, CFSAN-based workflow and PHEnix-based workflow, were able to correctly group the confirmed outbreak isolates and isolates from the same patient with all combinations of reference genomes and datasets. However, the workflows differed strongly with respect to the SNP distances between isolates and sensitivity towards sequencing coverage, which could be linked to the specific data analysis strategies used therein. To demonstrate the effect of particular data analysis steps, several modifications of the existing workflows were also tested. This allowed us to propose data analysis schemes most suitable for routine SNP-based subtyping applied to S. Typhimurium and S. 1,4,[5],12:i:-. Results presented in this study illustrate the importance of using correct data analysis strategies and to define benchmark and fine-tune parameters applied within routine data analysis pipelines to obtain optimal results.
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Affiliation(s)
- Assia Saltykova
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
| | - Véronique Wuyts
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
| | - Wesley Mattheus
- Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Sophie Bertrand
- Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Nancy H. C. Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB, Ghent, Belgium
- University of Pretoria, Pretoria, South Africa
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165
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Kendall M, Ayabina D, Xu Y, Stimson J, Colijn C. Estimating Transmission from Genetic and Epidemiological Data: A Metric to Compare Transmission Trees. Stat Sci 2018. [DOI: 10.1214/17-sts637] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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166
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Ye M, Bian LF. Association of serum leptin levels and pulmonary tuberculosis: a meta-analysis. J Thorac Dis 2018; 10:1027-1036. [PMID: 29607177 DOI: 10.21037/jtd.2018.01.70] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Background We performed a meta-analysis to investigate the association of serum leptin levels with the pathogenesis of pulmonary tuberculosis (PTB). Methods The retrieval of related articles was achieved through searching the electronic databases according to strict inclusion criteria. The STATA version 12.0 statistical software was employed to calculate the standardized mean difference (SMD) and 95% confidence interval (CI) during the statistical analysis. Results Twelve case-control studies were enrolled in this meta-analysis. Our finding showed that serum leptin levels of healthy controls were markedly higher than those of PTB patients (SMD =0.70, 95% CI =0.51-0.89, P<0.001). Stratified analysis based on ethnicity presented that lower serum leptin levels were apparently associated with the development of PTB among both Asians and Caucasians (Asians: SMD =0.38, 95% CI =0.15-0.61, P=0.001; Caucasians: SMD =1.54, 95% CI =1.17-1.91, P<0.001). Furthermore, subgroups analysis based on the detecting method also showed that there was an association between the serum leptin levels and the development of PTB in both ELISA subgroup and RIA subgroup (ELISA: SMD =1.03, 95% CI =0.81-1.26, P<0.001; RIA: SMD =-0.41, 95% CI =-0.82 to -0.01, P=0.045). Conclusions In conclusion, our present findings suggest that decreased serum leptin levels may be associated with the pathogenesis of PTB.
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Affiliation(s)
- Mao Ye
- The 2nd Department of Respiratory, Zhuji People's Hospital of Zhejiang Province, Zhuji 311800, China
| | - Lv-Fei Bian
- The 2nd Department of Respiratory, Zhuji People's Hospital of Zhejiang Province, Zhuji 311800, China
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167
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Rito T, Matos C, Carvalho C, Machado H, Rodrigues G, Oliveira O, Ferreira E, Gonçalves J, Maio L, Morais C, Ramos H, Guimarães JT, Santos CL, Duarte R, Correia-Neves M. A complex scenario of tuberculosis transmission is revealed through genetic and epidemiological surveys in Porto. BMC Infect Dis 2018; 18:53. [PMID: 29370774 PMCID: PMC5785791 DOI: 10.1186/s12879-018-2968-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 01/17/2018] [Indexed: 01/30/2023] Open
Abstract
Background Tuberculosis (TB) incidence is decreasing worldwide and eradication is becoming plausible. In low-incidence countries, intervention on migrant populations is considered one of the most important strategies for elimination. However, such measures are inappropriate in European areas where TB is largely endemic, such as Porto in Portugal. We aim to understand transmission chains in Porto through a genetic characterization of Mycobacterium tuberculosis strains and through a detailed epidemiological evaluation of cases. Methods We genotyped the M. tuberculosis strains using the MIRU-VNTR system. We performed an evolutionary reconstruction of the genotypes with median networks, used in this context for the first time. TB cases from a period of two years were evaluated combining genetic, epidemiological and georeferencing information. Results The data reveal a unique complex scenario in Porto where the autochthonous population acts as a genetic reservoir of M. tuberculosis diversity with discreet episodes of transmission, mostly undetected using classical epidemiology alone. Conclusions Although control policies have been successful in decreasing incidence in Porto, the discerned complexity suggests that, for elimination to be a realistic goal, strategies need to be adjusted and coupled with a continuous genetic characterization of strains and detailed epidemiological evaluation, in order to successfully identify and interrupt transmission chains.
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Affiliation(s)
- Teresa Rito
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal. .,ICVS/3B's, PT Government Associate Laboratory, Braga/4805-017, 4710-057, Guimarães, Portugal.
| | - Carlos Matos
- Eastern Porto Public Health Unit, (ACES Porto Oriental), 4200-510, Porto, Portugal
| | - Carlos Carvalho
- Northern Health Regional Administration, Department of Public Health, 4000-078, Porto, Portugal.,Multidisciplinary Unit for Biomedical Research (UMIB), Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-013, Porto, Portugal
| | - Henrique Machado
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/4805-017, 4710-057, Guimarães, Portugal
| | - Gabriela Rodrigues
- Northern Health Regional Administration, Department of Public Health, 4000-078, Porto, Portugal
| | - Olena Oliveira
- EPI Unit, Institute of Public Health, University of Porto, 4050-600, Porto, Portugal
| | - Eduarda Ferreira
- Eastern Porto Public Health Unit, (ACES Porto Oriental), 4200-510, Porto, Portugal
| | - Jorge Gonçalves
- Western Porto Public Health Unit, (ACES Porto Ocidental), 4100-503, Porto, Portugal
| | - Lurdes Maio
- Eastern Porto Public Health Unit, (ACES Porto Oriental), 4200-510, Porto, Portugal
| | - Clara Morais
- Porto TB Outpatient Centre, Centro Diagnóstico pneumológico, 4250-162, Porto, Portugal
| | - Helena Ramos
- Porto Hospital Centre, Hospital Santo António, 4099-001, Porto, Portugal
| | - João Tiago Guimarães
- EPI Unit, Institute of Public Health, University of Porto, 4050-600, Porto, Portugal.,Clinical Pathology, São João Hospital Centre, 4200-319, Porto, Portugal.,Biomedicine Department, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Catarina L Santos
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/4805-017, 4710-057, Guimarães, Portugal
| | - Raquel Duarte
- EPI Unit, Institute of Public Health, University of Porto, 4050-600, Porto, Portugal.,Pulmonology Department, Centro Hospitalar de Vila Nova de Gaia/Espinho EPE, 4400-129, Vila Nova de Gaia, Portugal.,Clinical Epidemiology, Predictive Medicine and Public Health Department, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Margarida Correia-Neves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Gualtar Campus, 4710-057, Braga, Portugal.,ICVS/3B's, PT Government Associate Laboratory, Braga/4805-017, 4710-057, Guimarães, Portugal
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168
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Occurrence and Nature of Double Alleles in Variable-Number Tandem-Repeat Patterns of More than 8,000 Mycobacterium tuberculosis Complex Isolates in The Netherlands. J Clin Microbiol 2018; 56:JCM.00761-17. [PMID: 29142049 PMCID: PMC5786718 DOI: 10.1128/jcm.00761-17] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 11/08/2017] [Indexed: 11/20/2022] Open
Abstract
Since 2004, variable-number tandem-repeat (VNTR) typing of Mycobacterium tuberculosis complex isolates has been applied on a structural basis in The Netherlands to study the epidemiology of tuberculosis (TB). Although this technique is faster and technically less demanding than the previously used restriction fragment length polymorphism (RFLP) typing, reproducibility remains a concern. In the period from 2004 to 2015, 8,532 isolates were subjected to VNTR typing in The Netherlands, with 186 (2.2%) of these exhibiting double alleles at one locus. Double alleles were most common in loci 4052 and 2163b. The variables significantly associated with double alleles were urban living (odds ratio [OR], 1.503; 95% confidence interval [CI], 1.084 to 2.084; P = 0.014) and pulmonary TB (OR, 1.703; 95% CI, 1.216 to 2.386; P = 0.002). Single-colony cultures of double-allele strains were produced and revealed single-allele profiles; a maximum of five single nucleotide polymorphisms (SNPs) was observed between the single- and double-allele isolates from the same patient when whole-genome sequencing (WGS) was applied. This indicates the presence of two bacterial populations with slightly different VNTR profiles in the parental population, related to genetic drift. This observation is confirmed by the fact that secondary cases from TB source cases with double-allele isolates sometimes display only one of the two alleles present in the source case. Double alleles occur at a frequency of 2.2% in VNTR patterns in The Netherlands. They are caused by biological variation rather than by technical aberrations and can be transmitted either as single- or double-allele variants.
