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Sadovska D, Ozere I, Pole I, Ķimsis J, Vaivode A, Vīksna A, Norvaiša I, Bogdanova I, Ulanova V, Čapligina V, Bandere D, Ranka R. Unraveling tuberculosis patient cluster transmission chains: integrating WGS-based network with clinical and epidemiological insights. Front Public Health 2024; 12:1378426. [PMID: 38832230 PMCID: PMC11144917 DOI: 10.3389/fpubh.2024.1378426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
Background Tuberculosis remains a global health threat, and the World Health Organization reports a limited reduction in disease incidence rates, including both new and relapse cases. Therefore, studies targeting tuberculosis transmission chains and recurrent episodes are crucial for developing the most effective control measures. Herein, multiple tuberculosis clusters were retrospectively investigated by integrating patients' epidemiological and clinical information with median-joining networks recreated based on whole genome sequencing (WGS) data of Mycobacterium tuberculosis isolates. Methods Epidemiologically linked tuberculosis patient clusters were identified during the source case investigation for pediatric tuberculosis patients. Only M. tuberculosis isolate DNA samples with previously determined spoligotypes identical within clusters were subjected to WGS and further median-joining network recreation. Relevant clinical and epidemiological data were obtained from patient medical records. Results We investigated 18 clusters comprising 100 active tuberculosis patients 29 of whom were children at the time of diagnosis; nine patients experienced recurrent episodes. M. tuberculosis isolates of studied clusters belonged to Lineages 2 (sub-lineage 2.2.1) and 4 (sub-lineages 4.3.3, 4.1.2.1, 4.8, and 4.2.1), while sub-lineage 4.3.3 (LAM) was the most abundant. Isolates of six clusters were drug-resistant. Within clusters, the maximum genetic distance between closely related isolates was only 5-11 single nucleotide variants (SNVs). Recreated median-joining networks, integrated with patients' diagnoses, specimen collection dates, sputum smear microscopy, and epidemiological investigation results indicated transmission directions within clusters and long periods of latent infection. It also facilitated the identification of potential infection sources for pediatric patients and recurrent active tuberculosis episodes refuting the reactivation possibility despite the small genetic distance of ≤5 SNVs between isolates. However, unidentified active tuberculosis cases within the cluster, the variable mycobacterial mutation rate in dormant and active states, and low M. tuberculosis genetic variability inferred precise transmission chain delineation. In some cases, heterozygous SNVs with an allelic frequency of 10-73% proved valuable in identifying direct transmission events. Conclusion The complex approach of integrating tuberculosis cluster WGS-data-based median-joining networks with relevant epidemiological and clinical data proved valuable in delineating epidemiologically linked patient transmission chains and deciphering causes of recurrent tuberculosis episodes within clusters.
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Affiliation(s)
- Darja Sadovska
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Ozere
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
- Department of Infectology, Riga Stradiņš University, Riga, Latvia
| | - Ilva Pole
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Jānis Ķimsis
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Annija Vaivode
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Anda Vīksna
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
- Department of Infectology, Riga Stradiņš University, Riga, Latvia
| | - Inga Norvaiša
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Ineta Bogdanova
- Centre of Tuberculosis and Lung Diseases, Riga East University Hospital, Upeslejas, Latvia
| | - Viktorija Ulanova
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Valentīna Čapligina
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Dace Bandere
- Department of Pharmaceutical Chemistry, Riga Stradiņš University, Riga, Latvia
| | - Renāte Ranka
- Laboratory of Molecular Microbiology, Latvian Biomedical Research and Study Centre, Riga, Latvia
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Putera I, Ten Berge JCEM, Thiadens AAHJ, Dik WA, Agrawal R, van Hagen PM, La Distia Nora R, Rombach SM. Relapse in ocular tuberculosis: relapse rate, risk factors and clinical management in a non-endemic country. Br J Ophthalmol 2024:bjo-2024-325207. [PMID: 38609164 DOI: 10.1136/bjo-2024-325207] [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: 01/12/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024]
Abstract
