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1. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Author

Coll, Francesc, Phelan, Jody, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ali, Shahjahan, Abdallah, Abdallah M., Alghamdi, Saad, Alsomali, Mona, Ahmed, Abdallah O., Portelli, Stephanie, Oppong, Yaa, Alves, Adriana, Bessa, Theolis Barbosa, Campino, Susana, Caws, Maxine, Chatterjee, Anirvan, Crampin, Amelia C., Dheda, Keertan, Furnham, Nicholas, Glynn, Judith R., Grandjean, Louis, Minh Ha, Dang, Hasan, Rumina, Hasan, Zahra, Hibberd, Martin L., Joloba, Moses, Jones-López, Edward C., Matsumoto, Tomoshige, Miranda, Anabela, Moore, David J., Mocillo, Nora, Panaiotov, Stefan, Parkhill, Julian, Penha, Carlos, Perdigão, João, Portugal, Isabel, Rchiad, Zineb, Robledo, Jaime, Sheen, Patricia, Shesha, Nashwa Talaat, Sirgel, Frik A., Sola, Christophe, Oliveira Sousa, Erivelton, Streicher, Elizabeth M., Helden, Paul Van, Viveiros, Miguel, Warren, Robert M., McNerney, Ruth, Pain, Arnab, and Clark, Taane G.

Published
2018
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3. Implications of Interspecies Transmission and Diagnosis of Mycobacterium bovis Infection in Free-Ranging Common Hippopotamus (Hippopotamus amphibius)

Author

Kerr, Tanya, primary, Goosen, Wynand, additional, Gumbo, Rachiel, additional, Lorist, Lin Mari deKlerk, additional, Pretorius, Oonagh, additional, Buss, Peter, additional, Kleynhans, L anie, additional, Lyashchenko, Konstantin, additional, Warren, Robin, additional, Helden, Paul van, additional, and Miller, Michele, additional

Published
2020
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5. Additional file 3: of Measuring antigen-specific responses in Mycobacterium bovis-infected warthogs (Phacochoerus africanus) using the intradermal tuberculin test

Author

Roos, Eduard, Olea-Popelka, Francisco, Buss, Peter, Hausler, Guy, Warren, Robin, Helden, Paul Van, Parsons, Sven, Lin-Mari De Klerk-Lorist, and Miller, Michele

Abstract

Table S2. Receiver operator characteristics curve analysis data for PPDb â PPDa. Warthog specific cut-off values and respective sensitivity and specificity, with 95% CI in parentheses. Youdenâ s index for each cut-off value is also indicated. (DOCX 14 kb)

Published
2018
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6. Additional file 2: of Measuring antigen-specific responses in Mycobacterium bovis-infected warthogs (Phacochoerus africanus) using the intradermal tuberculin test

Author

Roos, Eduard, Olea-Popelka, Francisco, Buss, Peter, Hausler, Guy, Warren, Robin, Helden, Paul Van, Parsons, Sven, Lin-Mari De Klerk-Lorist, and Miller, Michele

Abstract

Table S1. Receiver operator characteristics curve analysis data for Î PPDb. Warthog specific cut-off values and respective sensitivity and specificity, with 95% CI in parentheses. Youdenâ s index for each cut-off value is also indicated. (DOCX 15 kb)

Published
2018
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7. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis