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169
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Jeanes C, O'Grady J. Diagnosing tuberculosis in the 21st century - Dawn of a genomics revolution? Int J Mycobacteriol 2018; 5:384-391. [PMID: 27931678 DOI: 10.1016/j.ijmyco.2016.11.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tuberculosis (TB) ranks alongside HIV as the leading cause of death worldwide, killing 1.5million people in 2014. Traditional laboratory techniques do not provide sufficiently rapid results to inform clinicians on appropriate treatment, especially in the face of increasingly prevalent drug-resistant TB. Rapid molecular methods such as PCR and LAMP are vital tools in the fight against TB, however, rapid advances in next generation sequencing (NGS) technology are allowing increasingly rapid and accurate sequencing of entire bacterial genomes at ever decreasing cost, providing unprecedented depth of information. These advances mean NGS stands to revolutionise the diagnosis and epidemiological study of Mycobacterium tuberculosis infection. This review focuses on current applications of NGS for TB diagnosis including sequencing cultured isolates to predict drug resistance and, more desirably, direct diagnostic metagenomic sequencing of clinical samples. Also discussed is the potential impact of NGS on the epidemiological study of TB and some of the key challenges that need to be overcome to enable this promising technology to be translated into routine use.
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Affiliation(s)
- Christopher Jeanes
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
| | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
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170
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A cluster of multidrug-resistant Mycobacterium tuberculosis among patients arriving in Europe from the Horn of Africa: a molecular epidemiological study. THE LANCET. INFECTIOUS DISEASES 2018; 18:431-440. [PMID: 29326013 PMCID: PMC5864516 DOI: 10.1016/s1473-3099(18)30004-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Revised: 11/10/2017] [Accepted: 11/21/2017] [Indexed: 01/08/2023]
Abstract
Background The risk of tuberculosis outbreaks among people fleeing hardship for refuge in Europe is heightened. We describe the cross-border European response to an outbreak of multidrug-resistant tuberculosis among patients from the Horn of Africa and Sudan. Methods On April 29 and May 30, 2016, the Swiss and German National Mycobacterial Reference Laboratories independently triggered an outbreak investigation after four patients were diagnosed with multidrug-resistant tuberculosis. In this molecular epidemiological study, we prospectively defined outbreak cases with 24-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) profiles; phenotypic resistance to isoniazid, rifampicin, ethambutol, pyrazinamide, and capreomycin; and corresponding drug resistance mutations. We whole-genome sequenced all Mycobacterium tuberculosis isolates and clustered them using a threshold of five single nucleotide polymorphisms (SNPs). We collated epidemiological data from host countries from the European Centre for Disease Prevention and Control. Findings Between Feb 12, 2016, and April 19, 2017, 29 patients were diagnosed with multidrug-resistant tuberculosis in seven European countries. All originated from the Horn of Africa or Sudan, with all isolates two SNPs or fewer apart. 22 (76%) patients reported their travel routes, with clear spatiotemporal overlap between routes. We identified a further 29 MIRU-VNTR-linked cases from the Horn of Africa that predated the outbreak, but all were more than five SNPs from the outbreak. However all 58 isolates shared a capreomycin resistance-associated tlyA mutation. Interpretation Our data suggest that source cases are linked to an M tuberculosis clone circulating in northern Somalia or Djibouti and that transmission probably occurred en route before arrival in Europe. We hypothesise that the shared mutation of tlyA is a drug resistance mutation and phylogenetic marker, the first of its kind in M tuberculosis sensu stricto. Funding The Swiss Federal Office of Public Health, the University of Zurich, the Wellcome Trust, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre (BRC), the Medical Research Council, BELTA-TBnet, the European Union, the German Center for Infection Research, and Leibniz Science Campus Evolutionary Medicine of the Lung (EvoLUNG).
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171
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Ochoa-Díaz MM, Daza-Giovannetty S, Gómez-Camargo D. Bacterial Genotyping Methods: From the Basics to Modern. Methods Mol Biol 2018; 1734:13-20. [PMID: 29288442 DOI: 10.1007/978-1-4939-7604-1_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Bacterial genotyping methods have been used in several areas of microbiology and have facilitated the identification of bacterial strains, as well as the study of virulence and resistance factors, epidemiological surveillance, among others. Constituting, in this way, as complementary or alternative to phenotypic methods. This chapter reviews some of the methods of bacterial genotyping used nowadays, explains briefly how they are performed, and highlights some limitations and advantages they have.
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Affiliation(s)
- Margarita M Ochoa-Díaz
- Faculty of Medicine, Tropical Medicine Doctorate, UNIMOL, University of Cartagena, Cartagena, Colombia.
| | - Silvana Daza-Giovannetty
- Faculty of Medicine, Tropical Medicine Doctorate, UNIMOL, University of Cartagena, Cartagena, Colombia
| | - Doris Gómez-Camargo
- Faculty of Medicine, Tropical Medicine Doctorate, UNIMOL, University of Cartagena, Cartagena, Colombia
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172
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Bruning-Fann CS, Robbe-Austerman S, Kaneene JB, Thomsen BV, Tilden JD, Ray JS, Smith RW, Fitzgerald SD, Bolin SR, O'Brien DJ, Mullaney TP, Stuber TP, Averill JJ, Marks D. Use of whole-genome sequencing and evaluation of the apparent sensitivity and specificity of antemortem tuberculosis tests in the investigation of an unusual outbreak of Mycobacterium bovis infection in a Michigan dairy herd. J Am Vet Med Assoc 2017; 251:206-216. [PMID: 28671497 DOI: 10.2460/javma.251.2.206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To describe use of whole-genome sequencing (WGS) and evaluate the apparent sensitivity and specificity of antemortem tuberculosis tests during investigation of an unusual outbreak of Mycobacterium bovis infection in a Michigan dairy herd. DESIGN Bovine tuberculosis (bTB) outbreak investigation. ANIMALS Cattle, cats, dog, and wildlife. PROCEDURES All cattle in the index dairy herd were screened for bTB with the caudal fold test (CFT), and cattle ≥ 6 months old were also screened with a γ-interferon (γIFN) assay. The index herd was depopulated along with all barn cats and a dog that were fed unpasteurized milk from the herd. Select isolates from M bovis-infected animals from the index herd and other bTB-affected herds underwent WGS. Wildlife around all affected premises was examined for bTB. RESULTS No evidence of bTB was found in any wildlife examined. Within the index herd, 53 of 451 (11.8%) cattle and 12 of 21 (57%) cats were confirmed to be infected with M bovis. Prevalence of M bovis-infected cattle was greatest among 4- to 7-month-old calves (16/49 [33%]) followed by adult cows (36/203 [18%]). The apparent sensitivity and specificity were 86.8% and 92.7% for the CFT and 80.4% and 96.5% for the γIFN assay when results for those tests were interpreted separately and 96.1% and 91.7% when results were interpreted in parallel. Results of WGS revealed that M bovis-infected barn cats and cattle from the index herd and 6 beef operations were infected with the same strain of M bovis. Of the 6 bTB-affected beef operations identified during the investigation, 3 were linked to the index herd only by WGS results; there was no record of movement of livestock or waste milk from the index herd to those operations. CONCLUSIONS AND CLINICAL RELEVANCE Whole-genome sequencing enhanced the epidemiological investigation and should be used in all disease investigations. Performing the CFT and γIFN assay in parallel improved the antemortem ability to detect M bovis-infected animals. Contact with M bovis-infected cattle and contaminated milk were major risk factors for transmission of bTB within and between herds of this outbreak.
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Abstract
Tuberculosis is responsible for more deaths worldwide than any other infectious disease. For anyone looking to learn more about this persistent public health threat, this conversational "frequently asked questions" style review addresses a breadth of questions. It offers a brief, somewhat opinionated, review of what is and is not known, particularly in light of how findings in the lab do or do not help inform the understanding of human tuberculosis.
