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Bohada-Lizarazo DP, Bravo-Sanabria KD, Cárdenas-Malpica P, Rodríguez R. Comparative Genomic Analysis of Mycobacterium tuberculosis Isolates Circulating in North Santander, Colombia. Trop Med Infect Dis 2024; 9:197. [PMID: 39330886 PMCID: PMC11436241 DOI: 10.3390/tropicalmed9090197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/17/2024] [Accepted: 08/27/2024] [Indexed: 09/28/2024] Open
Abstract
Tuberculosis (TB) is an important infectious disease in relation to global public health and is caused species of the Mycobacterium tuberculosis complex (MTBC). In this study, we used whole-genome sequencing (WGS) and comparative genomics to investigate the genetic diversity of M. tuberculosis (Mtb) isolates circulating in North Santander (NS), Colombia. WGS was used for the phylogenetic and lineage characterization of 18 isolates of Mtb typed with orphan genotypes from 11 municipalities of NS between 2015 and 2018. The isolates studied were included in six sublineages from L4; the most frequent were 4.1.2.1, 4.3.3, and 4.3.4.2, corresponding to a proportion of 22.2%. The genome analysis conducted allowed the identification of a set of genetic variants mainly associated with determinants of virulence and evasion of the immune system (PPE34 and PE_PGRS2); adaptation and survival (PGL/p-HBAD); stress response (sigJ and sigM); geographic variability (PPE34); and carbohydrate and lipid metabolism (aldA, rocA, and cyp144). This is the first description of the molecular epidemiology of Mtb isolates circulating in NS achieved through WGS. It was possible to perform comparative genomics analyses between Mtb isolates against the universal reference H37Rv and Colombian UT205 genome, which can help us to understand the local genetic diversity and is relevant for epidemiological studies, providing insight into TB transmission dynamics in NS.
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Affiliation(s)
- Diana Patricia Bohada-Lizarazo
- Centro Experimental de Diagnóstico e Investigación Molecular-CEDIMOL, Universidad de Pamplona, Pamplona 503050, Colombia; (K.D.B.-S.); (R.R.)
- Grupo de Investigación en Recursos Naturales, Universidad de Pamplona, Pamplona 503050, Colombia;
- Departamento de Bacteriología y Laboratorio Clínico, Facultad de Salud, Universidad de Pamplona, Pamplona 503050, Colombia
| | - Karen Dayana Bravo-Sanabria
- Centro Experimental de Diagnóstico e Investigación Molecular-CEDIMOL, Universidad de Pamplona, Pamplona 503050, Colombia; (K.D.B.-S.); (R.R.)
- Departamento de Bacteriología y Laboratorio Clínico, Facultad de Salud, Universidad de Pamplona, Pamplona 503050, Colombia
| | - Paola Cárdenas-Malpica
- Grupo de Investigación en Recursos Naturales, Universidad de Pamplona, Pamplona 503050, Colombia;
- Departamento de Bacteriología y Laboratorio Clínico, Facultad de Salud, Universidad de Pamplona, Pamplona 503050, Colombia
| | - Raúl Rodríguez
- Centro Experimental de Diagnóstico e Investigación Molecular-CEDIMOL, Universidad de Pamplona, Pamplona 503050, Colombia; (K.D.B.-S.); (R.R.)
- Grupo de Investigación en Recursos Naturales, Universidad de Pamplona, Pamplona 503050, Colombia;
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Chen J, Qin Z, Jia Z. The application status of sequencing technology in global respiratory infectious disease diagnosis. Infection 2024:10.1007/s15010-024-02360-4. [PMID: 39152290 DOI: 10.1007/s15010-024-02360-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 07/22/2024] [Indexed: 08/19/2024]
Abstract
Next-generation sequencing (NGS) has revolutionized clinical microbiology, particularly in diagnosing respiratory infectious diseases and conducting epidemiological investigations. This narrative review summarizes conventional methods for routine respiratory infection diagnosis, including culture, smear microscopy, immunological assays, image techniques as well as polymerase chain reaction(PCR). In contrast to conventional methods, there is a new detection technology, sequencing technology, and here we mainly focus on the next-generation sequencing NGS, especially metagenomic NGS(mNGS). NGS offers significant advantages over traditional methods. Firstly, mNGS eliminates assumptions about pathogens, leading to faster and more accurate results, thus reducing diagnostic time. Secondly, it allows unbiased identification of known and novel pathogens, offering broad-spectrum coverage. Thirdly, mNGS not only identifies pathogens but also characterizes microbiomes, analyzes human host responses, and detects resistance genes and virulence factors. It can complement targeted sequencing for bacterial and fungal classification. Unlike traditional methods affected by antibiotics, mNGS is less influenced due to the extended survival of pathogen DNA in plasma, broadening its applicability. However, barriers to full integration into clinical practice persist, primarily due to cost constraints and limitations in sensitivity and turnaround time. Despite these challenges, ongoing advancements aim to improve cost-effectiveness and efficiency, making NGS a cornerstone technology for global respiratory infection diagnosis.
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Affiliation(s)
- Jingyuan Chen
- Department of Global Health, School of Public Health, Peking University, Beijing, China
| | - Zhen Qin
- School of Public Health, Peking University, Beijing, China
| | - Zhongwei Jia
- Department of Global Health, School of Public Health, Peking University, Beijing, China.
- Center for Intelligent Public Health, Institute for Artificial Intelligence, Peking University, Beijing, China.
- Center for Drug Abuse Control and Prevention, National Institute of Health Data Science, Peking University, Beijing, China.
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Zhang X, Lam C, Sim E, Martinez E, Crighton T, Marais BJ, Sintchenko V. Genomic characteristics of prospectively sequenced Mycobacterium tuberculosis from respiratory and non-respiratory sources. iScience 2024; 27:110327. [PMID: 39055934 PMCID: PMC11269812 DOI: 10.1016/j.isci.2024.110327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/23/2024] [Accepted: 06/18/2024] [Indexed: 07/28/2024] Open
Abstract
Understanding the differences between Mycobacterium tuberculosis strains isolated from respiratory and non-respiratory sources may inform clinical care and control strategies. We examined demographic and genomic characteristics of all culture-confirmed M. tuberculosis cultures isolated from respiratory and non-respiratory sources in New South Wales, Australia, from January 2017 to December 2021, using logistic regression models. M. tuberculosis strains from 1,831 patients were sequenced; 64.7% were from respiratory, 32.1% from non-respiratory, and 2.2% from both sources. Female patients had more frequent isolation from a non-respiratory source (p = 0.03), and older adults (≧65 years) from a respiratory source (p < 0.0001). Lineage 2 strains were relatively over-represented among respiratory isolates (p = 0.01). Among 39 cases with sequenced isolates from both sources, 43.6% had 1-10 single nucleotide polymorphism differences. The finding that older adults were more likely to have M. tuberculosis isolated from respiratory sources has relevance for TB control given the expected rise of TB among older adults.
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Affiliation(s)
- Xiaomei Zhang
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Connie Lam
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Eby Sim
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
| | - Elena Martinez
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Taryn Crighton
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
| | - Ben J. Marais
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, NSW, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, NSW, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, NSW, Australia
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Dippenaar A, Costa Conceição E, Wells F, Loubser J, Mann B, De Diego Fuertes M, Rennie V, Warren RM, Van Rie A. Exploring the potential of Oxford Nanopore Technologies sequencing for Mycobacterium tuberculosis sequencing: An assessment of R10 flowcells and V14 chemistry. PLoS One 2024; 19:e0303938. [PMID: 38843147 PMCID: PMC11156342 DOI: 10.1371/journal.pone.0303938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 05/03/2024] [Indexed: 06/09/2024] Open
Abstract
Oxford Nanopore Technologies (ONT) sequencing is a promising technology. We assessed the performance of the new ONT R10 flowcells and V14 rapid sequencing chemistry for Mtb whole genome sequencing of Mycobacterium tuberculosis (Mtb) DNA extracted from clinical primary liquid cultures (CPLCs). Using the recommended protocols for MinION Mk1C, R10.4.1 MinION flowcells, and the ONT Rapid Sequencing Kit V14 on six CPLC samples, we obtained a pooled library yield of 10.9 ng/μl, generated 1.94 Gb of sequenced bases and 214k reads after 48h in a first sequencing run. Only half (49%) of all generated reads met the Phred Quality score threshold (>8). To assess if the low data output and sequence quality were due to impurities present in DNA extracted directly from CPLCs, we added a pre-library preparation bead-clean-up step and included purified DNA obtained from an Mtb subculture as a control sample in a second sequencing run. The library yield for DNA extracted from four CPLCs and one Mtb subculture (control) was similar (10.0 ng/μl), 2.38 Gb of bases and 822k reads were produced. The quality was slightly better with 66% of the produced reads having a Phred Quality >8. A third run of DNA from six CPLCs with bead clean-up pre-processing produced a low library yield (±1 Gb of bases, 166k reads) of low quality (51% of reads with a Phred Quality score >8). A median depth of coverage above 10× was only achieved for five of 17 (29%) sequenced libraries. Compared to Illumina WGS of the same samples, accurate lineage predictions and full drug resistance profiles from the generated ONT data could not be determined by TBProfiler. Further optimization of the V14 ONT rapid sequencing chemistry and library preparation protocol is needed for clinical Mtb WGS applications.
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Affiliation(s)
- Anzaan Dippenaar
- Department of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Emilyn Costa Conceição
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Felicia Wells
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Johannes Loubser
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Brendon Mann
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Miguel De Diego Fuertes
- Department of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Vincent Rennie
- Department of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Robin Mark Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Department of Family Medicine and Population Health, Global Health Institute, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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Tram TTB, Trieu LPT, Nhat LTH, Thu DDA, Quang NL, Bang ND, Chau TTH, Thwaites GE, Walker TM, Ha VTN, Thuong NTT. Targeted sequencing from cerebrospinal fluid for rapid identification of drug-resistant tuberculous meningitis. J Clin Microbiol 2024; 62:e0128723. [PMID: 38466092 PMCID: PMC11005362 DOI: 10.1128/jcm.01287-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 02/03/2024] [Indexed: 03/12/2024] Open
Abstract
Mortality from tuberculous meningitis (TBM) remains around 30%, with most deaths occurring within 2 months of starting treatment. Mortality from drug-resistant strains is higher still, making early detection of drug resistance (DR) essential. Targeted next-generation sequencing (tNGS) produces high read depths, allowing the detection of DR-associated alleles with low frequencies. We applied Deeplex Myc-TB-a tNGS assay-to cerebrospinal fluid (CSF) samples from 72 adults with microbiologically confirmed TBM and compared its genomic drug susceptibility predictions to a composite reference standard of phenotypic susceptibility testing (pDST) and whole genome sequencing, as well as to clinical outcomes. Deeplex detected Mycobacterium tuberculosis complex DNA in 24/72 (33.3%) CSF samples and generated full DR reports for 22/24 (91.7%). The read depth generated by Deeplex correlated with semi-quantitative results from MTB/RIF Xpert. Alleles with <20% frequency were seen at canonical loci associated with first-line DR. Disregarding these low-frequency alleles, Deeplex had 100% concordance with the composite reference standard for all drugs except pyrazinamide and streptomycin. Three patients had positive CSF cultures after 30 days of treatment; reference tests and Deeplex identified isoniazid resistance in two, and Deeplex alone identified low-frequency rifampin resistance alleles in one. Five patients died, of whom one had pDST-identified pyrazinamide resistance. tNGS on CSF can rapidly and accurately detect drug-resistant TBM, but its application is limited to those with higher bacterial loads. In those with lower bacterial burdens, alternative approaches need to be developed for both diagnosis and resistance detection.
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Affiliation(s)
| | | | | | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Le Quang
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Guy E. Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Timothy M. Walker
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
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Patterson B, Dinkele R, Gessner S, Koch A, Hoosen Z, January V, Leonard B, McKerry A, Seldon R, Vazi A, Hermans S, Cobelens F, Warner DF, Wood R. Aerosolization of viable Mycobacterium tuberculosis bacilli by tuberculosis clinic attendees independent of sputum-Xpert Ultra status. Proc Natl Acad Sci U S A 2024; 121:e2314813121. [PMID: 38470917 PMCID: PMC10962937 DOI: 10.1073/pnas.2314813121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
Potential Mycobacterium tuberculosis (Mtb) transmission during different pulmonary tuberculosis (TB) disease states is poorly understood. We quantified viable aerosolized Mtb from TB clinic attendees following diagnosis and through six months' follow-up thereafter. Presumptive TB patients (n=102) were classified by laboratory, radiological, and clinical features into Group A: Sputum-Xpert Ultra-positive TB (n=52), Group B: Sputum-Xpert Ultra-negative TB (n=20), or Group C: TB undiagnosed (n=30). All groups were assessed for Mtb bioaerosol release at baseline, and subsequently at 2 wk, 2 mo, and 6 mo. Groups A and B were notified to the national TB program and received standard anti-TB chemotherapy; Mtb was isolated from 92% and 90% at presentation, 87% and 74% at 2 wk, 54% and 44% at 2 mo and 32% and 20% at 6 mo, respectively. Surprisingly, similar numbers were detected in Group C not initiating TB treatment: 93%, 70%, 48% and 22% at the same timepoints. A temporal association was observed between Mtb bioaerosol release and TB symptoms in all three groups. Persistence of Mtb bioaerosol positivity was observed in ~30% of participants irrespective of TB chemotherapy. Captured Mtb bacilli were predominantly acid-fast stain-negative and poorly culturable; however, three bioaerosol samples yielded sufficient biomass following culture for whole-genome sequencing, revealing two different Mtb lineages. Detection of viable aerosolized Mtb in clinic attendees, independent of TB diagnosis, suggests that unidentified Mtb transmitters might contribute a significant attributable proportion of community exposure. Additional longitudinal studies with sputum culture-positive and -negative control participants are required to investigate this possibility.