AIMS To assess the risk of uveitis relapse in ocular tuberculosis (OTB) following clinical inactivity, to analyse clinical factors associated with relapses and to describe the management strategies for relapses. METHODS A retrospective study was conducted on a 10-year patient registry of patients with OTB diagnosed at Erasmus MC in Rotterdam, The Netherlands. Time-to-relapse of uveitis was evaluated with Kaplan-Meier curve and risk factors for relapses were analysed. RESULTS 93 OTB cases were identified, of which 75 patients achieved clinical inactivity following treatment. The median time to achieve uveitis inactivity was 3.97 months. During a median follow-up of 20.7 months (Q1-Q3: 5.2-81.2) after clinical inactivity, uveitis relapse occurred in 25 of these 75 patients (33.3%). Patients who were considered poor treatment responders for their initial uveitis episode had a significantly higher risk of relapse after achieving clinical inactivity than good responders (adjusted HR=3.84, 95% CI: 1.28 to 11.51). 13 of the 25 relapsed patients experienced multiple uveitis relapse episodes, accounting for 78 eye-relapse episodes during the entire observation period. Over half (46 out of 78, 59.0%) of these episodes were anterior uveitis. A significant number of uveitis relapse episodes (31 episodes, 39.7%) were effectively managed with topical corticosteroids. CONCLUSIONS Our results suggest that approximately one-third of patients with OTB will experience relapse after achieving clinical inactivity. The initial disease course and poor response to treatment predict the likelihood of relapse in the long-term follow-up. Topical corticosteroids were particularly effective in relapse presenting as anterior uveitis.
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Affiliation(s)
- Ikhwanuliman Putera
- Department of Ophthalmology, Faculty of Medicine, University of Indonesia - Cipto Mangunkusumo Hospital, Jakarta, Indonesia
- Department of Ophthalmology, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine Section Allergy and Clinical Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | | | - Alberta A H J Thiadens
- Department of Ophthalmology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Willem A Dik
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Rupesh Agrawal
- National Healthcare Group Eye Institute, Tan Tock Seng Hospital, Singapore
- National Institute for Health Research Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust, London, UK
- Lee Kong Chian School of Medicine, Nanyang Technological University of Singapore, Singapore
- Duke NUS Medical School, Singapore
| | - P Martin van Hagen
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
- Department of Internal Medicine Section Allergy and Clinical Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Rina La Distia Nora
- Department of Ophthalmology, Faculty of Medicine, University of Indonesia - Cipto Mangunkusumo Hospital, Jakarta, Indonesia
- Laboratory Medical Immunology, Department of Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Saskia M Rombach
- Department of Internal Medicine Section Allergy and Clinical Immunology, Erasmus University Medical Centre, Rotterdam, The Netherlands
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Derendinger B, Dippenaar A, de Vos M, Huo S, Alberts R, Tadokera R, Limberis J, Sirgel F, Dolby T, Spies C, Reuter A, Folkerts M, Allender C, Lemmer D, Van Rie A, Gagneux S, Rigouts L, Te Riele J, Dheda K, Engelthaler DM, Warren R, Metcalfe J, Cox H, Theron G. Bedaquiline resistance in patients with drug-resistant tuberculosis in Cape Town, South Africa: a retrospective longitudinal cohort study. THE LANCET. MICROBE 2023; 4:e972-e982. [PMID: 37931638 PMCID: PMC10842724 DOI: 10.1016/s2666-5247(23)00172-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 04/26/2023] [Accepted: 05/24/2023] [Indexed: 11/08/2023]
Abstract
BACKGROUND Bedaquiline is a life-saving tuberculosis drug undergoing global scale-up. People at risk of weak tuberculosis drug regimens are a priority for novel drug access despite the potential source of Mycobacterium tuberculosis-resistant strains. We aimed to characterise bedaquiline resistance in individuals who had sustained culture positivity during bedaquiline-based treatment. METHODS We did a retrospective longitudinal cohort study of adults (aged ≥18 years) with culture-positive pulmonary tuberculosis who received at least 4 months of a bedaquiline-containing regimen from 12 drug-resistant tuberculosis treatment facilities in Cape Town, South Africa, between Jan 20, 2016, and Nov 20, 2017. Sputum was programmatically collected at baseline (ie, before bedaquiline initiation) and each month to monitor treatment response per the national algorithm. The last available isolate from the sputum collected at or after 4 months of bedaquiline was designated the follow-up isolate. Phenotypic drug susceptibility testing for bedaquiline was done on baseline and follow-up isolates in MGIT960 media (WHO-recommended critical concentration of 1 μg/mL). Targeted deep sequencing for Rv0678, atpE, and pepQ, as well as whole-genome sequencing were also done. FINDINGS In total, 40 (31%) of 129 patients from an estimated pool were eligible for this study. Overall, three (8%) of 38 patients assessable by phenotypic drug susceptibility testing for bedaquiline had primary resistance, 18 (47%) gained resistance (acquired or reinfection), and 17 (45%) were susceptible at both baseline and follow-up. Several Rv0678 and pepQ single-nucleotide polymorphisms and indels were associated with resistance. Although variants occurred in Rv0676c and Rv1979c, these variants were not associated with resistance. Targeted deep sequencing detected low-level variants undetected by whole-genome sequencing; however, none were in genes without variants already detected by whole-genome sequencing. Patients with baseline fluoroquinolone resistance, clofazimine exposure, and four or less effective drugs were more likely to