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Affiliation(s)
- Kristine M Guinn
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Eric J Rubin
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
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174
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Cazzaniga S, Apfelbacher C, Diepgen T, Ofenloch R, Weisshaar E, Molin S, Bauer A, Mahler V, Elsner P, Schmitt J, Ballmer‐Weber B, Spring P, Naldi L, Borradori L, Simon D. Patterns of chronic hand eczema: a semantic map analysis of the
CARPE
registry data. Br J Dermatol 2017; 178:229-237. [DOI: 10.1111/bjd.15660] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2017] [Indexed: 11/30/2022]
Affiliation(s)
- S. Cazzaniga
- Department of Dermatology, Inselspital Bern University Hospital Bern Switzerland
- Centro Studi GISED Bergamo Italy
| | - C. Apfelbacher
- Institute of Epidemiology and Preventive Medicine University of Regensburg Regensburg Germany
| | - T. Diepgen
- Department of Clinical Social Medicine Occupational and Environmental Dermatology University Hospital Ruprecht Karls University Heidelberg Germany
| | - R.F. Ofenloch
- Department of Clinical Social Medicine Occupational and Environmental Dermatology University Hospital Ruprecht Karls University Heidelberg Germany
| | - E. Weisshaar
- Department of Clinical Social Medicine Occupational and Environmental Dermatology University Hospital Ruprecht Karls University Heidelberg Germany
| | - S. Molin
- Department of Dermatology and Allergy Ludwig Maximilian University Munich Germany
| | - A. Bauer
- Department of Dermatology University Hospital Carl Gustav Carus Technical University Dresden Dresden Germany
| | - V. Mahler
- Department of Dermatology University Hospital of Erlangen Friedrich Alexander University Erlangen‐Nuremberg Erlangen Germany
| | - P. Elsner
- Department of Dermatology and Dermatological Allergy Friedrich Schiller University Jena Jena Germany
| | - J. Schmitt
- Centre for Evidence‐based Healthcare Medical Faculty Carl Gustav Carus Technical University Dresden Dresden Germany
| | - B.K. Ballmer‐Weber
- Allergy Unit Department of Dermatology University Hospital Zürich Zurich Switzerland
| | - P. Spring
- Department of Dermatology University Hospital of Lausanne CHUV Lausanne Switzerland
| | - L. Naldi
- Centro Studi GISED Bergamo Italy
- Department of Dermatology Papa Giovanni XXIII Hospital Bergamo Italy
| | - L. Borradori
- Department of Dermatology, Inselspital Bern University Hospital Bern Switzerland
| | - D. Simon
- Department of Dermatology, Inselspital Bern University Hospital Bern Switzerland
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175
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Andrés M, Göhring-Zwacka E, Fiebig L, Priwitzer M, Richter E, Rüsch-Gerdes S, Haas W, Niemann S, Brodhun B. Integration of molecular typing results into tuberculosis surveillance in Germany-A pilot study. PLoS One 2017; 12:e0188356. [PMID: 29166403 PMCID: PMC5699808 DOI: 10.1371/journal.pone.0188356] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2017] [Accepted: 11/06/2017] [Indexed: 11/19/2022] Open
Abstract
An integrated molecular surveillance for tuberculosis (TB) improves the understanding of ongoing TB transmission by combining molecular typing and epidemiological data. However, the implementation of an integrated molecular surveillance for TB is complex and requires thoughtful consideration of feasibility, demand, public health benefits and legal issues. We aimed to pilot the integration of molecular typing results between 2008 and 2010 in the German Federal State of Baden-Württemberg (population 10.88 Million) as preparation for a nationwide implementation. Culture positive TB cases were typed by IS6110 DNA fingerprinting and results were integrated into routine notification data. Demographic and clinical characteristics of cases and clusters were described and new epidemiological links detected after integrating typing data were calculated. Furthermore, a cross-sectional survey was performed among local public health offices to evaluate their perception and experiences. Overall, typing results were available for 83% of notified culture positive TB cases, out of which 25% were clustered. Age <15 years (OR = 4.96, 95% CI: 1.69–14.55) and being born in Germany (OR = 2.01, 95% CI: 1.44–2.80) were associated with clustering. At cluster level, molecular typing information allowed the identification of previously unknown epidemiological links in 11% of the clusters. In 59% of the clusters it was not possible to identify any epidemiological link. Clusters extending over different counties were less likely to have epidemiological links identified among their cases (OR = 11.53, 95% CI: 3.48–98.23). The majority of local public health offices found molecular typing useful for their work. Our study illustrates the feasibility of integrating typing data into the German TB notification system and depicts its added public health value as complementary strategy in TB surveillance, especially to uncover transmission events among geographically separated TB patients. It also emphasizes that special efforts are required to strengthen the communication between local public health offices in different counties to enhance TB control.
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Affiliation(s)
- Marta Andrés
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
- * E-mail:
| | - Elke Göhring-Zwacka
- State Health Department (Landesgesundheitsamt) Baden-Württemberg, Stuttgart, Germany
| | - Lena Fiebig
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Martin Priwitzer
- Local Public Health Office (Gesundheitsamt) Stuttgart, Stuttgart, Germany
| | | | - Sabine Rüsch-Gerdes
- National Reference Center (NRC) for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Walter Haas
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Stefan Niemann
- National Reference Center (NRC) for Mycobacteria, Research Center Borstel, Borstel, Germany
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Borstel, Germany
| | - Bonita Brodhun
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
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176
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Brites D, Gagneux S. The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:1-26. [DOI: 10.1007/978-3-319-64371-7_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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177
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Mathema B, Andrews JR, Cohen T, Borgdorff MW, Behr M, Glynn JR, Rustomjee R, Silk BJ, Wood R. Drivers of Tuberculosis Transmission. J Infect Dis 2017; 216:S644-S653. [PMID: 29112745 PMCID: PMC5853844 DOI: 10.1093/infdis/jix354] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Measuring tuberculosis transmission is exceedingly difficult, given the remarkable variability in the timing of clinical disease after Mycobacterium tuberculosis infection; incident disease can result from either a recent (ie, weeks to months) or a remote (ie, several years to decades) infection event. Although we cannot identify with certainty the timing and location of tuberculosis transmission for individuals, approaches for estimating the individual probability of recent transmission and for estimating the fraction of tuberculosis cases due to recent transmission in populations have been developed. Data used to estimate the probable burden of recent transmission include tuberculosis case notifications in young children and trends in tuberculin skin test and interferon γ-release assays. More recently, M. tuberculosis whole-genome sequencing has been used to estimate population levels of recent transmission, identify the distribution of specific strains within communities, and decipher chains of transmission among culture-positive tuberculosis cases. The factors that drive the transmission of tuberculosis in communities depend on the burden of prevalent tuberculosis; the ways in which individuals live, work, and interact (eg, congregate settings); and the capacity of healthcare and public health systems to identify and effectively treat individuals with infectious forms of tuberculosis. Here we provide an overview of these factors, describe tools for measurement of ongoing transmission, and highlight knowledge gaps that must be addressed.
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Affiliation(s)
- Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University, California
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut
| | - Martien W Borgdorff
- Centers for Disease Control and Prevention, Kisumu, Kenya
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, the Netherlands
| | - Marcel Behr
- McGill International TB Centre, Research Institute of the McGill University Health Centre, Montreal,Canada
| | - Judith R Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Roxana Rustomjee
- Tuberculosis Clinical Research Branch, Therapeutics Research Program, Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, Rockville, Maryland
| | - Benjamin J Silk
- Division of Tuberculosis Elimination, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Robin Wood
- Desmond Tutu HIV Centre, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
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178
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Satta G, Lipman M, Smith GP, Arnold C, Kon OM, McHugh TD. Mycobacterium tuberculosis and whole-genome sequencing: how close are we to unleashing its full potential? Clin Microbiol Infect 2017; 24:604-609. [PMID: 29108952 DOI: 10.1016/j.cmi.2017.10.030] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2017] [Revised: 10/21/2017] [Accepted: 10/30/2017] [Indexed: 01/16/2023]
Abstract
BACKGROUND Nearly two decades after completion of the genome sequence of Mycobacterium tuberculosis (MTB), and with the advent of next generation sequencing technologies (NGS), whole-genome sequencing (WGS) has been applied to a wide range of clinical scenarios. Starting in 2017, England is the first country in the world to pioneer its use on a national scale for the diagnosis of tuberculosis, detection of drug resistance, and typing of MTB. AIMS This narrative review critically analyses the current applications of WGS for MTB and explains how close we are to realizing its full potential as a diagnostic, epidemiologic, and research tool. SOURCES We searched for reports (both original articles and reviews) published in English up to 31 May 2017, with combinations of the following keywords: whole-genome sequencing, Mycobacterium, and tuberculosis. MEDLINE, Embase, and Scopus were used as search engines. We included articles that covered different aspects of whole-genome sequencing in relation to MTB. CONTENT This review focuses on three main themes: the role of WGS for the prediction of drug susceptibility, MTB outbreak investigation and genetic diversity, and research applications of NGS. IMPLICATIONS Many of the original expectations have been accomplished, and we believe that with its unprecedented sensitivity and power, WGS has the potential to address many unanswered questions in the near future. However, caution is still needed when interpreting WGS data as there are some important limitations to be aware of, from correct interpretation of drug susceptibilities to the bioinformatic support needed.