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Affiliation(s)
- Benjamin Patterson
- Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam1105, The Netherlands
| | - Ryan Dinkele
- South African Medical Research Council, National Health Laboratory Service, University of Cape Town Molecular Mycobacteriology Research Unit & Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
| | - Sophia Gessner
- South African Medical Research Council, National Health Laboratory Service, University of Cape Town Molecular Mycobacteriology Research Unit & Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
| | - Anastasia Koch
- South African Medical Research Council, National Health Laboratory Service, University of Cape Town Molecular Mycobacteriology Research Unit & Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
| | - Zeenat Hoosen
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Vanessa January
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Bryan Leonard
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Andrea McKerry
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Ronnett Seldon
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Andiswa Vazi
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
| | - Sabine Hermans
- Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam1105, The Netherlands
| | - Frank Cobelens
- Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam1105, The Netherlands
| | - Digby F. Warner
- South African Medical Research Council, National Health Laboratory Service, University of Cape Town Molecular Mycobacteriology Research Unit & Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
| | - Robin Wood
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town7925, South Africa
- Aerobiology and TB Research Unit, Desmond Tutu Health Foundation, Cape Town7975, South Africa
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Ogwang MO, Diero L, Ng'ong'a F, Magoma G, Mutharia L, Imbuga M, Ngugi C. Strain structure analysis of Mycobacterium tuberculosis circulating among HIV negative, positive and drug resistant TB patients attending chest clinics in Western Kenya. BMC Pulm Med 2023; 23:497. [PMID: 38071287 PMCID: PMC10709907 DOI: 10.1186/s12890-023-02802-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Despite global tuberculosis (TB) interventions, the disease remains one of the major public health concerns. Kenya is ranked 15th among 22 high burden TB countries globally. METHODS A cross-sectional study was conducted in Western Kenya, which comprises 10 counties. A multistage sampling method was used where a single sub-county was randomly selected followed by sampling two high volume health facility from each sub-county. Identification of spoligotype profiles and their family distribution and lineage level were achieved by comparison with SITVIT database. RESULTS Lineage distribution pattern revealed that the most predominant lineage was CAS 220 (39.8%) followed by Beijing 128 (23.1%). The other lineages identified were T, LAM, H, X, S and MANU which were quantified as 87 (15.7%), 67 (12.1%), 16 (2.8%), 10 (1.8%), 8 (1.4%) and 5 (0.9%) respectively. CAS and Beijing strains were the most predominant lineage in both HIV negative and positive TB patients. The Beijing lineage was also the most predominant in resistant M. tuberculosis strains as compared to wild type. A total of 12 (2.0%) were orphaned M. tuberculosis strains which were spread across all the 10 counties of the study site. In multivariate logistic regression adjusting for potential cofounders three potential risk factors were significant. HIV status (OR = 1.52, CI = 0.29-3.68 and P value of 0.001), Alcohol use (OR = 0.59, CI = 0.43-3.12 and P-value =0.001) and cross border travel (OR = 0.61, CI = 0.49-3.87 and P value = 0.026). Most M. tuberculosis clinical isolates showed genetic clustering with multivariate logistic regression indicating three potential risk factors to clustering. HIV status (OR = 1.52, CI = 0.29-3.68 and P value of 0.001), Alcohol use (OR = 0.59, CI = 0.43-3.12 and P-value =0.001) and cross border travel (OR = 0.61, CI = 0.49-3.87 and P value = 0.026). CONCLUSION There exist diverse strains of M. tuberculosis across the 10 counties of Western Kenya. Predominant distribution of clustered genotype points to the fact that most TB cases in this region are as a result of resent transmission other than activation of latent TB.
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Affiliation(s)
- Martin O Ogwang
- School of Public Health Nairobi Kenya, Jomo Kenyatta University of Agriculture and Technology, Juja, Kenya.
| | - Lameck Diero
- School of Medicine, Moi University, Eldoret, Kenya
| | - Florence Ng'ong'a
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Gabriel Magoma
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Lucy Mutharia
- Department of Cellular and Molecular Biology, University of Guelph, Guelph, ON, Canada
| | - Mabel Imbuga
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Caroline Ngugi
- School of Biomedical Sciences, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
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Mekonnen D, Munshea A, Nibret E, Adnew B, Getachew H, Kebede A, Gebrewahid A, Herrera-Leon S, Aramendia AA, Benito A, Abascal E, Jacqueline C, Aseffa A, Herrera-Leon L. Mycobacterium tuberculosis Sub-Lineage 4.2.2/SIT149 as Dominant Drug-Resistant Clade in Northwest Ethiopia 2020-2022: In-silico Whole-Genome Sequence Analysis. Infect Drug Resist 2023; 16:6859-6870. [PMID: 37908783 PMCID: PMC10614653 DOI: 10.2147/idr.s429001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 10/09/2023] [Indexed: 11/02/2023] Open
Abstract
Introduction Drug resistance (DR) in Mycobacterium tuberculosis complex (MTBC) is mainly associated with certain lineages and varies across regions and countries. The Beijing genotype is the leading resistant lineage in Asia and western countries. M. tuberculosis (Mtb) (sub) lineages responsible for most drug resistance in Ethiopia are not well described. Hence, this study aimed to identify the leading drug resistance sub-lineages and characterize first-line anti-tuberculosis drug resistance-associated single nucleotide polymorphisms (SNPs). Methods A facility-based cross-sectional study was conducted in 2020-2022 among new and presumptive multidrug resistant-TB (MDR-TB) cases in Northwest Ethiopia. Whole-genome sequencing (WGS) was performed on 161 isolates using Illumina NovaSeq 6000 technology. The SNP mutations associated with drug resistance were identified using MtbSeq and TB profiler Bioinformatics softwares. Results Of the 146 Mtb isolates that were successfully genotyped, 20 (13.7%) harbored one or more resistance-associated SNPs. L4.2.2.ETH was the leading drug-resistant sub-lineage, accounting for 10/20 (50%) of the resistant Mtb. MDR-TB isolates showed extensive mutations against first-line anti-TB drugs. Ser450Leu/(tcg/tTg) for Rifampicin (RIF), Ser315Thr/(agc/aCc) for Isoniazid (INH), Met306Ile/(atg/atA(C)) for Ethambutol (EMB), and Gly69Asp for Streptomycin (STR) were the leading resistance associated mutations which accounted for 56.5%, 89.5%, 47%, and 29.4%, respectively. The presence of both clustered and non-clustered drug resistance (DR) isolates indicated that the epidemics is driven by both new DR development and acquired resistance. Conclusion The high prevalence of drug-resistant TB due to geographically restricted sub-lineages (L4.2.2.ETH) indicates the ongoing local micro epidemics. The Mtb drug resistance surveillance system must be improved. Further evolutionary analysis of L4.2.2.ETH strain is highly desirable to understand evolutionary forces that leads L4.2.2.ETH in to high level DR and transmissible sub-lineage.
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Affiliation(s)
- Daniel Mekonnen
- Department of Medical Laboratory Sciences, School of Health Science, College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Abaineh Munshea
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | - Endalkachew Nibret
- Health Biotechnology Division, Institute of Biotechnology, Bahir Dar University, Bahir Dar, Ethiopia
- Department of Biology, Bahir Dar University, Bahir Dar, Ethiopia
| | | | | | - Amiro Kebede
- Amhara Public Health Institute, Bahir Dar, Ethiopia
| | | | - Silvia Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | | | - Agustín Benito
- National Center of Tropical Medicine, Institute of Health Carlos III, Centro de Investigación Biomédica En Red de Enfermedades Infecciosas, Madrid, Spain
| | - Estefanía Abascal
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Camille Jacqueline
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- European Public Health Microbiology Training Programme, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Laura Herrera-Leon
- National Centre for Microbiology, Instituto de Salud Carlos III, Madrid, Spain
- CIBER Epidemiologia y Salud Publica, Madrid, Spain
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Mann BC, Jacobson KR, Ghebrekristos Y, Warren RM, Farhat MR. Assessment and validation of enrichment and target capture approaches to improve Mycobacterium tuberculosis WGS from direct patient samples. J Clin Microbiol 2023; 61:e0038223. [PMID: 37728909 PMCID: PMC10595060 DOI: 10.1128/jcm.00382-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 07/20/2023] [Indexed: 09/22/2023] Open
Abstract
Within-host Mycobacterium tuberculosis (Mtb) diversity may detect antibiotic resistance or predict tuberculosis treatment failure and is best captured through sequencing directly from sputum. Here, we compared three sample pre-processing steps for DNA decontamination and studied the yield of a new target enrichment protocol for optimal whole-genome sequencing (WGS) from direct patient samples. Mtb-positive NALC-NaOH-treated patient sputum sediments were pooled, and heat inactivated, split in replicates, and treated by either a wash, DNase I, or benzonase digestion. Levels of contaminating host DNA and target Mtb DNA were assessed by quantitative PCR (qPCR), followed by WGS with and without custom dsDNA target enrichment. The pre-treatment sample has a high host-to-target ratio of DNA (6,168 ± 1,638 host copies/ng to 212.3 ± 59.4 Mtb copies/ng) that significantly decreased with all three treatments. Benzonase treatment resulted in the highest enrichment of Mtb DNA at 100-fold compared with control (3,422 ± 2,162 host copies/ng to 11,721 ± 7,096 Mtb copies/ng). The custom dsDNA probe panel successfully enriched libraries from as little as 0.45 pg of Mtb DNA (100 genome copies). Applied to direct sputum the dsDNA target enrichment panel increased the percent of sequencing reads mapping to the Mtb target for all three pre-processing methods. Comparing the results of the benzonase sample sequenced both with and without enrichment, the percent of sequencing reads mapping to the Mtb increased to 90.95% from 1.18%. We demonstrate a low limit of detection for a new custom dsDNA Mtb target enrichment panel that has a favorable cost profile. The results also demonstrate that pre-processing to remove contaminating extracellular DNA prior to cell lysis and DNA extraction improves the host-to-Mtb DNA ratio but is not adequate to support average coverage WGS without target capture.
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Affiliation(s)
- B. C. Mann
- Department of Biomedical Sciences, 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
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
| | - K. R. Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Y. Ghebrekristos
- Department of Biomedical Sciences, 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
- National Health Laboratory Service, Greenpoint Tuberculosis Laboratory, Cape Town, South Africa
| | - R. M. Warren
- Department of Biomedical Sciences, 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
| | - M. R. Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA
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10
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Ismail N, Dippenaar A, Morgan G, Grobbelaar M, Wells F, Caffry J, Morais C, Gizynski K, McGurk D, Boada E, Murton H, Warren RM, Van Rie A. Microfluidic Capture of Mycobacterium tuberculosis from Clinical Samples for Culture-Free Whole-Genome Sequencing. Microbiol Spectr 2023; 11:e0111423. [PMID: 37358439 PMCID: PMC10433858 DOI: 10.1128/spectrum.01114-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/25/2023] [Indexed: 06/27/2023] Open
Abstract
Mycobacterium tuberculosis whole-genome sequencing (WGS) is a powerful tool as it can provide data on population diversity, drug resistance, disease transmission, and mixed infections. Successful WGS is still reliant on high concentrations of DNA obtained through M. tuberculosis culture. Microfluidics technology plays a valuable role in single-cell research but has not yet been assessed as a bacterial enrichment strategy for culture-free WGS of M. tuberculosis. In a proof-of-principle study, we evaluated the use of Capture-XT, a microfluidic lab-on-chip cleanup and pathogen concentration platform to enrich M. tuberculosis bacilli from clinical sputum specimens for downstream DNA extraction and WGS. Three of the four (75%) samples processed by the microfluidics application passed the library preparation quality control, compared to only one of the four (25%) samples not enriched by the microfluidics M. tuberculosis capture application. WGS data were of sufficient quality, with mapping depth of ≥25× and 9 to 27% of reads mapping to the reference genome. These results suggest that microfluidics-based M. tuberculosis cell capture might be a promising method for M. tuberculosis enrichment in clinical sputum samples, which could facilitate culture-free M. tuberculosis WGS. IMPORTANCE Diagnosis of tuberculosis is effective using molecular methods; however, a comprehensive characterization of the resistance profile of Mycobacterium tuberculosis often requires culturing and phenotypic drug susceptibility testing or culturing followed by whole-genome sequencing (WGS). The phenotypic route can take anywhere from 1 to >3 months to result, by which point the patient may have acquired additional drug resistance. The WGS route is a very attractive option; however, culturing is the rate-limiting step. In this original article, we provide proof-of-principle evidence that microfluidics-based cell capture can be used on high-bacillary-load clinical samples for culture-free WGS.
