Items where Author is "Meehan, CJ"

Journal article

ARUHOMUKAMA, D., GALIWANGO, R., MEEHAN, C.J. and ASIIMWE, B., 2024. Enhancing genomics and bioinformatics access in Africa: an imperative leap. The Lancet Microbe. ISSN 2666-5247

DOMINGO-SANANES, M.R. and MEEHAN, C.J., 2024. The population genetics of prokaryotic pangenomes. Nature Ecology and Evolution. ISSN 2397-334X

MEAZA, A., RIVIERE, E., BONSA, Z., RENNIE, V., GEBREMICAEL, G., DE DIEGO-FUERTES, M., MEEHAN, C.J., MEDHIN, G., ABEBE, G., AMENI, G., VAN RIE, A. and GUMI, B., 2023. Genomic transmission clusters and circulating lineages of Mycobacterium tuberculosis among refugees residing in refugee camps in Ethiopia. Infection, Genetics and Evolution, 116: 105530. ISSN 1567-1348

LEMPENS, P., VAN DEUN, A., AUNG, K.J.M., HOSSAIN, M.A., BEHRUZNIA, M., DECROO, T., RIGOUTS, L., DE JONG, B.C. and MEEHAN, C.J., 2023. Borderline rpoB mutations transmit at the same rate as common rpoB mutations in a tuberculosis cohort in Bangladesh. Microbial Genomics, 9 (9): 001109. ISSN 2057-5858

NAPIER, G., COUVIN, D., REFRÉGIER, G., GUYEUX, C., MEEHAN, C.J., SOLA, C., CAMPINO, S., PHELAN, J. and CLARK, T.G., 2023. Comparison of in silico predicted Mycobacterium tuberculosis spoligotypes and lineages from whole genome sequencing data. Scientific Reports, 13: 11368. ISSN 2045-2322

NGABONZIZA, J.C.S., RIGOUTS, L., TORREA, G., DECROO, T., KAMANZI, E., LEMPENS, P., RUCOGOZA, A., HABIMANA, Y.M., LAENEN, L., NIYIGENA, B.E., UWIZEYE, C., USHIZIMPUMU, B., MULDERS, W., IVAN, E., TZFADIA, O., MUVUNYI, C.M., MIGAMBI, P., ANDRE, E., MAZARATI, J.B., AFFOLABI, D., UMUBYEYI, A.N., NSANZIMANA, S., PORTAELS, F., GASANA, M., DE JONG, B.C. and MEEHAN, C.J., 2022. Multidrug-resistant tuberculosis control in Rwanda overcomes a successful clone that causes most disease over a quarter century. Journal of Clinical Tuberculosis and Other Mycobacterial Diseases, 27: 100299.

OOSTVOGELS, S., LEY, S.D., HEUPINK, T.H., DIPPENAAR, A., STREICHER, E.M., DE VOS, E., MEEHAN, C.J., DHEDA, K., WARREN, R. and VAN RIE, A., 2022. Transmission, distribution and drug resistance-conferring mutations of extensively drug-resistant tuberculosis in the Western Cape Province, South Africa. Microbial Genomics, 8 (4): 000815. ISSN 2057-5858

MEEHAN, C.J., BARCO, R.A., LOH, Y.-H.E., COGNEAU, S. and RIGOUTS, L., 2021. Reconstituting the genus Mycobacterium. International Journal of Systematic and Evolutionary Microbiology, 71 (9). ISSN 1466-5026

PEČERSKA, J., KÜHNERT, D., MEEHAN, C.J., COSCOLLÁ, M., DE JONG, B.C., GAGNEUX, S. and STADLER, T., 2021. Quantifying transmission fitness costs of multi-drug resistant tuberculosis. Epidemics, 36: 100471. ISSN 1755-4365

GUAN, Q., GARBATI, M., MFARREJ, S., ALMUTAIRI, T., LAVAL, T., SINGH, A., FAGBO, S., SMYTH, A., BROWNE, J., URRAHMAN, M., ALRUWAILI, A., HOOSEN, A., MEEHAN, C.J., NAKAJIMA, C., SUZUKI, Y., DEMANGEL, C., BHATT, A., GORDON, S., ALASMARI, F. and PAIN, A., 2021. Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense. NAR Genomics and Bioinformatics, 3 (3). ISSN 2631-9268