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Affiliation(s)
- G Satta
- UCL-TB and UCL Centre for Clinical Microbiology, Department of Infection, University College London, UK; Imperial College Healthcare NHS Trust, London, UK.
| | - M Lipman
- UCL-TB and UCL Respiratory, University College London, UK; Royal Free London NHS Foundation Trust, London, UK
| | - G P Smith
- National Mycobacterium Reference Laboratory, Public Health England, UK; Heart of England NHS Foundation Trust, Birmingham, UK
| | - C Arnold
- UCL-TB and UCL Centre for Clinical Microbiology, Department of Infection, University College London, UK; Genomic Services and Development Unit, Public Health England, UK
| | - O M Kon
- Imperial College Healthcare NHS Trust, London, UK; National Heart and Lung Institute, Imperial College London, UK
| | - T D McHugh
- UCL-TB and UCL Centre for Clinical Microbiology, Department of Infection, University College London, UK
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179
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Tagini F, Greub G. Bacterial genome sequencing in clinical microbiology: a pathogen-oriented review. Eur J Clin Microbiol Infect Dis 2017; 36:2007-2020. [PMID: 28639162 PMCID: PMC5653721 DOI: 10.1007/s10096-017-3024-6] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/22/2017] [Indexed: 12/11/2022]
Abstract
In recent years, whole-genome sequencing (WGS) has been perceived as a technology with the potential to revolutionise clinical microbiology. Herein, we reviewed the literature on the use of WGS for the most commonly encountered pathogens in clinical microbiology laboratories: Escherichia coli and other Enterobacteriaceae, Staphylococcus aureus and coagulase-negative staphylococci, streptococci and enterococci, mycobacteria and Chlamydia trachomatis. For each pathogen group, we focused on five different aspects: the genome characteristics, the most common genomic approaches and the clinical uses of WGS for (i) typing and outbreak analysis, (ii) virulence investigation and (iii) in silico antimicrobial susceptibility testing. Of all the clinical usages, the most frequent and straightforward usage was to type bacteria and to trace outbreaks back. A next step toward standardisation was made thanks to the development of several new genome-wide multi-locus sequence typing systems based on WGS data. Although virulence characterisation could help in various particular clinical settings, it was done mainly to describe outbreak strains. An increasing number of studies compared genotypic to phenotypic antibiotic susceptibility testing, with mostly promising results. However, routine implementation will preferentially be done in the workflow of particular pathogens, such as mycobacteria, rather than as a broadly applicable generic tool. Overall, concrete uses of WGS in routine clinical microbiology or infection control laboratories were done, but the next big challenges will be the standardisation and validation of the procedures and bioinformatics pipelines in order to reach clinical standards.
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Affiliation(s)
- F Tagini
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland
| | - G Greub
- Institute of Microbiology, Department of Laboratory, University of Lausanne & University Hospital, Lausanne, Switzerland.
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180
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Roycroft E, O'Toole RF, Fitzgibbon MM, Montgomery L, O'Meara M, Downes P, Jackson S, O'Donnell J, Laurenson IF, McLaughlin AM, Keane J, Rogers TR. Molecular epidemiology of multi- and extensively-drug-resistant Mycobacterium tuberculosis in Ireland, 2001-2014. J Infect 2017; 76:55-67. [PMID: 29031637 DOI: 10.1016/j.jinf.2017.10.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 09/05/2017] [Accepted: 10/03/2017] [Indexed: 12/16/2022]
Abstract
OBJECTIVES The primary objective of this work was to examine the acquisition and spread of multi-drug resistant (MDR) tuberculosis (TB) in Ireland. METHODS All available Mycobacterium tuberculosis complex (MTBC) isolates (n = 42), from MDR-TB cases diagnosed in Ireland between 2001 and 2014, were analysed using phenotypic drug-susceptibility testing, Mycobacterial-Interspersed-Repetitive-Units Variable-Number Tandem-Repeat (MIRU-VNTR) genotyping, and whole-genome sequencing (WGS). RESULTS The lineage distribution of the MDR-TB isolates comprised 54.7% Euro-American, 33.3% East Asian, 7.2% East African Indian, and 4.8% Indo-Oceanic. A significant association was identified between the East Asian Beijing sub-lineage and the relative risk of an isolate being MDR. Over 75% of MDR-TB cases were confirmed in non-Irish born individuals and 7 MIRU-VNTR genotypes were identical to clusters in other European countries indicating cross-border spread of MDR-TB to Ireland. WGS data provided the first evidence in Ireland of in vivo microevolution of MTBC isolates from drug-susceptible to MDR, and from MDR to extensively-drug resistant (XDR). In addition, they found that the katG S315T isoniazid and rpoB S450L rifampicin resistance mutations were dominant across the different MTBC lineages. CONCLUSIONS Our molecular epidemiological analyses identified the spread of MDR-TB to Ireland from other jurisdictions and its potential to evolve to XDR-TB.
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Affiliation(s)
- E Roycroft
- Irish Mycobacteria Reference Laboratory, Labmed Directorate, St. James's Hospital, Dublin, Ireland; Department of Clinical Microbiology, Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland.
| | - R F O'Toole
- Department of Clinical Microbiology, Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland; School of Medicine, Faculty of Health, University of Tasmania, Hobart, Australia
| | - M M Fitzgibbon
- Irish Mycobacteria Reference Laboratory, Labmed Directorate, St. James's Hospital, Dublin, Ireland; Department of Clinical Microbiology, Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - L Montgomery
- Irish Mycobacteria Reference Laboratory, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - M O'Meara
- Department of Public Health, Dr. Steeven's Hospital, Dublin, Ireland
| | - P Downes
- Department of Public Health, Dr. Steeven's Hospital, Dublin, Ireland
| | - S Jackson
- Health Protection Surveillance Centre, Dublin, Ireland
| | - J O'Donnell
- Health Protection Surveillance Centre, Dublin, Ireland
| | - I F Laurenson
- Scottish Mycobacteria Reference Laboratory, Edinburgh, UK
| | - A M McLaughlin
- Department of Respiratory Medicine, St. James's Hospital and Trinity Translational Medicine Institute Trinity College Dublin, Ireland
| | - J Keane
- Department of Respiratory Medicine, St. James's Hospital and Trinity Translational Medicine Institute Trinity College Dublin, Ireland
| | - T R Rogers
- Irish Mycobacteria Reference Laboratory, Labmed Directorate, St. James's Hospital, Dublin, Ireland; Department of Clinical Microbiology, Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
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181
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O'Toole RF, Gautam SS. Limitations of the Mycobacterium tuberculosis reference genome H37Rv in the detection of virulence-related loci. Genomics 2017; 109:471-474. [DOI: 10.1016/j.ygeno.2017.07.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 10/19/2022]
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182
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Michael Dunne W, Pouseele H, Monecke S, Ehricht R, van Belkum A. Epidemiology of transmissible diseases: Array hybridization and next generation sequencing as universal nucleic acid-mediated typing tools. INFECTION GENETICS AND EVOLUTION 2017; 63:332-345. [PMID: 28943408 DOI: 10.1016/j.meegid.2017.09.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 09/14/2017] [Accepted: 09/15/2017] [Indexed: 02/05/2023]
Abstract
The magnitude of interest in the epidemiology of transmissible human diseases is reflected in the vast number of tools and methods developed recently with the expressed purpose to characterize and track evolutionary changes that occur in agents of these diseases over time. Within the past decade a new suite of such tools has become available with the emergence of the so-called "omics" technologies. Among these, two are exponents of the ongoing genomic revolution. Firstly, high-density nucleic acid probe arrays have been proposed and developed using various chemical and physical approaches. Via hybridization-mediated detection of entire genes or genetic polymorphisms in such genes and intergenic regions these so called "DNA chips" have been successfully applied for distinguishing very closely related microbial species and strains. Second and even more phenomenal, next generation sequencing (NGS) has facilitated the assessment of the complete nucleotide sequence of entire microbial genomes. This technology currently provides the most detailed level of bacterial genotyping and hence allows for the resolution of microbial spread and short-term evolution in minute detail. We will here review the very recent history of these two technologies, sketch their usefulness in the elucidation of the spread and epidemiology of mostly hospital-acquired infections and discuss future developments.
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Affiliation(s)
- W Michael Dunne
- Data Analytics Unit, bioMerieux, 100 Rodolphe Street, Durham, NC 27712, USA.
| | - Hannes Pouseele
- Data Analytics Unit, bioMerieux, 100 Rodolphe Street, Durham, NC 27712, USA; Applied Maths NV, Keistraat 120, 9830 Sint-Martens-Latem, Belgium.
| | - Stefan Monecke
- Alere Technologies GmbH, Jena, Germany; InfectoGnostics Research Campus, Jena, Germany; Institute for Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - Ralf Ehricht
- Alere Technologies GmbH, Jena, Germany; InfectoGnostics Research Campus, Jena, Germany.
| | - Alex van Belkum
- Data Analytics Unit, bioMérieux, 3, Route de Port Michaud, 38390 La Balme Les Grottes, France.