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Affiliation(s)
- Nabila Ismail
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Anzaan Dippenaar
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Melanie Grobbelaar
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Felicia Wells
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | | | | | - David McGurk
- QuantuMDx Ltd., Newcastle upon Tyne, United Kingdom
| | | | | | - Robin M. Warren
- Division of Molecular Biology and Human Genetics, South African Medical Research Council Centre for Tuberculosis Research, DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Annelies Van Rie
- Tuberculosis Omics Research Consortium, Family Medicine and Population Health, Institute of Global Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
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11
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Beviere M, Reissier S, Penven M, Dejoies L, Guerin F, Cattoir V, Piau C. The Role of Next-Generation Sequencing (NGS) in the Management of Tuberculosis: Practical Review for Implementation in Routine. Pathogens 2023; 12:978. [PMID: 37623938 PMCID: PMC10459500 DOI: 10.3390/pathogens12080978] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 08/26/2023] Open
Abstract
Next-generation sequencing (NGS) has modernized the field of tuberculosis (TB) research by enabling high-throughput sequencing of the entire genome of Mycobacterium tuberculosis (MTB), which is the causative agent of TB. NGS has provided insights into the genetic diversity of MTB, which are crucial for understanding the evolution and transmission of the disease, and it has facilitated the identification of drug-resistant strains, enabling rapid and accurate tailoring of treatment. However, the high cost and the technical complexities of NGS currently limit its widespread use in clinical settings. International recommendations are thus necessary to facilitate the interpretation of polymorphisms, and an experimental approach is still necessary to correlate them to phenotypic data. This review aims to present a comparative, step-by-step, and up-to-date review of the techniques available for the implementation of this approach in routine laboratory workflow. Ongoing research on NGS for TB holds promise for improving our understanding of the disease and for developing more efficacious treatments.
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Affiliation(s)
- Marion Beviere
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35043 Rennes, France
| | - Sophie Reissier
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35043 Rennes, France
- Inserm U1230, Université de Rennes 1, F-35043 Rennes, France
| | - Malo Penven
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35043 Rennes, France
- Inserm U1230, Université de Rennes 1, F-35043 Rennes, France
| | - Loren Dejoies
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35043 Rennes, France
- Inserm U1230, Université de Rennes 1, F-35043 Rennes, France
| | - François Guerin
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35043 Rennes, France
- Inserm U1230, Université de Rennes 1, F-35043 Rennes, France
- CNR de La Résistance Aux Antibiotiques (Laboratoire Associé ‘Entérocoques’), F-35033 Rennes, France
| | - Vincent Cattoir
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35043 Rennes, France
- Inserm U1230, Université de Rennes 1, F-35043 Rennes, France
- CNR de La Résistance Aux Antibiotiques (Laboratoire Associé ‘Entérocoques’), F-35033 Rennes, France
| | - Caroline Piau
- Service de Bactériologie-Hygiène Hospitalière, CHU de Rennes, F-35043 Rennes, France
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12
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Mvubu NE, Salig A, Moopanar K, Nyide A, Govender D, Mankayi E. A quick, easy and efficient protocol for extracting high-quality RNA from Mycobacterium tuberculosis using a spin column commercial kit. BMC Res Notes 2023; 16:145. [PMID: 37443138 DOI: 10.1186/s13104-023-06424-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/04/2023] [Indexed: 07/15/2023] Open
Abstract
RNA extraction from Mycobacterium tuberculosis has been a historically challenging task for researchers due to the thick lipids associated with the cell wall of this "notorious" pathogen that is responsible for Tuberculosis (TB) outbreaks. Several studies have successfully extracted RNA from M. tuberculosis using a Trizol reagent combined with organic solvents. Recently, our laboratory has successfully extracted high quality total RNA using a commercial kit from clinical strains belonging to F15/LAM4/KZN, Beijing and F11 strain families and H37Rv laboratory strain by exploiting high speed homogenizer for cell lysis and spin columns for RNA purification. The quality and integrity of the extracted RNA was analyzed and confirmed through the Nanodrop, Bioanalyzer and RNA 3-(N-morpholino) propanesulfonic acid (MOPS) gel electrophoresis. Furthermore, to confirm the integrity of small RNA (sRNA) molecules due to their vulnerability to degradation, the RNA samples were converted to cDNA and sRNAs were amplified and confirmed through PCR. This detailed RNA extraction protocol proposes to carve a new path into TB transcriptome research without the use of organic solvent for downstream purification steps while yielding high quality RNA that can be used to understand M. tuberculosis transcriptome regulation.
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Affiliation(s)
- N E Mvubu
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Science, Medical School, University of KwaZulu Natal, Private Bag X54001, Durban, 4000, South Africa.
| | - A Salig
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
| | - K Moopanar
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
| | - Asg Nyide
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
| | - D Govender
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
| | - E Mankayi
- Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu Natal, Durban, South Africa
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13
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Comín J, Viñuelas J, Lafoz C, Cebollada A, Ibarz D, Iglesias MJ, Samper S. Rapid Identification of Lineage and Drug Resistance in Clinical Samples of Mycobacterium tuberculosis. Microorganisms 2023; 11:1467. [PMID: 37374968 DOI: 10.3390/microorganisms11061467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/25/2023] [Accepted: 05/27/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Mycobacterium tuberculosis is a slow-growing bacterium, which could delay its diagnosis and, therefore, promote the spread of the disease. Whole-genome sequencing allows us to obtain the complete drug-resistance profile of the strain; however, bacterial cultivation of clinical samples, along with complex processing, is required. METHODS In this work, we explore AmpliSeq, an amplicon-based enrichment method for preparing libraries for targeted next-generation sequencing, to identify lineage and drug resistance directly from clinical samples. RESULTS In our study, 111 clinical samples were tested. The lineage was identified in 100% of the culture-derived samples (52/52), in 95% of the smear (BK)-positive clinical samples (38/40) and in 42.1% of the BK-negative clinical samples (8/19). The drug-resistance profile was accurately identified in all but 11 samples, in which some phenotypic and genotypic discrepancies were found. In this respect, our panels were not exact in the detection of streptomycin resistance for isolates derived from clinical samples, as an extremely high number of SNPs in the rrs and rrl genes were detected due to cross-contamination. CONCLUSION This technique has demonstrated high sensitivity in obtaining the drug-resistance profile of the isolates, as even those samples with DNA concentrations below the detection limit of Qubit produced a result. AmpliSeq technology is cheaper than whole-genome sequencing, easy to perform by laboratory technicians and applicable to any microorganism using the Ion Torrent platform.
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Affiliation(s)
- Jéssica Comín
- Instituto Aragonés de Ciencias de la Salud, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
| | - Jesús Viñuelas
- Servicio de Microbiología, Hospital Universitario Miguel Servet, Paseo Isabel la Católica 1-3, 50009 Zaragoza, Spain
- Grupo de Estudio de Infecciones por Micobacterias (GEIM), Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, C/Agustín de Bentacourt, No. 13, 28003 Madrid, Spain
| | - Carmen Lafoz
- Servicio General de Apoyo a la Investigación, Servicio de Análisis Microbiológico, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Alberto Cebollada
- Unidad de Biocomputación, Instituto Aragonés de Ciencias de la Salud, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
| | - Daniel Ibarz
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, C/Domingo Miral S/N, 50009 Zaragoza, Spain
| | - María-José Iglesias
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, C/Domingo Miral S/N, 50009 Zaragoza, Spain
- Fundación IIS Aragón, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
- CIBER de Enfermedades Respiratorias, Av. Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
- Grupo de Genética de Micobacterias, Facultad de Medicina, Universidad de Zaragoza, C/Domingo Miral S/N, 50009 Zaragoza, Spain
- Fundación IIS Aragón, C/de San Juan Bosco 13, 50009 Zaragoza, Spain
- CIBER de Enfermedades Respiratorias, Av. Monforte de Lemos 3-5, Pabellón 11, Planta 0, 28029 Madrid, Spain
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14
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Huang W, Lee MKT, Sin ATK, Nazari RS, Chua SY, Sng LH. Evaluation of Xpert MTB/RIF ultra assay for detection of Mycobacterium tuberculosis and rifampicin resistance. Pathology 2023:S0031-3025(23)00116-2. [PMID: 37268484 DOI: 10.1016/j.pathol.2023.03.002] [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: 09/13/2022] [Revised: 01/05/2023] [Accepted: 03/14/2023] [Indexed: 06/04/2023]
Abstract
Tuberculosis (TB) is a public health challenge globally, and molecular testing is recommended to expedite diagnosis. Concerns that Xpert MTB/RIF assay (Xpert) may be less sensitive when testing paucibacillary samples led to the development of the Xpert MTB/RIF Ultra assay (Ultra). We evaluated the performance of Ultra against Xpert on clinical samples sent to the national reference laboratory in Singapore. In total, 149 samples collected between January 2019 and November 2020 were analysed. Mycobacterium tuberculosis complex (MTBC) was isolated from 55 cultures. Using culture as the reference standard, Ultra demonstrated higher sensitivity (96.4% vs 85.5%) and marginally lower specificity (88.3% vs 89.4%) compared to Xpert in the full cohort. When considering only paucibacillary specimens such as extrapulmonary and smear-negative samples, similar results were obtained. Reclassifying Ultra trace results (low levels of MTB are detected but no rifampicin resistant result is detected) as negative in the full cohort led to a decrease in sensitivity by 10.9% and a marginal increase in specificity by 1.1%. In instances of low bacillary load, Ultra also identified rifampicin resistance more accurately than Xpert, when corroborated against other methods such as broth microdilution, line probe assay and whole genome sequencing (WGS). One isolate tested rifampicin-resistant using Xpert and Ultra, but was phenotypically susceptible and WGS demonstrated the presence of the silent mutation Thr444Thr. Ultra is more sensitive than Xpert in the detection of MTBC and rifampicin resistance in our local setting. Nevertheless, the results of molecular testing should still be correlated with phenotypic studies.
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Affiliation(s)
- Wenjie Huang
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore.
| | - Melody Kee Tai Lee
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | - Amanda Teo Kai Sin
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | | | - Syn Yu Chua
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | - Li-Hwei Sng
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
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15
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van Tonder AJ, Ellis HC, Churchward CP, Kumar K, Ramadan N, Benson S, Parkhill J, Moffatt MF, Loebinger MR, Cookson WOC. M ycobacterium avium complex genomics and transmission in a London hospital. Eur Respir J 2023; 61:2201237. [PMID: 36517182 PMCID: PMC10116071 DOI: 10.1183/13993003.01237-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/23/2022] [Indexed: 12/23/2022]
Abstract
BACKGROUND Non-tuberculous mycobacteria (NTM) are environmental microorganisms and opportunistic pathogens in individuals with pre-existing lung conditions such as cystic fibrosis (CF) and non-CF bronchiectasis. While recent studies of Mycobacterium abscessus have identified transmission within single CF centres as well as nationally and globally, transmission of other NTM species is less well studied. METHODS To investigate the potential for transmission of the Mycobacterium avium complex (MAC) we sequenced 996 isolates from 354 CF and non-CF patients at the Royal Brompton Hospital (London, UK; collected 2013-2016) and analysed them in a global context. Epidemiological links were identified from patient records. Previously published genomes were used to characterise global population structures. RESULTS We identified putative transmission clusters in three MAC species, although few epidemiological links could be identified. For M. avium, lineages were largely limited to single countries, while for Mycobacterium chimaera, global transmission clusters previously associated with heater-cooler units (HCUs) were found. However, the immediate ancestor of the lineage causing the major HCU-associated outbreak was a lineage already circulating in patients. CONCLUSIONS CF and non-CF patients shared transmission chains, although the lack of epidemiological links suggested that most transmission is indirect and may involve environmental intermediates or asymptomatic carriage in the wider population.