RIVIÈRE, E., HEUPINK, T.H., ISMAIL, N., DIPPENAAR, A., CLARKE, C., ABEBE, G., HEUSDEN, P., WARREN, R., MEEHAN, C.J. and VAN RIE, A., 2021. Capacity building for whole genome sequencing of Mycobacterium tuberculosis and bioinformatics in high TB burden countries. Briefings in Bioinformatics, 22 (4): bbaa246. ISSN 1467-5463

SANOUSSI, C.N., COSCOLLA, M., OFORI-ANYINAM, B., OTCHERE, I.D., ANTONIO, M., NIEMANN, S., PARKHILL, J., HARRIS, S., YEBOAH-MANU, D., GAGNEUX, S., RIGOUTS, L., AFFOLABI, D., DE JONG, B.C. and MEEHAN, C.J., 2021. Mycobacterium tuberculosis complex lineage 5 exhibits high levels of within-lineage genomic diversity and differing gene content compared to the type strain H37Rv. Microbial Genomics, 7 (7). ISSN 2057-5858

DIPPENAAR, A., GOOSSENS, S.N., GROBBELAAR, M., OOSTVOGELS, S., CUYPERS, B., LAUKENS, K., MEEHAN, C.J., WARREN, R.M. and VAN RIE, A., 2021. Nanopore sequencing for Mycobacterium tuberculosis: a critical review of the literature, new developments and future opportunities. Journal of Clinical Microbiology. ISSN 0095-1137

VAN RIE, A., DE VIEDMA, D.G., MEEHAN, C.J., COMAS, I., HEUPINK, T.H., DE VOS, E., DE OÑATE, W.A., MATHYS, V., CEYSSENS, P.-J., GROENEN, G., GONZÁLEZ‐CANDELAS, F., FORIER, A. and JUENGST, E., 2021. Whole-genome sequencing for TB source investigations: principles of ethical precision public health. The International Journal of Tuberculosis and Lung Disease, 25 (3), pp. 222-227. ISSN 1027-3719

COSCOLLA, M., GAGNEUX, S., MENARDO, F., LOISEAU, C., RUIZ-RODRIGUEZ, P., BORRELL, S., OTCHERE, I.D., ASANTE-POKU, A., ASARE, P., SÁNCHEZ-BUSÓ, L., GEHRE, F., SANOUSSI, C.N., ANTONIO, M., AFFOLABI, D., FYFE, J., BECKERT, P., NIEMANN, S., ALABI, A.S., GROBUSCH, M.P., KOBBE, R., PARKHILL, J., BEISEL, C., FENNER, L., BÖTTGER, E.C., MEEHAN, C.J., HARRIS, S.R., DE JONG, B.C., YEBOAH-MANU, D. and BRITES, D., 2021. Phylogenomics of Mycobacterium africanum reveals a new lineage and a complex evolutionary history. Microbial Genomics, 7 (2): 000477. ISSN 2057-5858

HEINZ, E., HOLT, K.E., MEEHAN, C.J. and SHEPPARD, S.K., 2021. Addressing parachute research and removing barriers for LMIC researchers in Microbial Genomics. Microbial Genomics, 7 (10): 000722. ISSN 2057-5858

LEMPENS, P., DECROO, T., AUNG, K.J.M., HOSSAIN, M.A., RIGOUTS, L., MEEHAN, C.J., VAN DEUN, A. and DE JONG, B.C., 2020. Initial resistance to companion drugs should not be considered an exclusion criterion for the shorter multidrug-resistant tuberculosis treatment regimen. International Journal of Infectious Diseases, 100, pp. 357-365. ISSN 1201-9712