Author

King Abdullah University of Science and Technology, Wellcome Trust, Burroughs Wellcome Fund, Fundação para a Ciência e a Tecnologia (Portugal), Fundação Calouste Gulbenkian, European Society of Clinical Microbiology and Infectious Diseases, Medical Research Council (UK), Biotechnology and Biological Sciences Research Council (UK), Japan Agency for Medical Research and Development, Coll, Francesc [0000-0002-7882-2325], Coll, Francesc, Phelan, Jody, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ali, Shahjahan, Abdallah, Abdallah M., Alghamdi, Saad, Alsomali, Mona, Ahmed, Abdallah O., Portelli, Stephanie, Oppong, Yaa, Alves, Adriana, Barbosa Bessa, Theolis, Campino, Susana, Caws, Maxine, Chatterjee, Anirvan, Crampin, Amelia C., Dheda, Keertan, Furnham, Nicholas, Glynn, Judith R., Grandjean, Louis Louis, Ha, Dang Minh, Hasan, Rumina, Hasan, Zahra, Hibberd, Martin L., Joloba, Moses, Jones-López, Edward C., Matsumoto, Tomoshige, Miranda, Anabela, Moore, David J., Mocillo, Nora, Panaiotov, Stefan, Parkhill, Julian, Penha, Carlos, Perdigão, João, Portugal, Isabel, Rchiad, Zineb, Robledo, Jaime, Sheen, Patricia, Shesha, Nashwa Talaat, Sirgel, Frik A., Sola, Christophe, Oliveira Sousa, Erivelton, Streicher, Elizabeth M., Helden, Paul Van, Viveiros, Miguel, Warren, Robert M., McNerney, Ruth, Pain, Arnab, Clark, Taane G., King Abdullah University of Science and Technology, Wellcome Trust, Burroughs Wellcome Fund, Fundação para a Ciência e a Tecnologia (Portugal), Fundação Calouste Gulbenkian, European Society of Clinical Microbiology and Infectious Diseases, Medical Research Council (UK), Biotechnology and Biological Sciences Research Council (UK), Japan Agency for Medical Research and Development, Coll, Francesc [0000-0002-7882-2325], Coll, Francesc, Phelan, Jody, Hill-Cawthorne, Grant A., Nair, Mridul B., Mallard, Kim, Ali, Shahjahan, Abdallah, Abdallah M., Alghamdi, Saad, Alsomali, Mona, Ahmed, Abdallah O., Portelli, Stephanie, Oppong, Yaa, Alves, Adriana, Barbosa Bessa, Theolis, Campino, Susana, Caws, Maxine, Chatterjee, Anirvan, Crampin, Amelia C., Dheda, Keertan, Furnham, Nicholas, Glynn, Judith R., Grandjean, Louis Louis, Ha, Dang Minh, Hasan, Rumina, Hasan, Zahra, Hibberd, Martin L., Joloba, Moses, Jones-López, Edward C., Matsumoto, Tomoshige, Miranda, Anabela, Moore, David J., Mocillo, Nora, Panaiotov, Stefan, Parkhill, Julian, Penha, Carlos, Perdigão, João, Portugal, Isabel, Rchiad, Zineb, Robledo, Jaime, Sheen, Patricia, Shesha, Nashwa Talaat, Sirgel, Frik A., Sola, Christophe, Oliveira Sousa, Erivelton, Streicher, Elizabeth M., Helden, Paul Van, Viveiros, Miguel, Warren, Robert M., McNerney, Ruth, Pain, Arnab, and Clark, Taane G.

Abstract

To characterize the genetic determinants of resistance to antituberculosis drugs, we performed a genome-wide association study (GWAS) of 6,465 Mycobacterium tuberculosis clinical isolates from more than 30 countries. A GWAS approach within a mixed-regression framework was followed by a phylogenetics-based test for independent mutations. In addition to mutations in established and recently described resistance-associated genes, novel mutations were discovered for resistance to cycloserine, ethionamide and para-aminosalicylic acid. The capacity to detect mutations associated with resistance to ethionamide, pyrazinamide, capreomycin, cycloserine and para-aminosalicylic acid was enhanced by inclusion of insertions and deletions. Odds ratios for mutations within candidate genes were found to reflect levels of resistance. New epistatic relationships between candidate drug-resistance-associated genes were identified. Findings also suggest the involvement of efflux pumps (drrA and Rv2688c) in the emergence of resistance. This study will inform the design of new diagnostic tests and expedite the investigation of resistance and compensatory epistatic mechanisms.

Published
2018

18. MYCOBACTERIUM BOVIS IN FREE-RANGING LIONS (PANTHERA LEO) — EVALUATION OF SEROLOGICAL AND TUBERCULIN SKIN TESTS FOR DETECTION OF INFECTION AND DISEASE.