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Affiliation(s)
| | - Huw C Ellis
- Host Defence Unit, Department of Respiratory Medicine, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Kartik Kumar
- Host Defence Unit, Department of Respiratory Medicine, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Newara Ramadan
- Department of Microbiology, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Susan Benson
- Department of Microbiology, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, UK
- These three authors contributed equally
| | - Michael R Loebinger
- Host Defence Unit, Department of Respiratory Medicine, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- These three authors contributed equally
| | - William O C Cookson
- Host Defence Unit, Department of Respiratory Medicine, Royal Brompton Hospital, Guy's and St Thomas' NHS Foundation Trust, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
- These three authors contributed equally
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16
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Dhital R, Mustapha A. DNA concentration by solid phase reversible immobilization improves its yield and purity, and detection time of E. coli O157:H7 in foods by high resolution melt curve qPCR. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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17
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Macedo R, Isidro J, Ferreira R, Pinto M, Borges V, Duarte S, Vieira L, Gomes JP. Molecular Capture of Mycobacterium tuberculosis Genomes Directly from Clinical Samples: A Potential Backup Approach for Epidemiological and Drug Susceptibility Inferences. Int J Mol Sci 2023; 24:ijms24032912. [PMID: 36769230 PMCID: PMC9918089 DOI: 10.3390/ijms24032912] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/20/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The application of whole genome sequencing of Mycobacterium tuberculosis directly on clinical samples has been investigated as a means to avoid the time-consuming need for culture isolation that can lead to a potential prolonged suboptimal antibiotic treatment. We aimed to provide a proof-of-concept regarding the application of the molecular capture of M. tuberculosis genomes directly from positive sputum samples as an approach for epidemiological and drug susceptibility predictions. Smear-positive sputum samples (n = 100) were subjected to the SureSelectXT HS Target Enrichment protocol (Agilent Technologies, Santa Clara, CA, USA) and whole-genome sequencing analysis. A higher number of reads on target were obtained for higher smear grades samples (i.e., 3+ followed by 2+). Moreover, 37 out of 100 samples showed ≥90% of the reference genome covered with at least 10-fold depth of coverage (27, 9, and 1 samples were 3+, 2+, and 1+, respectively). Regarding drug-resistance/susceptibility prediction, for 42 samples, ≥90% of the >9000 hits that are surveyed by TB-profiler were detected. Our results demonstrated that M. tuberculosis genome capture and sequencing directly from clinical samples constitute a potential valid backup approach for phylogenetic inferences and resistance prediction, essentially in settings when culture is not routinely performed or for samples that fail to grow.
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Affiliation(s)
- Rita Macedo
- National Reference Laboratory for Mycobacteria, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Joana Isidro
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Rita Ferreira
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Miguel Pinto
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Vítor Borges
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Sílvia Duarte
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - Luís Vieira
- Innovation and Technology Unit, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
| | - João Paulo Gomes
- Genomics and Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health (INSA), 1649-016 Lisbon, Portugal
- Correspondence:
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18
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Ness TE, DiNardo A, Farhat MR. High Throughput Sequencing for Clinical Tuberculosis: An Overview. Pathogens 2022; 11:pathogens11111343. [PMID: 36422596 PMCID: PMC9695813 DOI: 10.3390/pathogens11111343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/07/2022] [Accepted: 11/10/2022] [Indexed: 11/16/2022] Open
Abstract
High throughput sequencing (HTS) can identify the presence of Mycobacterium tuberculosis DNA in a clinical sample while also providing information on drug susceptibility. Multiple studies have provided a context for exploring the clinical application of HTS for TB diagnosis. The workflow challenges, strengths and limitations of the various sequencing platforms, and tools used for analysis are presented to provide a framework for further innovations in the field.
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Affiliation(s)
- Tara E. Ness
- Division of Pediatric Infectious Diseases, Baylor College of Medicine/Texas Children’s Hospital, Houston, TX 77030, USA
- Global TB Program, Baylor College of Medicine/Texas Childrens Hospital, Houston, TX 77030, USA
- Correspondence:
| | - Andrew DiNardo
- Global TB Program, Baylor College of Medicine/Texas Childrens Hospital, Houston, TX 77030, USA
| | - Maha R. Farhat
- Harvard Medical School Biomedical Informatics and Pulmonary and Critical Care Massachusetts General Hospital, Boston, MA 02115, USA
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19
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Dale K, Globan M, Horan K, Sherry N, Ballard S, Tay EL, Bittmann S, Meagher N, Price DJ, Howden BP, Williamson DA, Denholm J. Whole genome sequencing for tuberculosis in Victoria, Australia: A genomic implementation study from 2017 to 2020. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 28:100556. [PMID: 36034164 PMCID: PMC9405109 DOI: 10.1016/j.lanwpc.2022.100556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Background Whole genome sequencing (WGS) is increasingly used by tuberculosis (TB) programs to monitor Mycobacterium tuberculosis (Mtb) transmission. We aimed to characterise the molecular epidemiology of TB and Mtb transmission in the low-incidence setting of Victoria, Australia, and assess the utility of WGS. Methods WGS was performed on all first Mtb isolates from TB cases from 2017 to 2020. Potential clusters (≤12 single nucleotide polymorphisms [SNPs]) were investigated for epidemiological links. Transmission events in highly-related (≤5 SNPs) clusters were classified as likely or possible, based on the presence or absence of an epidemiological link, respectively. Case characteristics and transmission settings (as defined by case relationship) were summarised. Poisson regression was used to examine associations with secondary case number. Findings Of 1844 TB cases, 1276 (69.2%) had sequenced isolates, with 182 (14.2%) in 54 highly-related clusters, 2-40 cases in size. Following investigation, 140 cases (11.0% of sequenced) were classified as resulting from likely/possible local-transmission, including 82 (6.4%) for which transmission was likely. Common identified transmission settings were social/religious (26.4%), household (22.9%) and family living in different households (7.1%), but many were uncertain (41.4%). While household transmission featured in many clusters (n = 24), clusters were generally smaller (median = 3 cases) than the fewer that included transmission in social/religious settings (n = 12, median = 7.5 cases). Sputum-smear-positivity was associated with higher secondary case numbers. Interpretation WGS results suggest Mtb transmission commonly occurs outside the household in our low-incidence setting. Further work is required to optimise the use of WGS in public health management of TB. Funding The Victorian Tuberculosis Program receives block funding for activities including case management and contact tracing from the Victorian Department of Health. No specific funding for this report was received by manuscript authors or the Victorian Tuberculosis Program, and the funders had no role in the study design, data collection, data analysis, interpretation or report writing.
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Affiliation(s)
- Katie Dale
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Maria Globan
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Ee Laine Tay
- Communicable Disease Epidemiology and Surveillance, Health Protection Branch, Public Health Division, Department of Health, Victoria, Australia
| | - Simone Bittmann
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Niamh Meagher
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - David J. Price
- Department of Infectious Diseases at the Doherty Institute for Infection & Immunity, The University of Melbourne and Royal Melbourne Hospital, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Deborah A. Williamson
- Victorian Infectious Diseases Reference Laboratory (VIDRL), at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
- Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
| | - Justin Denholm
- Victorian Tuberculosis Program, Melbourne Health, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, The University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
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20
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Mycobacterium tuberculosis Genotypes and Drug Susceptibility Test Results from Timor-Leste: A Pilot Study. Genes (Basel) 2022; 13:genes13101733. [PMID: 36292618 PMCID: PMC9602296 DOI: 10.3390/genes13101733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 09/13/2022] [Accepted: 09/22/2022] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis (TB) is prevalent and a major public health problem in Timor-Leste. The government of Timor-Leste is prioritising the surveillance of TB and drug-susceptibility testing (DST) to understand the burden of TB and TB drug resistance in the country. Moreover, little is known about the origin of Mycobacterium tuberculosis (MTB) in Timor-Leste. This study reports MTB DST and sequencing for Timor-Leste. A pilot study was carried out in which a convenience sample of TB isolates from mucopurulent sputum collected from presumptive TB patients in the capital Dili between July and December 2016 was tested for phenotypic and genotypic evidence of drug resistance. Standard MTB culture was performed at the Timor-Leste National Health Laboratory (NHL). The MTB isolates were sent to the Victorian Infectious Diseases Reference Laboratory (VIDRL) in Australia for DST and sequencing. Overall, 36 MTB isolates were detected at the NHL; 20 isolates were recovered during sub-culturing at VIDRL. All 20 isolates were susceptible to rifampicin, isoniazid, pyrazinamide, and ethambutol, with no genotypic markers of resistance identified. On sequencing, lineage 4 was the most common. The results of this study provide a small snapshot of MTB diversity and resistance in an under-sampled region with very high TB incidence. Future investment in whole-genome sequencing capacity in Timor-Leste will make it possible to undertake further, more representative analyses that may be used to evaluate transmission dynamics and epidemiology of genotypic markers of resistance.
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21
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Shea J, Smith C, Halse TA, Kohlerschmidt D, Rourke AK, Musser KA, Escuyer V, Lapierre P. Novel Mycobacterium tuberculosis Complex Genotype Related to M. caprae. Emerg Infect Dis 2022; 28:1431-1436. [PMID: 35731170 PMCID: PMC9239888 DOI: 10.3201/eid2807.212353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report the unusual genotypic characterization of a bacterium isolated from a clinical sample of a patient who grew up in Bangladesh and lives in the United States. Using whole-genome sequencing, we identified the bacterium as a member of the Mycobacterium tuberculosis complex (MTBC). Phylogenetic placement of this strain suggests a new MTBC genotype. Even though it had the same spoligotype as M. caprae strains, single-nucleotide polymorphism-based phylogenetic analysis placed the isolate as a sister lineage distinct from M. caprae, most closely related to 5 previously sequenced genomes isolated from primates and elephants in Asia. We propose a new animal-associated lineage, La4, within MTBC.
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22
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Walker TM, Choisy M, Dedicoat M, Drennan PG, Wyllie D, Yang-Turner F, Crook DW, Robinson ER, Walker AS, Smith EG, Peto TE. Mycobacterium tuberculosis transmission in Birmingham, UK, 2009-19: An observational study. THE LANCET REGIONAL HEALTH. EUROPE 2022; 17:100361. [PMID: 35345560 PMCID: PMC8956939 DOI: 10.1016/j.lanepe.2022.100361] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Background Over 10-years of whole-genome sequencing (WGS) of Mycobacterium tuberculosis in Birmingham presents an opportunity to explore epidemiological trends and risk factors for transmission in new detail. Methods Between 1st January 2009 and 15th June 2019, we obtained the first WGS isolate from every patient resident in a postcode district covered by Birmingham's centralised tuberculosis service. Data on patients' sex, country of birth, social risk-factors, anatomical locus of disease, and strain lineage were collected. Poisson harmonic regression was used to assess seasonal variation in case load and a mixed-effects multivariable Cox proportionate hazards model was used to assess risk factors for a future case arising in clusters defined by a 5 single nucleotide polymorphism (SNP) threshold, and by 12 SNPs in a sensitivity analysis. Findings 511/1653 (31%) patients were genomically clustered with another. A seasonal variation in diagnoses was observed, peaking in spring, but only among clustered cases. Risk-factors for a future clustered case included UK-birth (aHR=2·03 (95%CI 1·35-3·04), p < 0·001), infectious (pulmonary/laryngeal/miliary) tuberculosis (aHR=3·08 (95%CI 1·98-4·78), p < 0·001), and M. tuberculosis lineage 3 (aHR=1·91 (95%CI 1·03-3·56), p = 0·041) and 4 (aHR=2·27 (95%CI 1·21-4·26), p = 0·011), vs. lineage 1. Similar results pertained to 12 SNP clusters, for which social risk-factors were also significant (aHR 1·72 (95%CI 1·02-2·93), p = 0·044). There was marked heterogeneity in transmission patterns between postcode districts. Interpretation There is seasonal variation in the diagnosis of genomically clustered, but not non-clustered, cases. Risk factors for clustering include UK-birth, infectious forms of tuberculosis, and infection with lineage 3 or 4. Funding Wellcome Trust, MRC, UKHSA.