have bedaquiline-resistant gain. Resistance gain was primarily due to acquisition; however, some reinfection by resistant strains occurred. INTERPRETATION Bedaquiline-resistance gain, for which we identified risk factors, was common in these programmatically treated patients with sustained culture positivity. Our study highlights risks associated with implementing life-saving new drugs and shows evidence of bedaquiline-resistance transmission. Routine drug susceptibility testing should urgently accompany scale-up of new drugs; however, rapid drug susceptibility testing for bedaquiline remains challenging given the diversity of variants observed. FUNDING Doris Duke Charitable Foundation, US National Institute of Allergy and Infectious Diseases, South African Medical Research Council, National Research Foundation, Research Foundation Flanders, Stellenbosch University Faculty of Medicine Health Sciences, South African National Research Foundation, Swiss National Science Foundation, and Wellcome Trust.
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Affiliation(s)
- Brigitta Derendinger
- DSI-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
| | - Anzaan Dippenaar
- DSI-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; Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Department of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | - Margaretha de Vos
- DSI-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; FIND, Geneva, Switzerland
| | | | - Rencia Alberts
- DSI-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
| | - Rebecca Tadokera
- DSI-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
| | - Jason Limberis
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, CA, USA
| | - Frik Sirgel
- DSI-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
| | - Tania Dolby
- National Health Laboratory Services Green Point, Cape Town, South Africa
| | - Claudia Spies
- DSI-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
| | - Anja Reuter
- Médecins Sans Frontières, Khayelitsha, South Africa
| | - Megan Folkerts
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | | | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ, USA
| | - Annelies Van Rie
- Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Leen Rigouts
- Department of Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Keertan Dheda
- Division of Pulmonology, Department of Medicine, Centre for Lung Infection and Immunity, University of Cape Town Lung Institute, Cape Town, South Africa; Centre for the Study of Antimicrobial Resistance, South African Medical Research Council, Cape Town, South Africa; Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | - Robin Warren
- DSI-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
| | - John Metcalfe
- Division of Pulmonary and Critical Care Medicine, Zuckerberg San Francisco General Hospital and Trauma Center, University of California San Francisco, CA, USA
| | - Helen Cox
- Division of Medical Microbiology, Department of Pathology, University of Cape Town, Cape Town, South Africa; Institute of Infectious Disease and Molecular Medicine and Wellcome Centre for Infectious Disease Research, University of Cape Town, South Africa
| | - Grant Theron
- DSI-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.
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4
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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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5
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Kapp E, Calitz H, Streicher EM, Dippenaar A, Egieyeh S, Jordaan A, Warner DF, Joubert J, Malan SF, Sampson SL. Discovery and biological evaluation of an adamantyl-amide derivative with likely MmpL3 inhibitory activity. Tuberculosis (Edinb) 2023; 141:102350. [PMID: 37244249 DOI: 10.1016/j.tube.2023.102350] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 05/02/2023] [Accepted: 05/07/2023] [Indexed: 05/29/2023]
Abstract
A series of molecules containing bulky lipophilic scaffolds was screened for activity against Mycobacterium tuberculosis and a number of compounds with antimycobacterial activity were identified. The most active compound, (2E)-N-(adamantan-1-yl)-3-phenylprop-2-enamide (C1), has a low micromolar minimum inhibitory concentration, low cytotoxicity (therapeutic index = 32.26), low mutation frequency and is active against intracellular Mycobacterium tuberculosis. Whole genome sequencing of mutants resistant to C1 showed a mutation in mmpL3 which may point to the involvement of MmpL3 in the antimycobacterial activity of the compound. In silico mutagenesis and molecular modelling studies were performed to better understand the binding of C1 within MmpL3 and the role that the specific mutation may play in the interaction at protein level. These analyses revealed that the mutation increases the energy required for binding of C1 within the protein translocation channel of MmpL3. The mutation also decreases the solvation energy of the protein, suggesting that the mutant protein might be more solvent-accessible, thereby restricting its interaction with other molecules. The results reported here describe a new molecule that may interact with the MmpL3 protein, providing insights into the effect of mutations on protein-ligand interactions and enhancing our understanding of this essential protein as a priority drug target.