Author

Miller, Michele A., Buss, Peter, Sylvester, Tashnica Taime, Lyashchenko, Konstantin P., deKlerk-Lorist, Lin-Mari, Bengis, Roy, Hofmeyr, Markus, Hofmeyr, Jennifer, Mathebula, Nomkhosi, Hausler, Guy, Helden, Paul van, Stout, Eliza, Parsons, Sven D.C., and Olea-Popelka, Francisco

Abstract

Bovine tuberculosis (bTB), caused by Mycobacterium bovis infection, causes morbidity and mortality in free-ranging lions in bTB-endemic areas of South Africa. However, the only currently used diagnostic test is the tuberculin skin test (TST). This test is logistically challenging to perform because it requires immobilization of lions twice in a 72-hr period. Blood-based diagnostic tests, such as serological assays, have been previously reported for M. bovis detection in lion populations, and have the advantage of only requiring a single immobilization. In addition, serological assays can be used for retrospective testing. Therefore, the aim of this study was to test free-ranging lions with the STAT-PAKt (Chembio Diagnostics Systems, Medford, NY 11763, USA) and DPPt VetTB (Chembio Diagnostics Systems) serological assays and compare those results with the tuberculin skin test. The serological assays were also used to determine prevalence in bTB-endemic and uninfected lion populations. The results showed that the serological assays could distinguish between M. bovis culture-positive and -negative lions. In addition, antigen-specific humoral responses were present in lions that had clinical signs of bTB disease or were shedding M. bovis antemortem. Although the seroprevalence of M. bovis infection in Kruger National Park lions was similar to that obtained from antemortem mycobacterial culture (4.8 and 3.3%, respectively), it was less than that estimated by the TST (72%). These findings support the hypothesis that assays based on cell-mediated immune responses are more sensitive than serology is in detecting M. bovis infection in lions. However, serological assays can have a role in bTB disease detection in lions and are especially useful for retrospective studies. [ABSTRACT FROM AUTHOR]

Published
2019
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19. Classification of drug-resistant tuberculosis

Author

Helden, Paul van, Warren, Rob, Enarson, Don, Beyers, Nulda, Rie, Annelies van, DeRiemer, Kathy, Garcia, Ma de Lourdes Garcia, Garduno, Alfredo Ponce de Leon, Osornio, Jose Sifuentes, Small, Peter M, Sonnenberg, Pamela, Godfrey-Faussett, Peter, Glynn, Judith R, Shearer, Stuart, and Murray, Jill

Subjects
Tuberculosis, Drug resistance in microorganisms -- Development and progression
Published
2000

24. SNP/RD Typing of Mycobacterium tuberculosis Beijing Strains Reveals Local and Worldwide Disseminated Clonal Complexes.

Author

Schürch, Anita C., Kremer, Kristin, Hendriks, Amber C. A., Freyee, Benthe, McEvoy, Christopher R. E., Crevel, Reinout van, Boeree, Martin J., Helden, Paul van, Warren, Robin M., Siezen, Roland J., and Soolingen, Dick van

Subjects
LUNG diseases, MYCOBACTERIAL diseases, CHEST diseases, TUBERCULOSIS, EMIGRATION & immigration, MYCOBACTERIUM
Abstract

The Beijing strain is one of the most successful genotypes of Mycobacterium tuberculosis worldwide and appears to be highly homogenous according to existing genotyping methods. To type Beijing strains reliably we developed a robust typing scheme using single nucleotide polymorphisms (SNPs) and regions of difference (RDs) derived from whole-genome sequencing data of eight Beijing strains. SNP/RD typing of 259 M. tuberculosis isolates originating from 45 countries worldwide discriminated 27 clonal complexes within the Beijing genotype family. A total of 16 Beijing clonal complexes contained more than one isolate of known origin, of which two clonal complexes were strongly associated with South African origin. The remaining 14 clonal complexes encompassed isolates from different countries. Even highly resolved clonal complexes comprised isolates from distinct geographical sites. Our results suggest that Beijing strains spread globally on multiple occasions and that the tuberculosis epidemic caused by the Beijing genotype is at least partially driven by modern migration patterns. The SNPs and RDs presented in this study will facilitate future molecular epidemiological and phylogenetic studies on Beijing strains. [ABSTRACT FROM AUTHOR]