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183
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Senghore M, Otu J, Witney A, Gehre F, Doughty EL, Kay GL, Butcher P, Salako K, Kehinde A, Onyejepu N, Idigbe E, Corrah T, de Jong B, Pallen MJ, Antonio M. Whole-genome sequencing illuminates the evolution and spread of multidrug-resistant tuberculosis in Southwest Nigeria. PLoS One 2017; 12:e0184510. [PMID: 28926571 PMCID: PMC5604961 DOI: 10.1371/journal.pone.0184510] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 08/27/2017] [Indexed: 11/18/2022] Open
Abstract
Nigeria has an emerging problem with multidrug-resistant tuberculosis (MDR-TB). Whole-genome sequencing was used to understand the epidemiology of tuberculosis and genetics of multi-drug resistance among patients from two tertiary referral centers in Southwest Nigeria. In line with previous molecular epidemiology studies, most isolates of Mycobacterium tuberculosis from this dataset belonged to the Cameroon clade within the Euro-American lineage. Phylogenetic analysis showed this clade was undergoing clonal expansion in this region, and suggests that it was involved in community transmission of sensitive and multidrug-resistant tuberculosis. Five patients enrolled for retreatment were infected with pre-extensively drug resistant (pre-XDR) due to fluoroquinolone resistance in isolates from the Cameroon clade. In all five cases resistance was conferred through a mutation in the gyrA gene. In some patients, genomic changes occurred in bacterial isolates during the course of treatment that potentially led to decreased drug susceptibility. We conclude that inter-patient transmission of resistant isolates, principally from the Cameroon clade, contributes to the spread of MDR-TB in this setting, underscoring the urgent need to curb the spread of multi-drug resistance in this region.
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MESH Headings
- Adolescent
- Adult
- Antitubercular Agents/pharmacology
- Bacterial Proteins/genetics
- Cameroon/epidemiology
- Child
- Child, Preschool
- DNA Gyrase/genetics
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Female
- Genome, Bacterial
- Humans
- Infant
- Infant, Newborn
- Male
- Mutation
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Nigeria/epidemiology
- Phylogeny
- Sequence Analysis, DNA
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/microbiology
- Young Adult
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Affiliation(s)
- Madikay Senghore
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Jacob Otu
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | - Adam Witney
- Institute of Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Florian Gehre
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
| | - Emma L. Doughty
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Gemma L. Kay
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
| | - Phillip Butcher
- Institute of Infection and Immunity, St George’s University of London, London, United Kingdom
| | - Kayode Salako
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Nigeria
| | - Aderemi Kehinde
- Department of Medical Microbiology & Parasitology, University College Hospital, Ibadan, Nigeria
| | - Nneka Onyejepu
- National Tuberculosis Reference Laboratory, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Emmanuel Idigbe
- National Tuberculosis Reference Laboratory, Nigeria Institute of Medical Research, Lagos, Nigeria
| | - Tumani Corrah
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
| | | | - Mark J. Pallen
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
- Quadram Institute, Norwich Research Park, Norwich, Norfolk, NR4 7UA
| | - Martin Antonio
- Vaccines and Immunity Theme, Medical Research Council Unit The Gambia, Fajara, The Gambia
- Microbiology and Infection Unit, The University of Warwick, Coventry, United Kingdom
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail:
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184
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Folkvardsen DB, Norman A, Andersen ÅB, Michael Rasmussen E, Jelsbak L, Lillebaek T. Genomic Epidemiology of a Major Mycobacterium tuberculosis Outbreak: Retrospective Cohort Study in a Low-Incidence Setting Using Sparse Time-Series Sampling. J Infect Dis 2017; 216:366-374. [PMID: 28666374 DOI: 10.1093/infdis/jix298] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/20/2017] [Indexed: 11/14/2022] Open
Abstract
Since 1992, Denmark has documented the largest outbreak of tuberculosis in Scandinavia ascribed to a single genotype, termed C2/1112-15. As of spring 2017, the International Reference Laboratory of Mycobacteriology in Copenhagen has collected and identified isolates from more than a thousand cases belonging to this outbreak via routine mycobacterial interspersed repetitive units-variable number of tandem repeats typing. Here, we present a retrospective analysis of the C2/1112-15 dataset, based on whole-genome data from a sparse time series consisting of 5 randomly selected isolates from 23 years of sampling. Even if these data are derived from only 12% of the collected isolates, we have been able to extract important key information, such as mutation rate and conserved single-nucleotide polymorphisms to identify discrete transmission chains, as well as the possible historical origins of the outbreak.
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Affiliation(s)
- Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby
| | - Åse Bengård Andersen
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet.,Research Unit for Infectious Diseases, Department of Clinical Research, University of Southern Denmark, Odense
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen
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185
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Hallmaier-Wacker LK, Munster VJ, Knauf S. Disease reservoirs: from conceptual frameworks to applicable criteria. Emerg Microbes Infect 2017; 6:e79. [PMID: 28874791 PMCID: PMC5625316 DOI: 10.1038/emi.2017.65] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 06/20/2017] [Accepted: 06/28/2017] [Indexed: 11/25/2022]
Abstract
Central to the One Health approach and any disease eradication program is the question of whether a pathogen has a non-human reservoir. Despite well-established conceptual frameworks that define a reservoir of infection, empirical characterization of reservoirs often remains controversial, challenging and sometimes misleading. What is essentially missing are applicable requirements that standardize the use of the term ‘reservoir of infection’ across multiple disciplines. We propose an empirical framework, considering maintenance and feasible transmission of a pathogen, to standardize the acceptance of a disease reservoir across multiple disciplines. We demonstrate the intended use of these requirements by applying them to different diseases that are known to infect both humans and animals.
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Affiliation(s)
- Luisa K Hallmaier-Wacker
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen 37077, Germany.,Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen 37077, Germany
| | - Vincent J Munster
- Virus Ecology Unit, Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rocky Mountain Laboratories, Hamilton, MT 59840, USA
| | - Sascha Knauf
- Work Group Neglected Tropical Diseases, Pathology Unit, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, Göttingen 37077, Germany
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186
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Zhang H, Huang H, Liu C, Jia T, Zhang L, Zhou D, Wei S, Wang C. Genotyping and drug-resistance epidemiology of mycobacterium tuberculosis in Xuzhou, China. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2017; 10:9675-9682. [PMID: 31966848 PMCID: PMC6965968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 08/09/2017] [Indexed: 06/10/2023]
Abstract
BACKGROUND To explore the genetic diversity and drug resistance status of MTB in Xuzhou, China. METHODS A total of 325 clinical MTB strains were genotyped by spacer-oligonucleotide typing (spoligotyping) and mycobacterial interspersed repetitive unit variable number of tandem repeats (MIRU-VNTR). Phenotypic resistance was assessed by drug susceptibility testing (DST). RESULT Based on the spoligotyping method, 325 MTB isolates were classified into 5 known genotypes and 12 unknown genotypes, and the largest branch comprised 268 strains belonging to the Beijing family. Based on the 15-loci VNTR typing method, 325 MTB isolates were divided into 35 clusters and 220 unique patterns. Compared to the low discriminatory power of spoligotyping genotyping (HGDI = 0.3444), 15-loci VNTR genotyping had a significantly higher discriminatory power for all strains (HGDI = 0.9980), particularly for the Beijing family strains (HGDI = 0.9892). When spoligotyping and 15-loci VNTR methods were used together, the discriminatory power increased to 0.9991. The Beijing family strain presented increased risks for developing multi-drug resistance TB (P < 0.05). CONCLUSION The Beijing family isolates is the most prevalent strains in Xuzhou. Spoligotyping, in combination with 15-loci MIRU-VNTR, is useful for epidemiological analysis of MTB transmission in Xuzhou.
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Affiliation(s)
- Haiqing Zhang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Haibin Huang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Chengyong Liu
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Tong Jia
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Limao Zhang
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Dongqing Zhou
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Sumei Wei
- Department of Tuberculosis, Xuzhou Infectious Disease HospitalXuzhou, China
| | - Chunying Wang
- Department of Infectious Diseases, Xuzhou Infectious Disease HospitalXuzhou, China
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187
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Abstract
The tuberculosis agent Mycobacterium tuberculosis has undergone a long and selective evolution toward human infection and represents one of the most widely spread pathogens due to its efficient aerosol-mediated human-to-human transmission. With the availability of more and more genome sequences, the evolutionary trajectory of this obligate pathogen becomes visible, which provides us with new insights into the molecular events governing evolution of the bacterium and its ability to accumulate drug-resistance mutations. In this review, we summarize recent developments in mycobacterial research related to this matter that are important for a better understanding of the current situation and future trends and developments in the global epidemiology of tuberculosis, as well as for possible public health intervention possibilities.