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Affiliation(s)
- Erika Kapp
- School of Pharmacy, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; University of the Western Cape, Private Bag x17, Bellville, 7535, South Africa.
| | - Hanri Calitz
- DSI/NRF Centre of 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, P.O. Box 241, Cape Town, 8000, South Africa.
| | - Elizabeth M Streicher
- DSI/NRF Centre of 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, P.O. Box 241, Cape Town, 8000, South Africa.
| | - Anzaan Dippenaar
- DSI/NRF Centre of 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, P.O. Box 241, Cape Town, 8000, South Africa; Global Health Institute, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium; Gouverneur Kinsbergencentrum, Doornstraat 331, 2610, Wilrijk, Belgium.
| | - Samuel Egieyeh
- School of Pharmacy, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; University of the Western Cape, Private Bag x17, Bellville, 7535, South Africa.
| | - Audrey Jordaan
- Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag X3, Rondebosch, 7701, Cape Town, South Africa.
| | - Digby F Warner
- Molecular Mycobacteriology Research Unit, DSI/NRF Centre of Excellence for Biomedical Tuberculosis Research, Department of Pathology and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag X3, Rondebosch, 7701, Cape Town, South Africa.
| | - Jacques Joubert
- School of Pharmacy, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; University of the Western Cape, Private Bag x17, Bellville, 7535, South Africa.
| | - Sarel F Malan
- School of Pharmacy, Faculty of Natural Sciences, University of the Western Cape, Cape Town, South Africa; University of the Western Cape, Private Bag x17, Bellville, 7535, South Africa.
| | - Samantha L Sampson
- DSI/NRF Centre of 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, P.O. Box 241, Cape Town, 8000, South Africa.
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6
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Ismail N, Dippenaar A, Warren RM, Peters RPH, Omar SV. Emergence of Canonical and Noncanonical Genomic Variants following In Vitro Exposure of Clinical Mycobacterium tuberculosis Strains to Bedaquiline or Clofazimine. Antimicrob Agents Chemother 2023; 67:e0136822. [PMID: 36892309 PMCID: PMC10112258 DOI: 10.1128/aac.01368-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 02/09/2023] [Indexed: 03/10/2023] Open
Abstract
In Mycobacterium tuberculosis, bedaquiline and clofazimine resistance occurs primarily through Rv0678 variants, a gene encoding a repressor protein that regulates mmpS5/mmpL5 efflux pump gene expression. Despite the shared effect of both drugs on efflux, little else is known about other pathways affected. We hypothesized that in vitro generation of bedaquiline- or clofazimine-resistant mutants could provide insight into additional mechanisms of action. We performed whole-genome sequencing and determined phenotypic MICs for both drugs on progenitor and mutant progenies. Mutants were induced through serial passage on increasing concentrations of bedaquiline or clofazimine. Rv0678 variants were identified in both clofazimine- and bedaquiline-resistant mutants, with concurrent atpE SNPs occurring in the latter. Of concern was the acquisition of variants in the F420 biosynthesis pathway in clofazimine-resistant mutants obtained from either a fully susceptible (fbiD: del555GCT) or rifampicin mono-resistant (fbiA: 283delTG and T862C) progenitor. The acquisition of these variants possibly implicates a shared pathway between clofazimine and nitroimidazoles. Pathways associated with drug tolerance and persistence, F420 biosynthesis, glycerol uptake and metabolism, efflux, and NADH homeostasis appear to be affected following exposure to these drugs. Shared genes affected by both drugs include Rv0678, glpK, nuoG, and uvrD1. Genes with variants in the bedaquiline resistant mutants included atpE, fadE28, truA, mmpL5, glnH, and pks8, while clofazimine-resistant mutants displayed ppsD, fbiA, fbiD, mutT3, fadE18, Rv0988, and Rv2082 variants. These results show the importance of epistatic mechanisms as a means of responding to drug pressure and highlight the complexity of resistance acquisition in M. tuberculosis.