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Affiliation(s)
- Timothy M. Walker
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Marc Choisy
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Martin Dedicoat
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Philip G. Drennan
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, UK
- Oxford University Hospitals NHS Foundation Trust, UK
| | - David Wyllie
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Fan Yang-Turner
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - Derrick W. Crook
- Oxford University Hospitals NHS Foundation Trust, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - Esther R. Robinson
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - A. Sarah Walker
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - E. Grace Smith
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Timothy E.A. Peto
- Oxford University Hospitals NHS Foundation Trust, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
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23
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Novel Screening System of Virulent Strains for the Establishment of a Mycobacterium avium Complex Lung Disease Mouse Model Using Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0045122. [PMID: 35579455 PMCID: PMC9241706 DOI: 10.1128/spectrum.00451-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The establishment of animal models reflecting human Mycobacterium avium complex (MAC) lung disease (LD) pathology has the potential to expand our understanding of the disease pathophysiology. However, inducing sustained infection in immunocompetent mice is difficult since MAC generally shows less virulence and higher genetic variability than M. tuberculosis. To overcome this hurdle, we developed a screening system for identifying virulent MAC strains using whole-genome sequencing (WGS). We obtained nine clinical strains from Mycobacterium avium complex lung disease (MAC-LD) patients and divided them into two groups to make the mixed strain inocula for infection. Intranasal infection with the strain mixture of both groups in BALB/c mice resulted in progressive infection and extensive granuloma formation in the lungs, suggesting the existence of highly pathogenic strains in each group. We hypothesized that the change in the abundance of strain-specific single-nucleotide variants (SNVs) reflects the change in bacterial number of each strain in infected lungs. Based on this hypothesis, we quantified individual strain-specific SNVs in bacterial DNA from infected lungs. Specific SNVs for four strains were detected, suggesting the pathogenicity of these four strains. Consistent with these results, individual infection with these four strains induced a high lung bacterial burden, forming extensive peribronchial granuloma, while the other strains showed a decreased lung bacterial burden. The current method combining mixed infection and WGS accurately identified virulent strains that induced sustained infection in mice. This method will contribute to the establishment of mouse models that reflect human MAC-LD and lead to antimycobacterial drug testing. IMPORTANCE To promote research on Mycobacterium avium complex (MAC) pathogenicity, animal models reflecting human progressive MAC lung disease (MAC-LD) are needed. Because there is high genetic and virulence diversity among clinical MAC strains, choosing a suitable strain is an important process for developing a mouse model. In this study, we developed a screening system for virulent strains in mice by combining mixed infection and whole-genome sequencing analysis. This approach is designed on the hypothesis that in vivo virulence of MAC strains can be examined simultaneously by comparing changes in the abundance of strain-specific single-nucleotide variants in the mouse lungs after infection with mixed strains. The identified strains were shown to induce high bacterial burdens and cause extensive peribronchial granuloma resembling the pulmonary pathology of human MAC-LD. The current method will help researchers develop mouse models that reflect human MAC-LD and will lead to further investigation of MAC pathogenicity.
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24
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Jabeen MF, Sanderson ND, Foster D, Crook DW, Cane JL, Borg C, Connolly C, Thulborn S, Pavord ID, Klenerman P, Street TL, Hinks TSC. Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies. Microbiol Spectr 2022; 10:e0227921. [PMID: 35323032 PMCID: PMC9045196 DOI: 10.1128/spectrum.02279-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/02/2022] [Indexed: 12/11/2022] Open
Abstract
Previous metagenomic studies in asthma have been limited by inadequate sequencing depth for species-level bacterial identification and by heterogeneity in clinical phenotyping. We hypothesize that chronic bacterial airways infection is a key "treatable trait" whose prevalence, clinical phenotype and reliable biomarkers need definition. In this study, we have applied a method for Oxford Nanopore sequencing for the unbiased metagenomic characterization of severe asthma. We optimized methods to compare performance of Illumina MiSeq, Nanopore sequencing, and RT-qPCR on total sputum DNA extracts against culture/MALDI-TOF for analysis of induced sputum samples from highly phenotyped severe asthma during clinical stability. In participants with severe asthma (n = 23) H. influenzae was commonly cultured (n = 8) and identified as the dominant bacterial species by metagenomic sequencing using an optimized method for Illumina MiSeq and Oxford Nanopore. Alongside superior operational characteristics, Oxford Nanopore achieved near complete genome coverage of H. influenzae and demonstrated a high level of agreement with Illumina MiSeq data. Clinically significant infection was confirmed with validated H. influenzae plasmid-based quantitative PCR assay. H. influenzae positive patients were found to have sputum neutrophilia and lower FeNO. In conclusion, using an optimized method of direct sequencing of induced sputum samples, H. influenzae was identified as a clinically relevant pathogen in severe asthma and was identified reliably using metagenomic sequencing. Application of these protocols in ongoing analysis of large patient cohorts will allow full characterization of this clinical phenotype. IMPORTANCE The human airways were once thought sterile in health. Now metagenomic techniques suggest bacteria may be present, but their role in asthma is not understood. Traditional culture lacks sensitivity and current sequencing techniques are limited by operational problems and limited ability to identify pathogens at species level. We optimized a new sequencing technique-Oxford Nanopore technologies (ONT)-for use on human sputum samples and compared it with existing methods. We found ONT was effective for rapidly analyzing samples and could identify bacteria at the species level. We used this to show Haemophilus influenzae was a dominant bacterium in the airways in people with severe asthma. The presence of Haemophilus was associated with a "neutrophilic" form of asthma - a subgroup for which we currently lack specific treatments. Therefore, this technique could be used to target chronic antibiotic therapy and in research to characterize the full breadth of bacteria in the airways.
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Affiliation(s)
- Maisha F. Jabeen
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nicholas D. Sanderson
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Dona Foster
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
| | - Derrick W. Crook
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Jennifer L. Cane
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Catherine Borg
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Clare Connolly
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Samantha Thulborn
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Ian D. Pavord
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Paul Klenerman
- Peter Medawar Building for Pathogen Research and Translational Gastroenterology Unit, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Teresa L. Street
- Nuffield Department of Clinical Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Timothy S. C. Hinks
- Respiratory Medicine Unit, Experimental Medicine Division, Nuffield Department of Medicine, University of Oxford, John Radcliffe Hospital, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
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25
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Yadav RN, Bhalla M, Kumar G, Sah GC, Dewan RK, Singhal R. Diagnostic utility of GenoType MTBDR sl assay for the detection of moxifloxacin-resistant mycobacterium tuberculosis, as compared to phenotypic method and whole-genome sequencing. Int J Mycobacteriol 2022; 11:183-189. [PMID: 35775551 DOI: 10.4103/ijmy.ijmy_70_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Recently, moxifloxacin (MFX)-resistant results of Mycobacterium tuberculosis (Mtb) obtained by GenoType MTBDRsl (second-line line probe assay [SL-LPA]) have been stratified to determine their resistance level; however, its accuracy has not been well studied. Therefore, the study aimed to evaluate the diagnostic accuracy of SL-LPA, with phenotypic drug susceptibility testing (pDST) and whole-genome sequencing (WGS) for the detection of MFX-resistant Mtb and their resistance level. Methods A total of 111 sputum samples were subjected to SL-LPA according to the diagnostic algorithm of the National Tuberculosis Elimination Program. Results were compared with pDST of MFX (at critical concentration [CC, 0.25 μg/ml] and clinical breakpoint [CB, 1.0 μg/ml] using BACTEC mycobacterial growth indicator tube-960), and WGS. Results At CC, SL-LPA and pDST yielded concordant results of MFX for 104 of 111 (94%). However, at CB, 23 of 30 (77%) isolates carrying gyrA mutation known to confer low-level resistance to MFX were scored as susceptible by pDST. Among 46 Mtb isolates carrying gyrA mutations known to confer high-level resistance to MFX, 36 (78%) isolates yielded concordant results, while 10 (22%) isolates were scored as susceptible at CB by pDST. WGS identified gyrA mutations in all isolates suggested by SL-LPA. Conclusion It is concluded that the stratification of MFX-resistant results by SL-LPA/genotypic method is not very well correlated with pDST (at CB), and hence, pDST may not be completely replaced by SL-LPA. gyrA D94G and gyrAA90V are the most prevalent mutations in MFX-resistant Mtb.
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Affiliation(s)
- Raj Narayan Yadav
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Manpreet Bhalla
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Gavish Kumar
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Grish C Sah
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Ravindra Kumar Dewan
- Department of Thoracic Surgery and Surgical Anatomy, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
| | - Ritu Singhal
- Department of Microbiology, National Reference Laboratory and Canter of Excellence (TB) WHO, National Institute of Tuberculosis and Respiratory Diseases, New Delhi, India
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26
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Dippenaar A, Ismail N, Grobbelaar M, Oostvogels S, de Vos M, Streicher EM, Heupink TH, van Rie A, Warren RM. Optimizing liquefaction and decontamination of sputum for DNA extraction from Mycobacterium tuberculosis. Tuberculosis (Edinb) 2022; 132:102159. [PMID: 34906896 DOI: 10.1016/j.tube.2021.102159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 11/21/2021] [Accepted: 12/02/2021] [Indexed: 10/19/2022]
Abstract
Whole genome sequencing (WGS) can investigate the entire Mycobacterium tuberculosis (Mtb) genome but currently requires large amounts of mycobacterial DNA, necessitating culture. Culture-free Mtb WGS could revolutionize the clinical use of WGS but is hampered by the high viscosity, low mycobacterial load, and high contamination with bacterial and human DNA in sputum samples. To improve the sputum liquefaction and decontamination step prior to DNA extraction, we assessed the efficiency of Myco-TB, MycoPrep, and Sputolysin with/without TiKa-Kic in liquefying and decontaminating sputum and aimed to evaluate the effect of these approaches on mycobacterial viability, and Mtb DNA quality and quantity. Experiments using spiked sputum samples showed that Myco-TB and BD MycoPrep with standard (15 min) or increased (30 min) incubation time, but not reduced (7,5 min) incubation time performed well in liquefying and decontaminating sputum. No difference in DNA quality or quantity, contamination, or the amount of human DNA present was observed. In comparison, Sputolysin with/without TiKa-Kic was less effective for liquefaction and decontamination of sputum. PCR amplification of the human GAPDH gene after sputum treatment, showed the presence of human DNA in all samples, regardless of sputum treatment. Focused efforts are needed to deplete contaminating DNA for culture-free Mtb WGS.
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Affiliation(s)
- Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
| | - Nabila Ismail
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Melanie Grobbelaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Selien Oostvogels
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Margaretha de Vos
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Elizabeth M Streicher
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tim H Heupink
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Annelies van Rie
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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27
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Meumann EM, Horan K, Ralph AP, Farmer B, Globan M, Stephenson E, Popple T, Boyd R, Kaestli M, Seemann T, Vandelannoote K, Lowbridge C, Baird RW, Stinear TP, Williamson DA, Currie BJ, Krause VL. Tuberculosis in Australia's tropical north: a population-based genomic epidemiological study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2021; 15:100229. [PMID: 34528010 PMCID: PMC8350059 DOI: 10.1016/j.lanwpc.2021.100229] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/03/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022]
Abstract
BACKGROUND The Northern Territory (NT) has the highest tuberculosis (TB) rate of all Australian jurisdictions. We combined TB public health surveillance data with genomic sequencing of Mycobacterium tuberculosis isolates in the tropical 'Top End' of the NT to investigate trends in TB incidence and transmission. METHODS This retrospective observational study included all 741 culture-confirmed cases of TB in the Top End over three decades from 1989-2020. All 497 available M. tuberculosis isolates were sequenced. We used contact tracing data to define a threshold pairwise SNP distance for hierarchical single linkage clustering, and examined putative transmission clusters in the context of epidemiologic information. FINDINGS There were 359 (48%) cases born overseas, 329 (44%) cases among Australian First Nations peoples, and 52 (7%) cases were Australian-born and non-Indigenous. The annual incidence in First Nations peoples from 1989-2019 fell from average 50.4 to 11.0 per 100,000 (P<0·001). First Nations cases were more likely to die from TB (41/329, 12·5%) than overseas-born cases (11/359, 3·1%; P<0·001). Using a threshold of ≤12 SNPs, 28 clusters of between 2-64 individuals were identified, totalling 250 cases; 214 (86%) were First Nations cases and 189 (76%) were from a remote region. The time between cases and past epidemiologically- and genomically-linked contacts ranged from 4·5 months to 24 years. INTERPRETATION Our findings support prioritisation of timely case detection, contact tracing augmented by genomic sequencing, and latent TB treatment to break transmission chains in Top End remote hotspot regions.
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Affiliation(s)
- Ella M Meumann
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Australia
- Territory Pathology, Royal Darwin Hospital, Darwin, Australia
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anna P Ralph
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Australia
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Belinda Farmer
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Maria Globan
- Mycobacterium Reference Laboratory, Victorian Infectious Diseases Reference Laboratory, Royal Melbourne Hospital at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Elizabeth Stephenson
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Tracy Popple
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Rowena Boyd
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Mirjam Kaestli
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Koen Vandelannoote
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Christopher Lowbridge
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
| | - Robert W. Baird
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Australia
- Territory Pathology, Royal Darwin Hospital, Darwin, Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Deborah A. Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Bart J. Currie
- Global and Tropical Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, Australia
- Department of Infectious Diseases, Division of Medicine, Royal Darwin Hospital, Darwin, Australia
| | - Vicki L. Krause
- Nothern Territory Centre for Disease Control, Northern Territory Government, Darwin, Australia
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Characterizing Microbiomes via Sequencing of Marker Loci: Techniques To Improve Throughput, Account for Cross-Contamination, and Reduce Cost. mSystems 2021; 6:e0029421. [PMID: 34254828 PMCID: PMC8409480 DOI: 10.1128/msystems.00294-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
New approaches to characterizing microbiomes via high-throughput sequencing provide impressive gains in efficiency and cost reduction compared to approaches that were standard just a few years ago. However, the speed of method development has been such that staying abreast of the latest technological advances is challenging. Moreover, shifting laboratory protocols to include new methods can be expensive and time consuming. To facilitate adoption of new techniques, we provide a guide and review of recent advances that are relevant for single-locus sequence-based study of microbiomes—from extraction to library preparation—including a primer regarding the use of liquid-handling automation in small-scale academic settings. Additionally, we describe several amendments to published techniques to improve throughput, track contamination, and reduce cost. Notably, we suggest adding synthetic DNA molecules to each sample during nucleic acid extraction, thus providing a method of documenting incidences of cross-contamination. We also describe a dual-indexing scheme for Illumina sequencers that allows multiplexing of many thousands of samples with minimal PhiX input. Collectively, the techniques that we describe demonstrate that laboratory technology need not impose strict limitations on the scale of molecular microbial ecology studies. IMPORTANCE New methods to characterize microbiomes reduce technology-imposed limitations to study design, but many new approaches have not been widely adopted. Here, we present techniques to increase throughput and reduce contamination alongside a thorough review of current best practices.