BATTAGLIA, S., SPITALERI, A., CABIBBE, A.M., MEEHAN, C.J., UTPATEL, C., ISMAIL, N., TAHSEEN, S., SKRAHINA, A., ALIKHANOVA, N., MOSTOFA KAMAL, S.M., BARBOVA, A., NIEMANN, S., GROENHEIT, R., DEAN, A.S., ZIGNOL, M., RIGOUTS, L. and CIRILLO, D.M., 2020. Characterization of genomic variants associated with resistance to bedaquiline and delamanid in naive Mycobacterium tuberculosis clinical strains. Journal of Clinical Microbiology, 58 (11): e01304-20. ISSN 0095-1137

NGABONZIZA, J.C.S., DECROO, T., MIGAMBI, P., HABIMANA, Y.M., VAN DEUN, A., MEEHAN, C.J., TORREA, G., MASSOU, F., DE RIJK, W.B., USHIZIMPUMU, B., NIYIGENA, E.B., IVAN, E., SEMAHORE, J.M., MAZARATI, J.B., MERLE, C.S., SUPPLY, P., AFFOLABI, D., RIGOUTS, L. and DE JONG, B.C., 2020. Prevalence and drivers of false-positive rifampicin-resistant Xpert MTB/RIF results: a prospective observational study in Rwanda. The Lancet Microbe, 1 (2), e74-e83. ISSN 2666-5247

NGABONZIZA, S., HABIMANA, Y.M., DECROO, T., MIGAMBI, P., DUSHIME, A., MAZARATI, J.B., RIGOUTS, L., AFFOLABI, D., IVAN, E., MEEHAN, C.J., VAN DEUN, A., FISSETTE, K., HABIYAMBERE, I., NYARUHIRIRA, A.U., TURATE, I., SEMAHORE, J.M., NDJEKA, N., MUVUNYI, C.M., CONDO, J.U., GASANA, M., HASKER, E., TORREA, G. and DE JONG, B.C., 2020. Reduction of diagnostic and treatment delays reduces rifampicin-resistant tuberculosis mortality in Rwanda. International Journal of Tuberculosis and Lung Disease, 24 (3), pp. 329-339. ISSN 1027-3719

OFORI-ANYINAM, B., RILEY, A.J., JOBARTEH, T., GITTEH, E., SARR, B., FAAL-JAWARA, T.I., RIGOUTS, L., SENGHORE, M., KEHINDE, A., ONYEJEPU, N., ANTONIO, M., DE JONG, B.C., GEHRE, F. and MEEHAN, C.J., 2020. Comparative genomics shows differences in the electron transport and carbon metabolic pathways of Mycobacterium africanum relative to Mycobacterium tuberculosis and suggests an adaptation to low oxygen tension. Tuberculosis, 120: 101899. ISSN 1472-9792

GRÖSCHEL, M.I., MEEHAN, C.J., BARILAR, I., DIRICKS, M., GONZAGA, A., STEGLICH, M., CONCHILLO-SOLÉ, O., SCHERER, I.-C., MAMAT, U., LUZ, C.F., DE BRUYNE, K., UTPATEL, C., YERO, D., GIBERT, I., DAURA, X., KAMPMEIER, S., RAHMAN, N.A., KRESKEN, M., VAN DER WERF, T.S., ALIO, I., STREIT, W.R., ZHOU, K., SCHWARTZ, T., ROSSEN, J.W.A., FARHAT, M.R., SCHAIBLE, U.E., NÜBEL, U., RUPP, J., STEINMANN, J., NIEMANN, S. and KOHL, T.A., 2020. The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. Nature Communications, 11: 2044. ISSN 2041-1723

NGABONZIZA, J.C.S., LOISEAU, C., MARCEAU, M., JOUET, A., MENARDO, F., TZFADIA, O., ANTOINE, R., NIYIGENA, E.B., MULDERS, W., FISSETTE, K., DIELS, M., GAUDIN, C., DUTHOY, S., SSENGOOBA, W., ANDRÉ, E., KASWA, M.K., HABIMANA, Y.M., BRITES, D., AFFOLABI, D., MAZARATI, J.B., DE JONG, B.C., RIGOUTS, L., GAGNEUX, S., MEEHAN, C.J. and SUPPLY, P., 2020. A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nature Communications, 11: 2917.