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Affiliation(s)
- N. Ismail
- SAMRC Centre for Tuberculosis Research/DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Prinshof, Gauteng, South Africa
| | - A. Dippenaar
- Global Health Institute, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - R. M. Warren
- SAMRC Centre for Tuberculosis Research/DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - R. P. H. Peters
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Prinshof, Gauteng, South Africa
- Department of Medical Microbiology, School CAPHRI (Care and Public Health Research Institute), Maastricht University, Maastricht, The Netherlands
| | - S. V. Omar
- Department of Medical Microbiology, School CAPHRI (Care and Public Health Research Institute), Maastricht University, Maastricht, The Netherlands
- National Institute for Communicable Diseases/National Health Laboratory Service, Centre for Tuberculosis, National TB Reference Laboratory & WHO Supranational TB Reference Laboratory, Johannesburg, Gauteng, South Africa
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7
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Qiu B, Wu Z, Tao B, Li Z, Song H, Tian D, Wu J, Zhan M, Wang J. Risk factors for types of recurrent tuberculosis (reactivation versus reinfection): A global systematic review and meta-analysis. Int J Infect Dis 2021; 116:14-20. [PMID: 34954094 DOI: 10.1016/j.ijid.2021.12.344] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/13/2021] [Accepted: 12/17/2021] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The purpose of this meta-analysis (PROSPERO number: CRD42021243204) is to perform extensive and penetrating analyses on the risk factors associated with reactivation or reinfection. METHODS We searched PubMed and Embase using search terms. Risk factors (including sex, length of time between first onset and recurrent diagnosis, extrapulmonary tuberculosis, sputum smear, pulmonary cavity, Beijing family strains, diabetes, HIV infection, history of imprisonment, and immigration) were analyzed. The pooled risk ratio (RR) and 95% confidence interval (CI) were calculated with STATA 15.1. Heterogeneity was evaluated by I2 and P values. RESULTS The meta-analysis included 25 studies with a total of 1,477 patients. After subgroup analysis, sensitivity analysis, and testing for publication bias, it was concluded that time spanning less than two years (RR=1.56, 95% CI: 1.33-1.85) was a risk factor for endogenous reactivation, while coinfection with HIV (RR=0.72, 95% CI: 0.63-0.83), Beijing family genotype (RR=0.46, 95% CI: 0.32-0.67), history of imprisonment (RR=0.36, 95% CI: 0.16-0.81) and immigration (RR=0.66, 95% CI: 0.53-0.82) were associated with exogenous reinfection. CONCLUSIONS The recurrence interval is a risk factor for the endogenous reactivation of tuberculosis. Infection with Beijing family strains, coinfection with HIV, imprisonment, and immigration contribute to the risk of exogenous reinfection.
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Affiliation(s)
- Beibei Qiu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Zhuchao Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Bilin Tao
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Zhongqi Li
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Huan Song
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Dan Tian
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Jizhou Wu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Mengyao Zhan
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China
| | - Jianming Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China.
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8
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Melting the eis: Nondetection of Kanamycin Resistance Markers by Routine Diagnostic Tests and Identification of New eis Promoter Variants. Antimicrob Agents Chemother 2021; 65:e0250220. [PMID: 33903113 DOI: 10.1128/aac.02502-20] [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: 11/20/2022] Open
Abstract
Eis promoter mutations can confer reduced Mycobacterium tuberculosis kanamycin susceptibility. GenoType MTBDRsl, a widely used assay evaluating this region, wrongly classified 17/410 isolates as eis promoter wild type. Six out of seventeen isolates harbored mutations known to confer kanamycin resistance, and the remainder harbored either novel eis promoter mutations (7/11) or disputed mutations (4/11). GenoType MTBDRsl can miss established and new variants that cause reduced susceptibility. These data highlight the importance of reflex phenotypic kanamycin testing.