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29
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Almaw G, Mekonnen GA, Mihret A, Aseffa A, Taye H, Conlan AJK, Gumi B, Zewude A, Aliy A, Tamiru M, Olani A, Lakew M, Sombo M, Gebre S, Diguimbaye C, Hilty M, Fané A, Müller B, Hewinson RG, Ellis RJ, Nunez-Garcia J, Palkopoulou E, Abebe T, Ameni G, Parkhill J, Wood JLN, Berg S, van Tonder AJ. Population structure and transmission of Mycobacterium bovis in Ethiopia. Microb Genom 2021; 7:000539. [PMID: 33945462 PMCID: PMC8209724 DOI: 10.1099/mgen.0.000539] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 02/02/2021] [Indexed: 12/03/2022] Open
Abstract
Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis, which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of M. bovis in Ethiopia. A total of 134 M. bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis, based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.
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Affiliation(s)
- Gizat Almaw
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Getnet Abie Mekonnen
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Adane Mihret
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Hawult Taye
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | | | - Balako Gumi
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Aboma Zewude
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abde Aliy
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Mekdes Tamiru
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Abebe Olani
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Matios Lakew
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Melaku Sombo
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Solomon Gebre
- National Animal Health Diagnostic and Investigation Center, Sebeta, Ethiopia
| | - Colette Diguimbaye
- Institut de Recherches en Elevage pour le Développement & Clinique Médico-Chirurgicale PROVIDENCE, N'Djaména, Chad
| | - Markus Hilty
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Adama Fané
- Laboratoire Centrale Vétérinaire, Bamako, Mali
| | | | | | | | | | | | - Tamrat Abebe
- Department of Microbiology, Immunology and Parasitology, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Veterinary Medicine, College of Food and Agriculture, United Arab Emirates University, Al Ain, UAE
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - James L. N. Wood
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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30
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Lam C, Martinez E, Crighton T, Furlong C, Donnan E, Marais BJ, Sintchenko V. Value of routine whole genome sequencing for Mycobacterium tuberculosis drug resistance detection. Int J Infect Dis 2021; 113 Suppl 1:S48-S54. [PMID: 33753222 DOI: 10.1016/j.ijid.2021.03.033] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/02/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022] Open
Abstract
Routine whole genome sequencing (WGS) of pathogens is becoming more feasible as sequencing costs decrease and access to benchtop sequencing equipment and bioinformatics pipelines increases. This study examined the added value gained from implementing routine WGS of all Mycobacterium tuberculosis isolates in New South Wales, Australia. Drug resistance markers inferred from WGS data were compared to commercial genotypic drug susceptibility testing (DST) assays and conventional phenotypic DST in all isolates sequenced between 2016 and 2019. Of the 1107 clinical M. tuberculosis isolates sequenced, 29 (2.6%) were multi-drug resistant (MDR); most belonged to Beijing (336; 30.4%) or East-African Indian (332; 30%) lineages. Compared with conventional phenotypic DST, WGS identified an additional 1% of isolates which were likely drug resistant, explained by mutations previously associated with treatment failure and mixed bacterial populations. However, WGS provided a 20% increase in drug resistance detection in comparison with commercial genotypic assays by identifying mutations outside of the classic resistance determining regions in rpoB, inhA, katG, pncA and embB genes. Gains in drug resistance detection were significant (p = 0.0137, paired t-test), but varied substantially for different phylogenetic lineages. In low incidence settings, routine WGS of M. tuberculosis provides better guidance for person-centered management of drug resistant tuberculosis than commercial genotypic assays.
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Affiliation(s)
- Connie Lam
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia.
| | - Elena Martinez
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia
| | - Taryn Crighton
- NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia
| | - Catriona Furlong
- New South Wales Tuberculosis Program, Health Protection NSW, Sydney, New South Wales, Australia
| | - Ellen Donnan
- New South Wales Tuberculosis Program, Health Protection NSW, Sydney, New South Wales, Australia
| | - Ben J Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity and Centre for Research Excellence in Tuberculosis (TB-CRE), The University of Sydney, Sydney, New South Wales, Australia; Children's Hospital at Westmead, Westmead, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Western Sydney Local Health District, Sydney, New South Wales, Australia; NSW Mycobacterium Reference Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology - Western, Sydney, New South Wales, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity and Centre for Research Excellence in Tuberculosis (TB-CRE), The University of Sydney, Sydney, New South Wales, Australia
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31
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Low-Level Rifampin Resistance and rpoB Mutations in Mycobacterium tuberculosis: an Analysis of Whole-Genome Sequencing and Drug Susceptibility Test Data in New York. J Clin Microbiol 2021; 59:JCM.01885-20. [PMID: 32999007 DOI: 10.1128/jcm.01885-20] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 09/05/2020] [Indexed: 01/02/2023] Open
Abstract
Rapid and reliable detection of rifampin (RIF) resistance is critical for the diagnosis and treatment of drug-resistant and multidrug-resistant (MDR) tuberculosis. Discordant RIF phenotype/genotype susceptibility results remain a challenge due to the presence of rpoB mutations that do not confer high levels of RIF resistance, as have been exhibited in strains with mutations such as Ser450Leu. These strains, termed low-level RIF resistant, exhibit elevated RIF MICs compared to fully susceptible strains but remain phenotypically susceptible by mycobacterial growth indicator tube (MGIT) testing and have been associated with poor patient outcomes. Here, we assess RIF resistance prediction by whole-genome sequencing (WGS) among a set of 1,779 prospectively tested strains by both prevalence of rpoB gene mutation and phenotype as part of routine clinical testing during a 2.5-year period. During this time, 139 strains were found to have nonsynonymous rpoB mutations, 53 of which were associated with RIF resistance, including both low-level and high-level resistance. Resistance to RIF (1.0 μg/ml in MGIT) was identified in 43 (81.1%) isolates. The remaining 10 (18.9%) strains were susceptible by MGIT but were confirmed to be low-level RIF resistant by MIC testing. Full rpoB gene sequencing overcame the limitations of critical concentration phenotyping, probe-based genotyping, and partial gene sequencing methods. Universal clinical WGS with concurrent phenotypic testing provided a more complete understanding of the prevalence and type of rpoB mutations and their association with RIF resistance in New York.
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DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples. J Clin Microbiol 2020; 58:JCM.00670-20. [PMID: 32719032 PMCID: PMC7512152 DOI: 10.1128/jcm.00670-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/15/2020] [Indexed: 02/03/2023] Open
Abstract
Mycobacterium tuberculosis is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from M. tuberculosis-positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat inactivation (99°C/30 min), and enrichment for mycobacteria DNA were achieved using an equal volume of thermo-protection buffer (4 M KCl, 0. Mycobacterium tuberculosis is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from M. tuberculosis-positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat inactivation (99°C/30 min), and enrichment for mycobacteria DNA were achieved using an equal volume of thermo-protection buffer (4 M KCl, 0.05 M HEPES buffer, pH 7.5, 0.1% dithiothreitol [DTT]). The buffer emulated intracellular conditions found in hyperthermophiles, thus protecting DNA from rapid thermodegradation, which renders it a poor template for sequencing. Initial validation experiments employed mycobacteria DNA, either extracted or intracellular. Next, mock clinical samples (infection-negative human sputum spiked with 0 to 105Mycobacterium bovis BCG cells/ml) underwent liquefaction in thermo-protection buffer and heat inactivation. DNA was extracted and sequenced. Human DNA degraded faster than mycobacteria DNA, resulting in target enrichment. Four replicate experiments achieved M. tuberculosis detection at 101 BCG cells/ml, with 31 to 59 M. tuberculosis complex reads. Maximal genome coverage (>97% at 5× depth) occurred at 104 BCG cells/ml; >91% coverage (1× depth) occurred at 103 BCG cells/ml. Final validation employed M. tuberculosis-positive clinical samples (n = 20), revealing that initial sample volumes of ≥1 ml typically yielded higher mean depths of M. tuberculosis genome coverage, with an overall range of 0.55 to 81.02. A mean depth of 3 gave >96% 1-fold tuberculosis (TB) genome coverage (in 15/20 clinical samples). A mean depth of 15 achieved >99% 5-fold genome coverage (in 9/20 clinical samples). In summary, direct-from-sample sequencing of M. tuberculosis genomes was facilitated by a low-cost thermo-protection buffer.
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Crispell J, Cassidy S, Kenny K, McGrath G, Warde S, Cameron H, Rossi G, MacWhite T, White PCL, Lycett S, Kao RR, Moriarty J, Gordon SV. Mycobacterium bovis genomics reveals transmission of infection between cattle and deer in Ireland. Microb Genom 2020; 6:mgen000388. [PMID: 32553050 PMCID: PMC7641417 DOI: 10.1099/mgen.0.000388] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 05/19/2020] [Indexed: 12/13/2022] Open
Abstract
Control of bovine tuberculosis (bTB), caused by Mycobacterium bovis, in the Republic of Ireland costs €84 million each year. Badgers are recognized as being a wildlife source for M. bovis infection of cattle. Deer are thought to act as spillover hosts for infection; however, population density is recognized as an important driver in shifting their epidemiological role, and deer populations across the country have been increasing in density and range. County Wicklow represents one specific area in the Republic of Ireland with a high density of deer that has had consistently high bTB prevalence for over a decade, despite control operations in both cattle and badgers. Our research used whole-genome sequencing of M. bovis sourced from infected cattle, deer and badgers in County Wicklow to evaluate whether the epidemiological role of deer could have shifted from spillover host to source. Our analyses reveal that cattle and deer share highly similar M. bovis strains, suggesting that transmission between these species is occurring in the area. In addition, the high level of diversity observed in the sampled deer population suggests deer may be acting as a source of infection for local cattle populations. These findings have important implications for the control and ultimate eradication of bTB in Ireland.
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Affiliation(s)
- Joseph Crispell
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- Data Science Campus, Office for National Statistics, Newport, UK
| | - Sophie Cassidy
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Kevin Kenny
- Central Veterinary Research Laboratory, Backweston, County Kildare, Ireland
| | - Guy McGrath
- UCD Centre for Veterinary Epidemiology and Risk Analysis (CVERA), School of Veterinary Medicine, University College Dublin, Dublin, Ireland
| | - Susan Warde
- Central Veterinary Research Laboratory, Backweston, County Kildare, Ireland
| | - Henrietta Cameron
- Central Veterinary Research Laboratory, Backweston, County Kildare, Ireland
| | - Gianluigi Rossi
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Teresa MacWhite
- Department of Agriculture, Food and the Marine, Backweston, County Kildare, Ireland
| | - Piran C. L. White
- Department of Environment and Geography, University of York, Wentworth Way, York YO10 5NG, UK
| | | | - Rowland R. Kao
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - John Moriarty
- Central Veterinary Research Laboratory, Backweston, County Kildare, Ireland
| | - Stephen V. Gordon
- School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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34
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Asare P, Otchere ID, Bedeley E, Brites D, Loiseau C, Baddoo NA, Asante-Poku A, Osei-Wusu S, Prah DA, Borrell S, Reinhard M, Forson A, Koram KA, Gagneux S, Yeboah-Manu D. Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana. Front Med (Lausanne) 2020; 7:161. [PMID: 32509791 PMCID: PMC7248928 DOI: 10.3389/fmed.2020.00161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/09/2020] [Indexed: 01/08/2023] Open
Abstract
Whole genome sequencing (WGS) is progressively being used to investigate the transmission dynamics of Mycobacterium tuberculosis complex (MTBC). We used WGS analysis to resolve traditional genotype clusters and explored the spatial distribution of confirmed recent transmission clusters. Bacterial genomes from a total of 452 MTBC isolates belonging to large traditional clusters from a population-based study spanning July 2012 and December 2015 were obtained through short read next-generation sequencing using the illumina HiSeq2500 platform. We performed clustering and spatial analysis using specified R packages and ArcGIS. Of the 452 traditional genotype clustered genomes, 314 (69.5%) were confirmed clusters with a median cluster size of 7.5 genomes and an interquartile range of 4–12. Recent tuberculosis (TB) transmission was estimated as 24.7%. We confirmed the wide spread of a Cameroon sub-lineage clone with a cluster size of 78 genomes predominantly from the Ablekuma sub-district of Accra metropolis. More importantly, we identified a recent transmission cluster associated with isoniazid resistance belonging to the Ghana sub-lineage of lineage 4. WGS was useful in detecting unsuspected outbreaks; hence, we recommend its use not only as a research tool but as a surveillance tool to aid in providing the necessary guided steps to track, monitor, and control TB.