TORTOLI, E., MEEHAN, C.J., GROTTOLA, A., FREGNI SERPINI, G., FABIO, A., TROVATO, A., PECORARI, M. and CIRILLO, D.M., 2019. Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium. Infection, Genetics and Evolution, 75: 103983. ISSN 1567-1348

WITTOUCK, S., WUYTS, S., MEEHAN, C.J., VAN NOORT, V. and LEBEER, S., 2019. A genome-based species taxonomy of the Lactobacillus genus complex. mSystems, 4 (5): e00264-19. ISSN 2379-5077

MEEHAN, C.J., GOIG, G.A., KOHL, T.A., VERBOVEN, L., DIPPENAAR, A., EZEWUDO, M., FARHAT, M.R., GUTHRIE, J.L., LAUKENS, K., MIOTTO, P., OFORI-ANYINAM, B., DREYER, V., SUPPLY, P., SURESH, A., UTPATEL, C., VAN SOOLINGEN, D., ZHOU, Y., ASHTON, P.M., BRITES, D., CABIBBE, A.M., DE JONG, B.C., DE VOS, M., MENARDO, F., GAGNEUX, S., GAO, Q., HEUPINK, T.H., LIU, Q., LOISEAU, C., RIGOUTS, L., RODWELL, T.C., TAGLIANI, E., WALKER, T.M., WARREN, R.M., ZHAO, Y., ZIGNOL, M., SCHITO, M., GARDY, J., CIRILLO, D.M., NIEMANN, S., COMAS, I. and VAN RIE, A., 2019. Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nature Reviews Microbiology, 17 (9), pp. 533-545. ISSN 1740-1526

NG, K.C.S., NGABONZIZA, J.C.S., LEMPENS, P., DE JONG, B.C., VAN LETH, F. and MEEHAN, C.J., 2019. Bridging the TB data gap: in silico extraction of rifampicin-resistant tuberculosis diagnostic test results from whole genome sequence data. PeerJ, 7: e7564. ISSN 2167-8359

DE JONG, B.C., GAYE, B.M., LUYTEN, J., VAN BUITENEN, B., ANDRÉ, E., MEEHAN, C.J., O’SIOCHAIN, C., TOMSU, K., URBAIN, J., GRIETENS, K.P., NJUE, M., PINXTEN, W., GEHRE, F., NYAN, O., BUVÉ, A., ROCA, A., RAVINETTO, R. and ANTONIO, M., 2019. Ethical considerations for movement mapping to identify disease transmission hotspots. Emerging Infectious Diseases, 25 (7). ISSN 1080-6040

SANOUSSI, C.N., DE JONG, B.C., AFFOLABI, D., MEEHAN, C.J., ODOUN, M. and RIGOUTS, L., 2019. Storage of sputum in cetylpyridinium chloride, OMNIgene.SPUTUM, and ethanol is compatible with molecular tuberculosis diagnostic testing. Journal of Clinical Microbiology, 57 (7): e00275-19. ISSN 0095-1137

OSBAK, K.K., MEEHAN, C.J., G RIBAS, S., HEYNDRICKX, L., ARIËN, K.K., TSOUMANIS, A., FLORENCE, E., ESBROECK, M.V., FRANSEN, K. and KENYON, C.R., 2019. Superimposing incident sexually transmitted infections on HIV phylogram to investigate possible misclassification of men who have sex with men as heterosexuals in a cohort in Antwerp, Belgium. International Journal of STD and AIDS, 30 (5), pp. 486-495. ISSN 0956-4624

VANDELANNOOTE, K., PHANZU, D.M., KIBADI, K., EDDYANI, M., MEEHAN, C.J., JORDAENS, K., LEIRS, H., PORTAELS, F., STINEAR, T.P., HARRIS, S.R. and DE JONG, B.C., 2019. Mycobacterium ulcerans population genomics to inform on the spread of Buruli ulcer across Central Africa. mSphere, 4 (1): e00472-18. ISSN 2379-5042