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9
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Byrne AS, Goudreau A, Bissonnette N, Shamputa IC, Tahlan K. Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review. Front Genet 2020; 11:600692. [PMID: 33408740 PMCID: PMC7779811 DOI: 10.3389/fgene.2020.600692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.
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Affiliation(s)
| | - Alex Goudreau
- Science & Health Sciences Librarian, University of New Brunswick, Saint John, NB, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Isdore Chola Shamputa
- Department of Nursing & Health Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
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10
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Meiring C, Higgitt R, Dippenaar A, Roos E, Buss P, Hewlett J, Cooper D, Rogers P, Klerk‐Lorist L, Schalkwyk L, Hausler G, Helden P, Möller M, Warren R, Miller M. Characterizing epidemiological and genotypic features of
Mycobacterium bovis
infection in wild dogs (
Lycaon pictus
). Transbound Emerg Dis 2020. [DOI: 10.1111/tbed.13947] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Christina Meiring
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Roxanne Higgitt
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Anzaan Dippenaar
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Eduard Roos
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Peter Buss
- Veterinary Wildlife Services South African National Parks Skukuza South Africa
| | - Jennie Hewlett
- Veterinary Wildlife Services South African National Parks Skukuza South Africa
- Paraclinical Department Faculty of Veterinary Science University of Pretoria Onderstepoort South Africa
| | - Dave Cooper
- Ezemvelo KZN Wildlife Mtubatuba South Africa
| | - Peter Rogers
- Provet Wildlife Services & Companion Animal Hospital Hoedspruit South Africa
| | - Lin‐Mari Klerk‐Lorist
- Department of Agriculture, Forestry and FisheriesOffice of the State Veterinarian Skukuza South Africa
| | - Louis Schalkwyk
- Department of Agriculture, Forestry and FisheriesOffice of the State Veterinarian Skukuza South Africa
| | - Guy Hausler
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Paul Helden
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Marlo Möller
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Rob Warren
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
| | - Michele Miller
- DSI‐NRF Centre of Excellence for Biomedical Tuberculosis Research Cape Town South Africa
- South African Medical Research Council Centre for Tuberculosis Research Cape Town South Africa
- Division of Molecular Biology and Human Genetics Faculty of Medicine and Health Sciences Stellenbosch University Cape Town South Africa
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11
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Preclinical Evidence of Nanomedicine Formulation to Target Mycobacterium tuberculosis at Its Bone Marrow Niche. Pathogens 2020; 9:pathogens9050372. [PMID: 32414000 PMCID: PMC7281663 DOI: 10.3390/pathogens9050372] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 04/24/2020] [Accepted: 04/26/2020] [Indexed: 12/13/2022] Open
Abstract
One-third of the world’s population is estimated to be latently infected with Mycobacterium tuberculosis (Mtb). Recently, we found that dormant Mtb hides in bone marrow mesenchymal stem cells (BM-MSCs) post-chemotherapy in mice model and in clinical subjects. It is known that residual Mtb post-chemotherapy may be responsible for increased relapse rates. However, strategies for Mtb clearance post-chemotherapy are lacking. In this study, we engineered and formulated novel bone-homing PEGylated liposome nanoparticles (BTL-NPs) which actively targeted the bone microenvironment leading to Mtb clearance. Targeting of BM-resident Mtb was carried out through bone-homing liposomes tagged with alendronate (Ald). BTL characterization using TEM and DLS showed that the size of bone-homing isoniazid (INH) and rifampicin (RIF) BTLs were 100 ± 16.3 nm and 84 ± 18.4 nm, respectively, with the encapsulation efficiency of 69.5% ± 4.2% and 70.6% ± 4.7%. Further characterization of BTLs, displayed by sustained in vitro release patterns, increased in vivo tissue uptake and enhanced internalization of BTLs in RAW cells and CD271+BM-MSCs. The efficacy of isoniazid (INH)- and rifampicin (RIF)-loaded BTLs were shown using a mice model where the relapse rate of the tuberculosis was decreased significantly in targeted versus non-targeted groups. Our findings suggest that BTLs may play an important role in developing a clinical strategy for the clearance of dormant Mtb post-chemotherapy in BM cells.
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