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188
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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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189
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Abstract
Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
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190
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van Ingen J, Kohl TA, Kranzer K, Hasse B, Keller PM, Katarzyna Szafrańska A, Hillemann D, Chand M, Schreiber PW, Sommerstein R, Berger C, Genoni M, Rüegg C, Troillet N, Widmer AF, Becker SL, Herrmann M, Eckmanns T, Haller S, Höller C, Debast SB, Wolfhagen MJ, Hopman J, Kluytmans J, Langelaar M, Notermans DW, Ten Oever J, van den Barselaar P, Vonk ABA, Vos MC, Ahmed N, Brown T, Crook D, Lamagni T, Phin N, Smith EG, Zambon M, Serr A, Götting T, Ebner W, Thürmer A, Utpatel C, Spröer C, Bunk B, Nübel U, Bloemberg GV, Böttger EC, Niemann S, Wagner D, Sax H. Global outbreak of severe Mycobacterium chimaera disease after cardiac surgery: a molecular epidemiological study. THE LANCET. INFECTIOUS DISEASES 2017; 17:1033-1041. [PMID: 28711585 DOI: 10.1016/s1473-3099(17)30324-9] [Citation(s) in RCA: 156] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 04/25/2017] [Accepted: 05/03/2017] [Indexed: 01/25/2023]
Abstract
BACKGROUND Since 2013, over 100 cases of Mycobacterium chimaera prosthetic valve endocarditis and disseminated disease were notified in Europe and the USA, linked to contaminated heater-cooler units (HCUs) used during cardiac surgery. We did a molecular epidemiological investigation to establish the source of these patients' disease. METHODS We included 24 M chimaera isolates from 21 cardiac surgery-related patients in Switzerland, Germany, the Netherlands, and the UK, 218 M chimaera isolates from various types of HCUs in hospitals, from LivaNova (formerly Sorin; London, UK) and Maquet (Rastatt, Germany) brand HCU production sites, and unrelated environmental sources and patients, as well as eight Mycobacterium intracellulare isolates. Isolates were analysed by next-generation whole-genome sequencing using Illumina and Pacific Biosciences technologies, and compared with published M chimaera genomes. FINDINGS Phylogenetic analysis based on whole-genome sequencing of 250 isolates revealed two major M chimaera groups. Cardiac surgery-related patient isolates were all classified into group 1, in which all, except one, formed a distinct subgroup. This subgroup also comprised isolates from 11 cardiac surgery-related patients reported from the USA, most isolates from LivaNova HCUs, and one from their production site. Isolates from other HCUs and unrelated patients were more widely distributed in the phylogenetic tree. INTERPRETATION HCU contamination with M chimaera at the LivaNova factory seems a likely source for cardiothoracic surgery-related severe M chimaera infections diagnosed in Switzerland, Germany, the Netherlands, the UK, the USA, and Australia. Protective measures and heightened clinician awareness are essential to guarantee patient safety. FUNDING Partly funded by the EU Horizon 2020 programme, its FP7 programme, the German Center for Infection Research (DZIF), the Swiss National Science Foundation, the Swiss Federal Office of Public Health, and National Institute of Health Research Oxford Health Protection Research Units on Healthcare Associated Infection and Antimicrobial Resistance.
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Affiliation(s)
- Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - Katharina Kranzer
- National Mycobacteriology Reference Laboratory, Forschungszentrum Borstel, Borstel, Germany
| | - Barbara Hasse
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; National Center for Mycobacteria, University of Zurich, Zurich, Switzerland
| | - Anna Katarzyna Szafrańska
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Doris Hillemann
- National Mycobacteriology Reference Laboratory, Forschungszentrum Borstel, Borstel, Germany
| | - Meera Chand
- National Infection Service, Public Health England, London, UK; Guy's and St Thomas' NHS Foundation Trust, London, UK; NIHR Health Protection Research Unit in Respiratory Infections, Imperial College London, London, UK
| | - Peter Werner Schreiber
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Rami Sommerstein
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland; Department of Infectious Diseases, Bern University Hospital, Bern, Switzerland
| | - Christoph Berger
- Infectious Diseases and Children's Research, University Children's Hospital Zurich, Zurich, Switzerland
| | - Michele Genoni
- Clinic for Cardiac Surgery, Stadtspital Triemli, Zurich, Switzerland
| | - Christian Rüegg
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland
| | - Nicolas Troillet
- Service of Infectious Diseases, Central Institute, Valais Hospital, Sion, Switzerland
| | - Andreas F Widmer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital and University of Basel, Basel, Switzerland
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany; Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Mathias Herrmann
- Institute of Medical Microbiology and Hygiene, Saarland University, Homburg/Saar, Germany
| | - Tim Eckmanns
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Sebastian Haller
- Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | | | - Sylvia B Debast
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, Netherlands
| | - Maurice J Wolfhagen
- Laboratory of Medical Microbiology and Infectious Diseases, Isala, Zwolle, Netherlands
| | - Joost Hopman
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, Netherlands
| | - Jan Kluytmans
- Laboratory for Microbiology and Infection Control, Amphia Hospital, Breda, Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, Netherlands
| | | | - Daan W Notermans
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Jaap Ten Oever
- Department of Internal Medicine, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Alexander B A Vonk
- Department of Cardio-Thoracic Surgery, VU University Medical Center, Amsterdam, Netherlands
| | - Margreet C Vos
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center, Rotterdam, Netherlands
| | - Nada Ahmed
- National Infection Service, Public Health England, London, UK
| | - Timothy Brown
- National Infection Service, Public Health England, London, UK
| | - Derrick Crook
- National Infection Service, Public Health England, London, UK; NIHR Health Protection Research Unit in AMR & HCAI, University of Oxford, Oxford, UK
| | - Theresa Lamagni
- National Infection Service, Public Health England, London, UK
| | - Nick Phin
- National Infection Service, Public Health England, London, UK
| | - E Grace Smith
- National Infection Service, Public Health England, London, UK; National Mycobacterial Reference Service, National Infection Service, Public Health Laboratory Birmingham, Birmingham, UK
| | - Maria Zambon
- National Infection Service, Public Health England, London, UK
| | - Annerose Serr
- Center for Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tim Götting
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Winfried Ebner
- Institute for Infection Prevention and Hospital Epidemiology, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Alexander Thürmer
- Institute of Medical Microbiology and Hygiene, Technische Universität Dresden, Dresden, Germany
| | - Christian Utpatel
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - Cathrin Spröer
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Boyke Bunk
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Ulrich Nübel
- Leibniz-Institute DSMZ, German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Guido V Bloemberg
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland; National Center for Mycobacteria, University of Zurich, Zurich, Switzerland
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research (DZIF), partner site Borstel, Borstel, Germany
| | - Dirk Wagner
- Division of Infectious Diseases, Department of Medicine II, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Hugo Sax
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Zurich, Switzerland.
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191
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Nübel U. Emergence and Spread of Antimicrobial Resistance: Recent Insights from Bacterial Population Genomics. Curr Top Microbiol Immunol 2017; 398:35-53. [PMID: 27738914 DOI: 10.1007/82_2016_505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Driven by progress of DNA sequencing technologies, recent population genomics studies have revealed that several bacterial pathogens constitute 'measurably evolving populations'. As a consequence, it was possible to reconstruct the emergence and spatial spread of drug-resistant bacteria on the basis of temporally structured samples of bacterial genome sequences. Based on currently available data, some general inferences can be drawn across different bacterial species as follows: (1) Resistance to various antibiotics evolved years to decades earlier than had been anticipated on the basis of epidemiological surveillance data alone. (2) Resistance traits are more rapidly acquired than lost and commonly persist in bacterial populations for decades. (3) Global populations of drug-resistant pathogens are dominated by very few clones, yet the features enabling such spreading success have not been revealed, aside from antibiotic resistance. (4) Whole-genome sequencing proved very effective at identifying bacterial isolates as parts of the same transmission networks.
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Affiliation(s)
- Ulrich Nübel
- DZIF Group on Microbial Genome Research, Leibniz Institute DSMZ, Braunschweig, Germany. .,Technical University Braunschweig, Braunschweig, Germany. .,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.
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192
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Petkau A, Mabon P, Sieffert C, Knox NC, Cabral J, Iskander M, Iskander M, Weedmark K, Zaheer R, Katz LS, Nadon C, Reimer A, Taboada E, Beiko RG, Hsiao W, Brinkman F, Graham M, Van Domselaar G. SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology. Microb Genom 2017; 3:e000116. [PMID: 29026651 PMCID: PMC5628696 DOI: 10.1099/mgen.0.000116] [Citation(s) in RCA: 88] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 04/12/2017] [Indexed: 11/18/2022] Open
Abstract
The recent widespread application of whole-genome sequencing (WGS) for microbial disease investigations has spurred the development of new bioinformatics tools, including a notable proliferation of phylogenomics pipelines designed for infectious disease surveillance and outbreak investigation. Transitioning the use of WGS data out of the research laboratory and into the front lines of surveillance and outbreak response requires user-friendly, reproducible and scalable pipelines that have been well validated. Single Nucleotide Variant Phylogenomics (SNVPhyl) is a bioinformatics pipeline for identifying high-quality single-nucleotide variants (SNVs) and constructing a whole-genome phylogeny from a collection of WGS reads and a reference genome. Individual pipeline components are integrated into the Galaxy bioinformatics framework, enabling data analysis in a user-friendly, reproducible and scalable environment. We show that SNVPhyl can detect SNVs with high sensitivity and specificity, and identify and remove regions of high SNV density (indicative of recombination). SNVPhyl is able to correctly distinguish outbreak from non-outbreak isolates across a range of variant-calling settings, sequencing-coverage thresholds or in the presence of contamination. SNVPhyl is available as a Galaxy workflow, Docker and virtual machine images, and a Unix-based command-line application. SNVPhyl is released under the Apache 2.0 license and available at http://snvphyl.readthedocs.io/ or at https://github.com/phac-nml/snvphyl-galaxy.