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Affiliation(s)
- Prince Asare
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Edmund Bedeley
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Diana Ahu Prah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Audrey Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Korle-Bu, Accra, Ghana
| | - Kwadwo Ansah Koram
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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35
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Karmakar M, Rodrigues CHM, Horan K, Denholm JT, Ascher DB. Structure guided prediction of Pyrazinamide resistance mutations in pncA. Sci Rep 2020; 10:1875. [PMID: 32024884 PMCID: PMC7002382 DOI: 10.1038/s41598-020-58635-x] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 11/28/2019] [Indexed: 11/29/2022] Open
Abstract
Pyrazinamide plays an important role in tuberculosis treatment; however, its use is complicated by side-effects and challenges with reliable drug susceptibility testing. Resistance to pyrazinamide is largely driven by mutations in pyrazinamidase (pncA), responsible for drug activation, but genetic heterogeneity has hindered development of a molecular diagnostic test. We proposed to use information on how variants were likely to affect the 3D structure of pncA to identify variants likely to lead to pyrazinamide resistance. We curated 610 pncA mutations with high confidence experimental and clinical information on pyrazinamide susceptibility. The molecular consequences of each mutation on protein stability, conformation, and interactions were computationally assessed using our comprehensive suite of graph-based signature methods, mCSM. The molecular consequences of the variants were used to train a classifier with an accuracy of 80%. Our model was tested against internationally curated clinical datasets, achieving up to 85% accuracy. Screening of 600 Victorian clinical isolates identified a set of previously unreported variants, which our model had a 71% agreement with drug susceptibility testing. Here, we have shown the 3D structure of pncA can be used to accurately identify pyrazinamide resistance mutations. SUSPECT-PZA is freely available at: http://biosig.unimelb.edu.au/suspect_pza/.
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Affiliation(s)
- Malancha Karmakar
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
- Victorian Tuberculosis Program, Melbourne Health and Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Carlos H M Rodrigues
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Kristy Horan
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at The Peter Doherty Institute for Infection &Immunity, Melbourne, Victoria, Australia
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health and Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - David B Ascher
- Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia.
- Department of Biochemistry and Molecular Biology, Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK.
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36
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Epperson LE, Strong M. A scalable, efficient, and safe method to prepare high quality DNA from mycobacteria and other challenging cells. J Clin Tuberc Other Mycobact Dis 2020; 19:100150. [PMID: 32154387 PMCID: PMC7052505 DOI: 10.1016/j.jctube.2020.100150] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The rapid development in sequencing technology is creating an increase in demand for largely intact DNA as starting material as very long strands of DNA are sequenced directly to generate reads that are thousands of bases long. Organisms with thick cell walls are difficult to lyse, often impacting both DNA recovery and quality. Consequently, most mycobacterial DNA extraction methods require bead-beating steps or toxic chemicals. Here we present an updated method that yields abundant, high quality genomic DNA from M. tuberculosis and diverse nontuberculous mycobacterial (NTM) species, in addition to complex biological communities from a variety of sources. This method eliminates the time-consuming phenol and chloroform extraction and ethanol precipitation steps, and high quality DNA from up to 96 samples can be extracted in about 2-3 h of hands-on time. This DNA is suitable for long and short read sequencing technologies as well as PCR and qPCR amplification.
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Affiliation(s)
- L Elaine Epperson
- Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, Colorado 80206, USA
| | - Michael Strong
- Center for Genes, Environment, and Health, National Jewish Health, 1400 Jackson Street, Denver, Colorado 80206, USA
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37
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Bouso JM, Planet PJ. Complete nontuberculous mycobacteria whole genomes using an optimized DNA extraction protocol for long-read sequencing. BMC Genomics 2019; 20:793. [PMID: 31666009 PMCID: PMC6822416 DOI: 10.1186/s12864-019-6134-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Background Nontuberculous mycobacteria (NTM) are a major cause of pulmonary and systemic disease in at-risk populations. Gaps in knowledge about transmission patterns, evolution, and pathogenicity during infection have prompted a recent surge in genomic NTM research. Increased availability and affordability of whole genome sequencing (WGS) techniques provide new opportunities to sequence and construct complete bacterial genomes faster and at a lower cost. However, extracting large quantities of pure genomic DNA is particularly challenging with NTM due to its slow growth and recalcitrant cell wall. Here we report a DNA extraction protocol that is optimized for long-read WGS of NTM, yielding large quantities of highly pure DNA with no additional clean-up steps. Results Our DNA extraction method was compared to 6 other methods with variations in timing of mechanical disruption and enzymatic digestion of the cell wall, quantity of matrix material, and reagents used in extraction and precipitation. We tested our optimized method on 38 clinical isolates from the M. avium and M. abscessus complexes, which yielded optimal quality and quantity measurements for Oxford Nanopore Technologies sequencing. We also present the efficient completion of circularized M. avium subspecies hominissuis genomes using our extraction technique and the long-read sequencing MinION platform, including the identification of a novel plasmid. Conclusions Our optimized extraction protocol and assembly pipeline was both sufficient and efficient for genome closure. We expect that our finely-tuned extraction method will prove to be a valuable tool in long-read sequencing and completion of mycobacterial genomes going forward. Utilization of comprehensive, long-read based approaches will advance the understanding evolution and pathogenicity of NTM infections.
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Affiliation(s)
- Jennifer M Bouso
- Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Paul J Planet
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA. .,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, USA.
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Zakham F, Laurent S, Esteves Carreira A, Corbaz A, Bertelli C, Masserey E, Nicod L, Greub G, Jaton K, Mazza-Stalder J, Opota O. Whole-genome sequencing for rapid, reliable and routine investigation of Mycobacterium tuberculosis transmission in local communities. New Microbes New Infect 2019; 31:100582. [PMID: 31388433 PMCID: PMC6669808 DOI: 10.1016/j.nmni.2019.100582] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/11/2019] [Accepted: 06/24/2019] [Indexed: 11/28/2022] Open
Abstract
Contact investigations following the diagnosis of active tuberculosis (TB) are paramount for the control of the disease. Epidemiological data are very powerful for contact tracing but might be delayed and/or difficult to integrate, especially in the setting of multiple contact-tracing investigations. The aim of this study was to address the added-value of whole-genome sequencing (WGS) to routine local TB surveillance systems. From November 2016 to July 2017, the local TB surveillance system identified three clusters that could constitute a unique larger outbreak. Epidemiological and clinical information were integrated with WGS genotyping data of Mycobacterium tuberculosis strains obtained using a simple DNA extraction method coupled with sequencing using an Illumina MiSeq platform and an in-house bioinformatics pipeline for single nucleotide polymorphism (SNP) analysis. Epidemiological investigations identified three putative TB clusters potentially interrelated including eight patients with active TB. Seven M. tuberculosis isolates were available and analysed by WGS. Using a 5-SNP threshold to define recent transmission, WGS-based genotyping supported the occurrence of the three clusters as well as a link between clusters 1 and 2 (SNP ≤1), constituting a larger outbreak. This outbreak was clearly delineated by refuting a potential link with the third cluster (SNP >500). Genotyping data did not support the belonging of patient 7 to any studied cluster. This study illustrates the usefulness of WGS genotyping for routine TB surveillance systems in local communities to rapidly confirm or disprove epidemiological hypotheses and delineate TB clusters, especially in the context of multiple contact-tracing investigations.
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Affiliation(s)
- F. Zakham
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - S. Laurent
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - A.L. Esteves Carreira
- Department of Pneumology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - A. Corbaz
- Department of Pneumology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - C. Bertelli
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - E. Masserey
- Public Health Department, Canton of Vaud, Lausanne Switzerland
| | - L. Nicod
- Department of Pneumology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - G. Greub
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - K. Jaton
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - J. Mazza-Stalder
- Department of Pneumology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
| | - O. Opota
- Institute of Microbiology, University of Lausanne and University Hospital of Lausanne, Lausanne Switzerland
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García de Viedma D. Pathways and strategies followed in the genomic epidemiology of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2019; 72:4-9. [DOI: 10.1016/j.meegid.2019.01.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 10/27/2022]
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40
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Khan PY, Yates TA, Osman M, Warren RM, van der Heijden Y, Padayatchi N, Nardell EA, Moore D, Mathema B, Gandhi N, Eldholm V, Dheda K, Hesseling AC, Mizrahi V, Rustomjee R, Pym A. Transmission of drug-resistant tuberculosis in HIV-endemic settings. THE LANCET. INFECTIOUS DISEASES 2019; 19:e77-e88. [PMID: 30554996 PMCID: PMC6474238 DOI: 10.1016/s1473-3099(18)30537-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022]
Abstract
The emergence and expansion of the multidrug-resistant tuberculosis epidemic is a threat to the global control of tuberculosis. Multidrug-resistant tuberculosis is the result of the selection of resistance-conferring mutations during inadequate antituberculosis treatment. However, HIV has a profound effect on the natural history of tuberculosis, manifesting in an increased rate of disease progression, leading to increased transmission and amplification of multidrug-resistant tuberculosis. Interventions specific to HIV-endemic areas are urgently needed to block tuberculosis transmission. These interventions should include a combination of rapid molecular diagnostics and improved chemotherapy to shorten the duration of infectiousness, implementation of infection control measures, and active screening of multidrug-resistant tuberculosis contacts, with prophylactic regimens for individuals without evidence of disease. Development and improvement of the efficacy of interventions will require a greater understanding of the factors affecting the transmission of multidrug-resistant tuberculosis in HIV-endemic settings, including population-based molecular epidemiology studies. In this Series article, we review what we know about the transmission of multidrug-resistant tuberculosis in settings with high burdens of HIV and define the research priorities required to develop more effective interventions, to diminish ongoing transmission and the amplification of drug resistance.
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Affiliation(s)
- Palwasha Y Khan
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; TB Centre, London School of Hygiene & Tropical Medicine, London, UK; Interactive Research and Development, Karachi, Pakistan
| | - Tom A Yates
- Institute for Global Health, University College London, London, UK; Institute of Child Health, University College London, London, UK
| | - Muhammad Osman
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M Warren
- Department of Science and Technology/National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Yuri van der Heijden
- Vanderbilt Tuberculosis Center and Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Nesri Padayatchi
- South African Medical Research Council HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Edward A Nardell
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, MA, USA
| | - David Moore
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; TB Centre, London School of Hygiene & Tropical Medicine, London, UK
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Neel Gandhi
- Rollins School of Public Health and Emory School of Medicine, Emory University, Atlanta, GA, USA
| | - Vegard Eldholm
- Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology and University of Cape Town Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - 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
| | - Valerie Mizrahi
- Department of Science and Technology/National Research Foundation Centre of Excellence in Biomedical Tuberculosis Research, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Roxana Rustomjee
- Division of AIDS, National Institutes of Health, Bethesda, MD, USA
| | - Alexander Pym
- Department of Infection and Immunity, University College London, London, UK; Africa Health Research Institute, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa.
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The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis. Microbiol Spectr 2019; 6. [PMID: 30338753 DOI: 10.1128/microbiolspec.mtbp-0002-2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The introduction of genotypic tools to analyze Mycobacterium tuberculosis isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of M. tuberculosis. This review integrates two approaches: on the one hand, it considers how genotyping techniques have evolved over the years; and on the other, it looks at how the way we think these techniques should be applied has changed. We begin by examining the application of fingerprinting tools to suspected outbreaks only, before moving on to universal genotyping schemes, and finally we describe the latest real-time strategies used in molecular epidemiology. We also analyze refined approaches to obtaining epidemiological data from patients and to increasing the discriminatory power of genotyping by techniques based on genomic characterization. Finally, we review the development of integrative solutions to reconcile the speed of PCR-based methods with the high discriminatory power of whole-genome sequencing in easily implemented formats adapted to low-resource settings. Our analysis of future considerations highlights the need to bring together the three key elements of high-quality surveillance of transmission in tuberculosis, namely, speed, precision, and ease of implementation.