Published
2011
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25. In Situ Detection of Mycobacterium tuberculosisTranscripts in Human Lung Granulomas Reveals Differential Gene Expression in Necrotic Lesions

Author

Fenhalls, Gael, Stevens, Liesel, Moses, Lorraine, Bezuidenhout, Juanita, Betts, Joanna C., Helden, Paul van, Lukey, Pauline T., and Duncan, Ken

Abstract

ABSTRACTWe have used RNA-RNA in situ hybridization to detect the expression of several Mycobacterium tuberculosisgenes in tuberculous granulomas in lung tissue sections from tuberculosis patients. The M. tuberculosisgenes chosen fall into two classes. Four genes (icl, narX, and Rv2557 and Rv2558) have been implicated in the persistence of the bacterium in the host, and two genes (iniBand kasA) are upregulated in response to isoniazid exposure. Both necrotic and nonnecrotic granulomas were identified in all of the patients. Necrotic granulomas were divided into three zones: an outer lymphocyte cuff containing lymphocytes and macrophages, a transition zone consisting of necrotic material interspersed with macrophages, and a central acellular necrotic region. Transcripts of all of the genes studied were found in nonnecrotic granulomas and in the lymphocyte cuff of necrotic granulomas. Mycobacterial gene expression was associated with CD68-positive myeloid cells. Rv2557 and/or its homologue Rv2558, kasA, and iniBwere expressed within the transition zone of necrotic granulomas, whereas icland narXtranscripts were absent from this area. There was no evidence of transcription of any of the genes examined in the central necrotic region, although mycobacterial DNA was present. The differential expression of genes within granulomas demonstrates that M. tuberculosisexists in a variety of metabolic states and may be indicative of the response to different microenvironments. These observations confirm that genes identified in models of persistence or in response to drug treatment in vitro are expressed in the human host.

Published
2002
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26. Additional file 5: of Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy

Author

Isobella Honeyborne, McHugh, Timothy, Iitu Kuittinen, Cichonska, Anna, Evangelopoulos, Dimitrios, Ronacher, Katharina, Helden, Paul Van, Gillespie, Stephen, Delmiro Fernandez-Reyes, Walzl, Gerhard, Rousu, Juho, Butcher, Philip, and Waddell, Simon

Subjects
3. Good health
Abstract

Figure S1. An illustration of the computation process to test associations between transcriptional signatures and patient variables. Figure S2. Venn diagrams describing the overlapping transcriptional signatures of bacilli in sputum relative to aerobic log phase growth. Figure S3. Box and whisker plots mapping the differential expression of gene families. Figure S4. Hierarchical clustering of the mean M.tb transcriptional profiles derived from sputa. Figure S5. Venn diagram highlighting genes significantly induced 3 days after the start of drug therapy. Figure S6. Contrasting patient trajectories as defined by principle component analysis plotting day 0 and day 3 timepoints only. (PDF 526 kb)

27. Additional file 5: of Profiling persistent tubercule bacilli from patient sputa during therapy predicts early drug efficacy

Author

Isobella Honeyborne, McHugh, Timothy, Iitu Kuittinen, Cichonska, Anna, Evangelopoulos, Dimitrios, Ronacher, Katharina, Helden, Paul Van, Gillespie, Stephen, Delmiro Fernandez-Reyes, Walzl, Gerhard, Rousu, Juho, Butcher, Philip, and Waddell, Simon

Subjects
3. Good health
Abstract

Figure S1. An illustration of the computation process to test associations between transcriptional signatures and patient variables. Figure S2. Venn diagrams describing the overlapping transcriptional signatures of bacilli in sputum relative to aerobic log phase growth. Figure S3. Box and whisker plots mapping the differential expression of gene families. Figure S4. Hierarchical clustering of the mean M.tb transcriptional profiles derived from sputa. Figure S5. Venn diagram highlighting genes significantly induced 3 days after the start of drug therapy. Figure S6. Contrasting patient trajectories as defined by principle component analysis plotting day 0 and day 3 timepoints only. (PDF 526 kb)