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Affiliation(s)
- Aaron Petkau
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Philip Mabon
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Cameron Sieffert
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Natalie C Knox
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Jennifer Cabral
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | | | - Mark Iskander
- 2University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Kelly Weedmark
- 3Health Canada - Bureau of Microbial Hazards, Ottawa, ON K1A 0K9, Canada
| | - Rahat Zaheer
- 4Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Lee S Katz
- 5Centers for Disease Control and Prevention, Atlanta, GA 30333, USA
| | - Celine Nadon
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Aleisha Reimer
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Eduardo Taboada
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | | | - William Hsiao
- 7BC Public Health Microbiology and Reference Laboratory, Vancouver, BC V5Z 4R4, Canada
| | | | - Morag Graham
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
| | - Gary Van Domselaar
- 1National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada
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193
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Validation and Implementation of Clinical Laboratory Improvements Act-Compliant Whole-Genome Sequencing in the Public Health Microbiology Laboratory. J Clin Microbiol 2017; 55:2502-2520. [PMID: 28592550 PMCID: PMC5527429 DOI: 10.1128/jcm.00361-17] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 05/26/2017] [Indexed: 11/24/2022] Open
Abstract
Public health microbiology laboratories (PHLs) are on the cusp of unprecedented improvements in pathogen identification, antibiotic resistance detection, and outbreak investigation by using whole-genome sequencing (WGS). However, considerable challenges remain due to the lack of common standards. Here, we describe the validation of WGS on the Illumina platform for routine use in PHLs according to Clinical Laboratory Improvements Act (CLIA) guidelines for laboratory-developed tests (LDTs). We developed a validation panel comprising 10 Enterobacteriaceae isolates, 5 Gram-positive cocci, 5 Gram-negative nonfermenting species, 9 Mycobacterium tuberculosis isolates, and 5 miscellaneous bacteria. The genome coverage range was 15.71× to 216.4× (average, 79.72×; median, 71.55×); the limit of detection (LOD) for single nucleotide polymorphisms (SNPs) was 60×. The accuracy, reproducibility, and repeatability of base calling were >99.9%. The accuracy of phylogenetic analysis was 100%. The specificity and sensitivity inferred from multilocus sequence typing (MLST) and genome-wide SNP-based phylogenetic assays were 100%. The following objectives were accomplished: (i) the establishment of the performance specifications for WGS applications in PHLs according to CLIA guidelines, (ii) the development of quality assurance and quality control measures, (iii) the development of a reporting format for end users with or without WGS expertise, (iv) the availability of a validation set of microorganisms, and (v) the creation of a modular template for the validation of WGS processes in PHLs. The validation panel, sequencing analytics, and raw sequences could facilitate multilaboratory comparisons of WGS data. Additionally, the WGS performance specifications and modular template are adaptable for the validation of other platforms and reagent kits.
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194
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Mulholland CV, Ruthe A, Cursons RT, Durrant R, Karalus N, Coley K, Bower J, Permina E, Coleman MJ, Roberts SA, Arcus VL, Cook GM, Aung HL. Rapid molecular diagnosis of the Mycobacterium tuberculosis Rangipo strain responsible for the largest recurring TB cluster in New Zealand. Diagn Microbiol Infect Dis 2017; 88:138-140. [DOI: 10.1016/j.diagmicrobio.2017.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 03/19/2017] [Accepted: 03/20/2017] [Indexed: 10/19/2022]
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195
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Epidemiology and whole genome sequencing of an ongoing point-source Salmonella Agona outbreak associated with sushi consumption in western Sydney, Australia 2015. Epidemiol Infect 2017; 145:2062-2071. [PMID: 28462733 DOI: 10.1017/s0950268817000693] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
During May 2015, an increase in Salmonella Agona cases was reported from western Sydney, Australia. We examine the public health actions used to investigate and control this increase. A descriptive case-series investigation was conducted. Six outbreak cases were identified; all had consumed cooked tuna sushi rolls purchased within a western Sydney shopping complex. Onset of illness for outbreak cases occurred between 7 April and 24 May 2015. Salmonella was isolated from food samples collected from the implicated premise and a prohibition order issued. No further cases were identified following this action. Whole genome sequence (WGS) analysis was performed on isolates recovered during this investigation, with additional S. Agona isolates from sporadic-clinical cases and routine food sampling in New South Wales, January to July 2015. Clinical isolates of outbreak cases were indistinguishable from food isolates collected from the implicated sushi outlet. Five additional clinical isolates not originally considered to be linked to the outbreak were genomically similar to outbreak isolates, indicating the point-source contamination may have started before routine surveillance identified an increase. This investigation demonstrated the value of genomics-guided public health action, where near real-time WGS enhanced the resolution of the epidemiological investigation.
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196
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Fiebig L, Kohl TA, Popovici O, Mühlenfeld M, Indra A, Homorodean D, Chiotan D, Richter E, Rüsch-Gerdes S, Schmidgruber B, Beckert P, Hauer B, Niemann S, Allerberger F, Haas W. A joint cross-border investigation of a cluster of multidrug-resistant tuberculosis in Austria, Romania and Germany in 2014 using classic, genotyping and whole genome sequencing methods: lessons learnt. ACTA ACUST UNITED AC 2017; 22:30439. [PMID: 28106529 PMCID: PMC5404487 DOI: 10.2807/1560-7917.es.2017.22.2.30439] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 09/28/2016] [Indexed: 11/30/2022]
Abstract
Molecular surveillance of multidrug-resistant tuberculosis (MDR-TB) using 24-loci MIRU-VNTR in the European Union suggests the occurrence of international transmission. In early 2014, Austria detected a molecular MDR-TB cluster of five isolates. Links to Romania and Germany prompted the three countries to investigate possible cross-border MDR-TB transmission jointly. We searched genotyping databases, genotyped additional isolates from Romania, used whole genome sequencing (WGS) to infer putative transmission links, and investigated pairwise epidemiological links and patient mobility. Ten isolates from 10 patients shared the same 24-loci MIRU-VNTR pattern. Within this cluster, WGS defined two subgroups of four patients each. The first comprised an MDR-TB patient from Romania who had sought medical care in Austria and two patients from Austria. The second comprised patients, two of them epidemiologically linked, who lived in three different countries but had the same city of provenance in Romania. Our findings strongly suggested that the two cases in Austrian citizens resulted from a newly introduced MDR-TB strain, followed by domestic transmission. For the other cases, transmission probably occurred in the same city of provenance. To prevent further MDR-TB transmission, we need to ensure universal access to early and adequate therapy and collaborate closely in tuberculosis care beyond administrative borders.
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Affiliation(s)
- Lena Fiebig
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany.,These authors contributed equally to this work
| | - Thomas A Kohl
- These authors contributed equally to this work.,Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Odette Popovici
- National Institute of Public Health - National Center for Communicable Diseases Surveillance and Control, Bucharest, Romania
| | | | - Alexander Indra
- Austrian Reference Laboratory for Mycobacteria, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Daniela Homorodean
- Clinical Hospital of Pneumology, Tuberculosis National Reference Laboratory, Cluj-Napoca, Romania
| | | | | | - Sabine Rüsch-Gerdes
- National Reference Center (NRC) for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Beatrix Schmidgruber
- Tuberculosis Patient Service, Health Service of the City of Vienna, Vienna, Austria
| | - Patrick Beckert
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Borstel, Germany
| | - Barbara Hauer
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany.,National Reference Center (NRC) for Mycobacteria, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner Site Hamburg-Borstel-Lübeck, Borstel, Germany
| | - Franz Allerberger
- Austrian Reference Laboratory for Mycobacteria, Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - Walter Haas
- Respiratory Infections Unit, Department for Infectious Disease Epidemiology, Robert Koch Institute, Berlin, Germany
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197
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Didelot X, Fraser C, Gardy J, Colijn C. Genomic Infectious Disease Epidemiology in Partially Sampled and Ongoing Outbreaks. Mol Biol Evol 2017; 34:997-1007. [PMID: 28100788 PMCID: PMC5850352 DOI: 10.1093/molbev/msw275] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Genomic data are increasingly being used to understand infectious disease epidemiology. Isolates from a given outbreak are sequenced, and the patterns of shared variation are used to infer which isolates within the outbreak are most closely related to each other. Unfortunately, the phylogenetic trees typically used to represent this variation are not directly informative about who infected whom-a phylogenetic tree is not a transmission tree. However, a transmission tree can be inferred from a phylogeny while accounting for within-host genetic diversity by coloring the branches of a phylogeny according to which host those branches were in. Here we extend this approach and show that it can be applied to partially sampled and ongoing outbreaks. This requires computing the correct probability of an observed transmission tree and we herein demonstrate how to do this for a large class of epidemiological models. We also demonstrate how the branch coloring approach can incorporate a variable number of unique colors to represent unsampled intermediates in transmission chains. The resulting algorithm is a reversible jump Monte-Carlo Markov Chain, which we apply to both simulated data and real data from an outbreak of tuberculosis. By accounting for unsampled cases and an outbreak which may not have reached its end, our method is uniquely suited to use in a public health environment during real-time outbreak investigations. We implemented this transmission tree inference methodology in an R package called TransPhylo, which is freely available from https://github.com/xavierdidelot/TransPhylo.