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42
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Packer S, Green C, Brooks-Pollock E, Chaintarli K, Harrison S, Beck CR. Social network analysis and whole genome sequencing in a cohort study to investigate TB transmission in an educational setting. BMC Infect Dis 2019; 19:154. [PMID: 30760211 PMCID: PMC6375175 DOI: 10.1186/s12879-019-3734-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 01/18/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND TB outbreaks in educational institutions can result in significant transmission and pose a considerable threat to TB control. Investigation using traditional microbiological and epidemiological tools can lead to imprecise screening strategies due to difficulties characterising complex transmission networks. Application of whole genome sequencing (WGS) and social network analysis can provide additional information that may facilitate rapid directed public health action. We report the utility of these methods in combination with traditional approaches for the first time to investigate a TB outbreak in an educational setting. METHODS Latent tuberculosis infection (LTBI) cases were screenees with a positive T-SPOT®.TB test. Active TB cases were defined through laboratory confirmation of M. tuberculosis on culture or through clinical or radiological findings consistent with infection. Epidemiological data were collected from institutional records and screenees. Samples were cultured and analysed using traditional M. tuberculosis typing and WGS. We undertook multivariable multinomial regression and social network analysis to identify exposures associated with case status and risk communities. RESULTS We identified 189 LTBI cases (13.7% positivity rate) and nine active TB cases from 1377 persons screened. The LTBI positivity rate was 39.1% (99/253) among persons who shared a course with an infectious case (odds ratio 7.3, 95% confidence interval [CI] 5.2 to 10.3). The community structure analysis divided the students into five communities based on connectivity, as opposed to the 11 shared courses. Social network analysis identified that the community including the suspected index case was at significantly elevated risk of active disease (odds ratio 7.5, 95% CI 1.3 to 44.0) and contained eight persons who were lost to follow-up. Five sputum samples underwent WGS, four had zero single nucleotide polymorphism (SNP) differences and one had a single SNP difference. CONCLUSION This study demonstrates the public health impact an undiagnosed case of active TB disease can have in an educational setting within a low incidence area. Social network analysis and whole genome sequencing provided greater insight to evolution of the transmission network and identification of communities of risk. These tools provide further information over traditional epidemiological and microbiological approaches to direct public health action in this setting.
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Affiliation(s)
- Simon Packer
- Field Epidemiology Service, Public Health England, Bristol, UK
| | - Claire Green
- Heart and Lung Unit, Torbay and South Devon NHS Foundation Trust, Torbay, UK
| | - Ellen Brooks-Pollock
- NIHR Health Protection Research Unit in Evaluation of Interventions at the University of Bristol, Bristol, UK
| | | | | | - Charles R Beck
- Field Epidemiology Service, Public Health England, Bristol, UK. .,NIHR Health Protection Research Unit in Evaluation of Interventions at the University of Bristol, Bristol, UK. .,School of Social and Community Medicine, University of Bristol, Bristol, UK.
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43
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Whole-Genome Sequencing for Predicting Clarithromycin Resistance in Mycobacterium abscessus. Antimicrob Agents Chemother 2018; 63:AAC.01204-18. [PMID: 30397069 DOI: 10.1128/aac.01204-18] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/25/2018] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium abscessus is emerging as an important pathogen in chronic lung diseases, with concern regarding patient-to-patient transmission. The recent introduction of routine whole-genome sequencing (WGS) as a replacement for existing reference techniques in England provides an opportunity to characterize the genetic determinants of resistance. We conducted a systematic review to catalogue all known resistance-determining mutations. This knowledge was used to construct a predictive algorithm based on mutations in the erm(41) and rrl genes which was tested on a collection of 203 sequentially acquired clinical isolates for which there were paired genotype/phenotype data. A search for novel resistance-determining mutations was conducted using a heuristic algorithm. The sensitivity of existing knowledge for predicting resistance in clarithromycin was 95% (95% confidence interval [CI], 89 to 98%), and the specificity was 66% (95% CI, 54 to 76%). The subspecies alone was a poor predictor of resistance to clarithromycin. Eight potential new resistance-conferring single nucleotide polymorphisms (SNPs) were identified. WGS demonstrated probable resistance-determining SNPs in regions that the NTM-DR line probe cannot detect. These mutations are potentially clinically important, as they all occurred in samples that were predicted to be inducibly resistant and for which a macrolide would therefore currently be indicated. We were unable to explain all resistance, raising the possibility of the involvement of other as yet unidentified genes.
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44
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Tagliani E, Nikolayevskyy V, Tortoli E, Cirillo DM. Laboratory diagnosis of tuberculosis. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10021318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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45
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Folkvardsen DB, Norman A, Andersen ÅB, Rasmussen EM, Lillebaek T, Jelsbak L. A Major Mycobacterium tuberculosis outbreak caused by one specific genotype in a low-incidence country: Exploring gene profile virulence explanations. Sci Rep 2018; 8:11869. [PMID: 30089859 PMCID: PMC6082827 DOI: 10.1038/s41598-018-30363-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/10/2018] [Indexed: 12/30/2022] Open
Abstract
Denmark, a tuberculosis low burden country, still experiences significant active Mycobacterium tuberculosis (Mtb) transmission, especially with one specific genotype named Cluster 2/1112-15 (C2), the most prevalent lineage in Scandinavia. In addition to environmental factors, antibiotic resistance, and human genetics, there is increasing evidence that Mtb strain variation plays a role for the outcome of infection and disease. In this study, we explore the reasons for the success of the C2 genotype by analysing strain specific polymorphisms identified through whole genome sequencing of all C2 isolates identified in Denmark between 1992 and 2014 (n = 952), and the demographic distribution of C2. Of 234 non-synonymous (NS) monomorphic SNPs found in C2 in comparison with Mtb reference strain H37Rv, 23 were in genes previously reported to be involved in Mtb virulence. Of these 23 SNPs, three were specific for C2 including a NS mutation in a gene associated with hyper-virulence. We show that the genotype is readily transmitted to different ethnicities and is also found outside Denmark. Our data suggest that strain specific virulence factor variations are important for the success of the C2 genotype. These factors, likely in combination with poor TB control, seem to be the main drivers of C2 success.
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Affiliation(s)
- Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Åse Bengård Andersen
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Research Unit for Infectious Diseases, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing. J Clin Microbiol 2018; 56:JCM.00666-18. [PMID: 29848567 PMCID: PMC6062781 DOI: 10.1128/jcm.00666-18] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
The current methods available to diagnose antimicrobial-resistant Mycobacterium tuberculosis infections require a positive culture or only test a limited number of resistance-associated mutations. A rapid accurate identification of antimicrobial resistance enables the prompt initiation of effective treatment. Here, we determine the utility of whole-genome sequencing (WGS) of M. tuberculosis directly from routinely obtained diagnostic sputum samples to provide a comprehensive resistance profile compared to that from mycobacterial growth indicator tube (MGIT) WGS. We sequenced M. tuberculosis from 43 sputum samples by targeted DNA enrichment using the Agilent SureSelectXT kit, and 43 MGIT positive samples from each participant. Thirty two (74%) sputum samples and 43 (100%) MGIT samples generated whole genomes. The times to antimicrobial resistance profiles and concordance were compared with Xpert MTB/RIF and phenotypic resistance testing from cultures of the same samples. Antibiotic susceptibility could be predicted from WGS of sputum within 5 days of sample receipt and up to 24 days earlier than WGS from MGIT culture and up to 31 days earlier than phenotypic testing. Direct sputum results could be reduced to 3 days with faster hybridization and if only regions encoding drug resistance are sequenced. We show that direct sputum sequencing has the potential to provide comprehensive resistance detection significantly faster than MGIT whole-genome sequencing or phenotypic testing of resistance from cultures in a clinical setting. This improved turnaround time enables prompt appropriate treatment with associated patient and health service benefits. Improvements in sample preparation are necessary to ensure comparable sensitivities and complete resistance profile predictions in all cases.
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47
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Gupta S, Kakkar V. Recent technological advancements in tuberculosis diagnostics - A review. Biosens Bioelectron 2018; 115:14-29. [PMID: 29783081 DOI: 10.1016/j.bios.2018.05.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Revised: 04/26/2018] [Accepted: 05/09/2018] [Indexed: 01/14/2023]
Abstract
Early diagnosis and on-time effective treatment are indispensable for Tuberculosis (TB) control - a life threatening infectious communicable disease. The conventional techniques for diagnosing TB normally take two to three weeks. This delay in diagnosis and further increase in detection complexity due to the emerging risks of XDR-TB (Extensively drug Resistant-TB) and MDR-TB (Multidrug Resistant-TB) are evoking interest of researchers in the field of developing rapid TB detection techniques such as biosensing and other point-of-care (POC) techniques. Biosensing technologies along with the collaboration with nanotechnology have enormous potential to boost the MTB detection and for overall management in clinical diagnosis. A diverse range of portable, sensitive and rapid biosensors based on different signal transducer principles and with different biomarkers detection capabilities have been developed for TB detection in the early stages. Further, a lot of progress has been achieved over the years in developing various point-of-care diagnostic tools including non-molecular methods and molecular techniques. The objective of this study is to present a succinct review of the available TB detection techniques that are either in use or under development. The focus of this review is on the current developments occurred in nano-biosensing technologies. A synopsis of ameliorations in different non-molecular diagnostic tools and progress in the field of molecular techniques along with the role of emerging Lab-on-Chip technology for diagnosing and mitigating the TB consequences have also been presented.
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Affiliation(s)
- Shagun Gupta
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra 182320, India.
| | - Vipan Kakkar
- School of Electronics and Communication Engineering, Shri Mata Vaishno Devi University, Katra 182320, India.
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Dookie N, Rambaran S, Padayatchi N, Mahomed S, Naidoo K. Evolution of drug resistance in Mycobacterium tuberculosis: a review on the molecular determinants of resistance and implications for personalized care. J Antimicrob Chemother 2018; 73:1138-1151. [PMID: 29360989 PMCID: PMC5909630 DOI: 10.1093/jac/dkx506] [Citation(s) in RCA: 166] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Drug-resistant TB (DR-TB) remains a significant challenge in TB treatment and control programmes worldwide. Advances in sequencing technology have significantly increased our understanding of the mechanisms of resistance to anti-TB drugs. This review provides an update on advances in our understanding of drug resistance mechanisms to new, existing drugs and repurposed agents. Recent advances in WGS technology hold promise as a tool for rapid diagnosis and clinical management of TB. Although the standard approach to WGS of Mycobacterium tuberculosis is slow due to the requirement for organism culture, recent attempts to sequence directly from clinical specimens have improved the potential to diagnose and detect resistance within days. The introduction of new databases may be helpful, such as the Relational Sequencing TB Data Platform, which contains a collection of whole-genome sequences highlighting key drug resistance mutations and clinical outcomes. Taken together, these advances will help devise better molecular diagnostics for more effective DR-TB management enabling personalized treatment, and will facilitate the development of new drugs aimed at improving outcomes of patients with this disease.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Santhuri Rambaran
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Sharana Mahomed
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC) - CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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Lange C, Chesov D, Heyckendorf J, Leung CC, Udwadia Z, Dheda K. Drug-resistant tuberculosis: An update on disease burden, diagnosis and treatment. Respirology 2018; 23:656-673. [PMID: 29641838 DOI: 10.1111/resp.13304] [Citation(s) in RCA: 139] [Impact Index Per Article: 23.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 03/14/2018] [Accepted: 03/14/2018] [Indexed: 01/02/2023]
Abstract
The emergence of antimicrobial resistance against Mycobacterium tuberculosis, the leading cause of mortality due to a single microbial pathogen worldwide, represents a growing threat to public health and economic growth. The global burden of multidrug-resistant tuberculosis (MDR-TB) has recently increased by an annual rate of more than 20%. According to the World Health Organization approximately only half of all patients treated for MDR-TB achieved a successful outcome. For many years, patients with drug-resistant tuberculosis (TB) have received standardized treatment regimens, thereby accelerating the development of MDR-TB through drug-specific resistance amplification. Comprehensive drug susceptibility testing (phenotypic and/or genotypic) is necessary to inform physicians about the best drugs to treat individual patients with tailor-made treatment regimens. Phenotypic drug resistance can now often, but with variable sensitivity, be predicted by molecular drug susceptibility testing based on whole genome sequencing, which in the future could become an affordable method for the guidance of treatment decisions, especially in high-burden/resource-limited settings. More recently, MDR-TB treatment outcomes have dramatically improved with the use of bedaquiline-based regimens. Ongoing clinical trials with novel and repurposed drugs will potentially further improve cure-rates, and may substantially decrease the duration of MDR-TB treatment necessary to achieve relapse-free cure.
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Affiliation(s)
- Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany.,Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Dumitru Chesov
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany.,Department of Pneumology and Allergology, State University of Medicine and Pharmacy "Nicolae Testemitanu", Chisinau, Republic of Moldova
| | - Jan Heyckendorf
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany.,German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany.,International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany
| | - Chi C Leung
- Department of Health, Tuberculosis and Chest Service, Centre for Health Protection, Hong Kong, China
| | - Zarir Udwadia
- Department of Pulmonology, Hinduja Hospital and Research Centre, Mumbai, India
| | - Keertan Dheda
- Lung Infection and Immunity Unit, Division of Pulmonology and UCT Lung Institute, Department of Medicine, University of Cape Town, Cape Town, South Africa
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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: 6] [Impact Index Per Article: 1.0] [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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