28. Additional file 1: Table S1. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

Author

Phelan, Jody, Coll, Francesc, Bergval, Indra, Anthony, Richard, Warren, Rob, Sampson, Samantha, Pittius, Nicolaas Gey Van, Glynn, Judith, Crampin, Amelia, Alves, Adriana, Theolis Bessa, Campino, Susana, Keertan Dheda, Grandjean, Louis, Rumina Hasan, Hasan, Zahra, Miranda, Anabela, Moore, David, Panaiotov, Stefan, Joao Perdigao, Portugal, Isabel, Sheen, Patricia, Erivelton De Oliveira Sousa, Streicher, Elizabeth, Helden, Paul Van, Viveiros, Miguel, Hibberd, Martin, Arnab Pain, McNerney, Ruth, and Taane Clark

Subjects
3. Good health
Abstract

a) The samples used for the assembly (*Malawi [55, 56], Netherlands [57], Pakistan [58], Portugal [59]) and b) the 21 reference strains. Table S2. Lineage, sequence coverage and polymorphism. Ď nucleotide diversity; Lineage 1 Indo-Oceanic; Lineage 2 East-Asian (Beijing); Lineage 3 East-African-Indian; Lineage 4 Euro-American. Table S3. Completeness of pe/ppe gene assemblies. Table S4. List of 87 pe/ppe lineage specific-markers. S synonymous, NS non-synonymous, * genes bolded if there are sites under selection using the Bayes Empirical Bayes method; Lineage 1 Indo-Oceanic; Lineage 2 East-Asian (Beijing); Lineage 3 East-African-Indian; Lineage 4 Euro-American. Table S5. Genes with more than 10 sites under selective pressure (dN/dS (Ď ) >1). Table S6. Epitopes. * identified using netMHCpan, ** epitopes that had sites under positive selection according to the Bayes Empirical Bayes (BEB) method. (DOCX 70 kb)

29. Additional file 1: Table S1. of Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages

Author

Phelan, Jody, Coll, Francesc, Bergval, Indra, Anthony, Richard, Warren, Rob, Sampson, Samantha, Pittius, Nicolaas Gey Van, Glynn, Judith, Crampin, Amelia, Alves, Adriana, Theolis Bessa, Campino, Susana, Keertan Dheda, Grandjean, Louis, Rumina Hasan, Hasan, Zahra, Miranda, Anabela, Moore, David, Panaiotov, Stefan, Joao Perdigao, Portugal, Isabel, Sheen, Patricia, Erivelton De Oliveira Sousa, Streicher, Elizabeth, Helden, Paul Van, Viveiros, Miguel, Hibberd, Martin, Arnab Pain, McNerney, Ruth, and Taane Clark

Subjects
3. Good health
Abstract

a) The samples used for the assembly (*Malawi [55, 56], Netherlands [57], Pakistan [58], Portugal [59]) and b) the 21 reference strains. Table S2. Lineage, sequence coverage and polymorphism. Ď nucleotide diversity; Lineage 1 Indo-Oceanic; Lineage 2 East-Asian (Beijing); Lineage 3 East-African-Indian; Lineage 4 Euro-American. Table S3. Completeness of pe/ppe gene assemblies. Table S4. List of 87 pe/ppe lineage specific-markers. S synonymous, NS non-synonymous, * genes bolded if there are sites under selection using the Bayes Empirical Bayes method; Lineage 1 Indo-Oceanic; Lineage 2 East-Asian (Beijing); Lineage 3 East-African-Indian; Lineage 4 Euro-American. Table S5. Genes with more than 10 sites under selective pressure (dN/dS (Ď ) >1). Table S6. Epitopes. * identified using netMHCpan, ** epitopes that had sites under positive selection according to the Bayes Empirical Bayes (BEB) method. (DOCX 70 kb)

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