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Affiliation(s)
- Xavier Didelot
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, United Kingdom
| | - Christophe Fraser
- Department of Infectious Disease Epidemiology, Imperial College London, Norfolk Place, London, United Kingdom
- Oxford Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Jennifer Gardy
- Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
| | - Caroline Colijn
- Department of Mathematics, Imperial College, London, United Kingdom
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198
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Fedrizzi T, Meehan CJ, Grottola A, Giacobazzi E, Fregni Serpini G, Tagliazucchi S, Fabio A, Bettua C, Bertorelli R, De Sanctis V, Rumpianesi F, Pecorari M, Jousson O, Tortoli E, Segata N. Genomic characterization of Nontuberculous Mycobacteria. Sci Rep 2017; 7:45258. [PMID: 28345639 PMCID: PMC5366915 DOI: 10.1038/srep45258] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 02/23/2017] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium tuberculosis and Mycobacterium leprae have remained, for many years, the primary species of the genus Mycobacterium of clinical and microbiological interest. The other members of the genus, referred to as nontuberculous mycobacteria (NTM), have long been underinvestigated. In the last decades, however, the number of reports linking various NTM species with human diseases has steadily increased and treatment difficulties have emerged. Despite the availability of whole genome sequencing technologies, limited effort has been devoted to the genetic characterization of NTM species. As a consequence, the taxonomic and phylogenetic structure of the genus remains unsettled and genomic information is lacking to support the identification of these organisms in a clinical setting. In this work, we widen the knowledge of NTMs by reconstructing and analyzing the genomes of 41 previously uncharacterized NTM species. We provide the first comprehensive characterization of the genomic diversity of NTMs and open new venues for the clinical identification of opportunistic pathogens from this genus.
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Affiliation(s)
| | - Conor J Meehan
- Mycobacteriology unit, Department of Biomedical Science, Institute of Tropical Medicine, Antwerp, Belgium
| | - Antonella Grottola
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | | | | | - Sara Tagliazucchi
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Anna Fabio
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Clotilde Bettua
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Roberto Bertorelli
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Italy
| | - Veronica De Sanctis
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Italy
| | - Fabio Rumpianesi
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Monica Pecorari
- Microbiology and Virology Unit, University Hospital Polyclinic, Modena, Italy
| | - Olivier Jousson
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Enrico Tortoli
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
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199
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Dheda K, Gumbo T, Maartens G, Dooley KE, McNerney R, Murray M, Furin J, Nardell EA, London L, Lessem E, Theron G, van Helden P, Niemann S, Merker M, Dowdy D, Van Rie A, Siu GKH, Pasipanodya JG, Rodrigues C, Clark TG, Sirgel FA, Esmail A, Lin HH, Atre SR, Schaaf HS, Chang KC, Lange C, Nahid P, Udwadia ZF, Horsburgh CR, Churchyard GJ, Menzies D, Hesseling AC, Nuermberger E, McIlleron H, Fennelly KP, Goemaere E, Jaramillo E, Low M, Jara CM, Padayatchi N, Warren RM. The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. THE LANCET. RESPIRATORY MEDICINE 2017; 5:S2213-2600(17)30079-6. [PMID: 28344011 DOI: 10.1016/s2213-2600(17)30079-6] [Citation(s) in RCA: 380] [Impact Index Per Article: 54.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/24/2016] [Accepted: 12/08/2016] [Indexed: 12/25/2022]
Abstract
Global tuberculosis incidence has declined marginally over the past decade, and tuberculosis remains out of control in several parts of the world including Africa and Asia. Although tuberculosis control has been effective in some regions of the world, these gains are threatened by the increasing burden of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis. XDR tuberculosis has evolved in several tuberculosis-endemic countries to drug-incurable or programmatically incurable tuberculosis (totally drug-resistant tuberculosis). This poses several challenges similar to those encountered in the pre-chemotherapy era, including the inability to cure tuberculosis, high mortality, and the need for alternative methods to prevent disease transmission. This phenomenon mirrors the worldwide increase in antimicrobial resistance and the emergence of other MDR pathogens, such as malaria, HIV, and Gram-negative bacteria. MDR and XDR tuberculosis are associated with high morbidity and substantial mortality, are a threat to health-care workers, prohibitively expensive to treat, and are therefore a serious public health problem. In this Commission, we examine several aspects of drug-resistant tuberculosis. The traditional view that acquired resistance to antituberculous drugs is driven by poor compliance and programmatic failure is now being questioned, and several lines of evidence suggest that alternative mechanisms-including pharmacokinetic variability, induction of efflux pumps that transport the drug out of cells, and suboptimal drug penetration into tuberculosis lesions-are likely crucial to the pathogenesis of drug-resistant tuberculosis. These factors have implications for the design of new interventions, drug delivery and dosing mechanisms, and public health policy. We discuss epidemiology and transmission dynamics, including new insights into the fundamental biology of transmission, and we review the utility of newer diagnostic tools, including molecular tests and next-generation whole-genome sequencing, and their potential for clinical effectiveness. Relevant research priorities are highlighted, including optimal medical and surgical management, the role of newer and repurposed drugs (including bedaquiline, delamanid, and linezolid), pharmacokinetic and pharmacodynamic considerations, preventive strategies (such as prophylaxis in MDR and XDR contacts), palliative and patient-orientated care aspects, and medicolegal and ethical issues.
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Affiliation(s)
- Keertan Dheda
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa.
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Kelly E Dooley
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruth McNerney
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Megan Murray
- Department of Global Health and Social Medicine, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jennifer Furin
- Department of Global Health and Social Medicine, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Edward A Nardell
- TH Chan School of Public Health, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Leslie London
- School of Public Health and Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Grant Theron
- SA MRC Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Paul van Helden
- SA MRC Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Schleswig-Holstein, Germany; German Centre for Infection Research (DZIF), Partner Site Borstel, Borstel, Schleswig-Holstein, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Schleswig-Holstein, Germany
| | - David Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Annelies Van Rie
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; International Health Unit, Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Gilman K H Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Jotam G Pasipanodya
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Camilla Rodrigues
- Department of Microbiology, P.D. Hinduja National Hospital & Medical Research Centre, Mumbai, India
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Frik A Sirgel
- SA MRC Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Aliasgar Esmail
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Hsien-Ho Lin
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Sachin R Atre
- Center for Clinical Global Health Education (CCGHE), Johns Hopkins University, Baltimore, MD, USA; Medical College, Hospital and Research Centre, Pimpri, Pune, India
| | - H Simon Schaaf
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kwok Chiu Chang
- Tuberculosis and Chest Service, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Christoph Lange
- Division of Clinical Infectious Diseases, German Center for Infection Research, Research Center Borstel, Borstel, Schleswig-Holstein, Germany; International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany; Department of Medicine, Karolinska Institute, Stockholm, Sweden; Department of Medicine, University of Namibia School of Medicine, Windhoek, Namibia
| | - Payam Nahid
- Division of Pulmonary and Critical Care, San Francisco General Hospital, University of California, San Francisco, CA, USA
| | - Zarir F Udwadia
- Pulmonary Department, Hinduja Hospital & Research Center, Mumbai, India
| | | | - Gavin J Churchyard
- Aurum Institute, Johannesburg, South Africa; School of Public Health, University of Witwatersrand, Johannesburg, South Africa; Advancing Treatment and Care for TB/HIV, South African Medical Research Council, Johannesburg, South Africa
| | - Dick Menzies
- Montreal Chest Institute, McGill University, Montreal, QC, Canada
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eric Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Helen McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Kevin P Fennelly
- Pulmonary Clinical Medicine Section, Division of Intramural Research, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Eric Goemaere
- MSF South Africa, Cape Town, South Africa; School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Marcus Low
- Treatment Action Campaign, Johannesburg, South Africa
| | | | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), MRC HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Robin M Warren
- SA MRC Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
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200
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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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