FARHAT, M.R., FRESCHI, L., CALDERON, R., IOERGER, T., SNYDER, M., MEEHAN, C.J., DE JONG, B., RIGOUTS, L., SLOUTSKY, A., KAUR, D., SUNYAEV, S., VAN SOOLINGEN, D., SHENDURE, J., SACCHETTINI, J. and MURRAY, M., 2019. GWAS for quantitative resistance phenotypes in Mycobacterium tuberculosis reveals resistance genes and regulatory regions. Nature Communications, 10: 2128. ISSN 2041-1723

MEEHAN, C.J., MORIS, P., KOHL, T.A., PEČERSKA, J., AKTER, S., MERKER, M., UTPATEL, C., BECKERT, P., GEHRE, F., LEMPENS, P., STADLER, T., KASWA, M.K., KÜHNERT, D., NIEMANN, S. and DE JONG, B.C., 2018. The relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology. EBioMedicine, 37, pp. 410-416. ISSN 2352-3964

OSBAK, K.K., VAN RAEMDONCK, G.A., DOM, M., CAMERON, C.E., MEEHAN, C.J., DEFORCE, D., OSTADE, X.V., KENYON, C.R. and DHAENENS, M., 2018. Candidate Treponema pallidum biomarkers uncovered in urine from individuals with syphilis using mass spectrometry. Future Microbiology, 13 (13), pp. 1497-1510. ISSN 1746-0913

NG, K.C.S., VAN DEUN, A., MEEHAN, C.J., TORREA, G., DRIESEN, M., GABRIËLS, S., RIGOUTS, L., ANDRÉ, E. and DE JONG, B.C., 2018. Xpert Ultra can unambiguously identify specific rifampin resistance-conferring mutations. Journal of Clinical Microbiology, 56 (9): 00686-18. ISSN 0095-1137

BUULTJENS, A.H., VANDELANNOOTE, K., MEEHAN, C.J., EDDYANI, M., DE JONG, B.C., FYFE, J.A.M., GLOBAN, M., TOBIAS, N.J., PORTER, J.L., TOMITA, T., TAY, E.L., SEEMANN, T., HOWDEN, B.P., JOHNSON, P.D.R. and STINEAR, T.P., 2018. Comparative genomics shows that Mycobacterium ulcerans migration and expansion preceded the rise of Buruli ulcer in southeastern Australia. Applied and Environmental Microbiology, 84 (8): e02612-17. ISSN 0099-2240

BRAET, S., VANDELANNOOTE, K., MEEHAN, C.J., BRUM FONTES, A.N., HASKER, E., ROSA, P.S., LUCENA-SILVA, N., RIGOUTS, L., SUFFYS, P.N. and DE JONG, B.C., 2018. The repetitive element RLEP is a highly specific target for detection of Mycobacterium leprae. Journal of Clinical Microbiology, 56 (3): e01924-17. ISSN 0095-1137

LEMPENS, P., MEEHAN, C.J., VANDELANNOOTE, K., FISSETTE, K., DE RIJK, P., VAN DEUN, A., RIGOUTS, L. and DE JONG, B.C., 2018. Isoniazid resistance levels of Mycobacterium tuberculosis can largely be predicted by high-confidence resistance-conferring mutations. Scientific Reports, 8 (1): 3246. ISSN 2045-2322

NG, K.C., MEEHAN, C.J., TORREA, G., GOEMINNE, L., DIELS, M., RIGOUTS, L., DE JONG, B.C. and ANDRÉ, E., 2018. Potential application of digitally linked tuberculosis diagnostics for real-time surveillance of drug-resistant tuberculosis transmission: validation and analysis of test results. JMIR Medical Informatics, 6 (1): e12.

Chapter in book

RIOJAS, M.A., FRANK, A.M., GREENFIELD, S.R., KING, S.P., MEEHAN, C.J., STRONG, M., WATTAM, A.R. and HAZBÓN, M.H., 2021. Identification and characterization of mycobacterial species using whole-genome sequences. In: T. PARISH and A. KUMAR, eds., Mycobacteria protocols. Methods in molecular biology (2314). New York: Humana Press, pp. 399-457. ISBN 9781071614594