{"doi":"10.1371/journal.pone.0232343","title":"Detection of drug resistant Mycobacterium tuberculosis by high-throughput sequencing of DNA isolated from acid fast bacilli smears","abstract":"BACKGROUND: Drug susceptibility testing for Mycobacterium tuberculosis (MTB) is difficult to perform in resource-limited settings where Acid Fast Bacilli (AFB) smears are commonly used for disease diagnosis and monitoring. We developed a simple method for extraction of MTB DNA from AFB smears for sequencing-based detection of mutations associated with resistance to all first and several second-line anti-tuberculosis drugs. METHODS: We isolated MTB DNA by boiling smear content in a Chelex solution, followed by column purification. We sequenced PCR-amplified segments of the rpoB, katG, embB, gyrA, gyrB, rpsL, and rrs genes, the inhA, eis, and pncA promoters and the entire pncA gene. RESULTS: We tested our assay on 1,208 clinically obtained AFB smears from Ghana (n = 379), Kenya (n = 517), Uganda (n = 262), and Zambia (n = 50). Coverage depth varied by target and slide smear grade, ranging from 300X to 12000X on average. Coverage of ≥20X was obtained for all targets in 870 (72%) slides overall. Mono-resistance (5.9%), multi-drug resistance (1.8%), and poly-resistance (2.4%) mutation profiles were detected in 10% of slides overall, and in over 32% of retreatment and follow-up cases. CONCLUSION: This rapid AFB smear DNA-based method for determining drug resistance may be useful for the diagnosis and surveillance of drug-resistant tuberculosis.","journal":"PLoS ONE","year":2020,"id":81112,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":14,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9529,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2020-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":419946,"name":"Naomi Aronson","orcid":"0000-0001-6386-0946","position":1,"is_corresponding":false},{"id":419947,"name":"Peicheng Du","orcid":"0000-0003-4367-0875","position":2,"is_corresponding":false},{"id":421163,"name":"Paige Sachs","orcid":null,"position":3,"is_corresponding":false},{"id":421164,"name":"Robert Blakemore","orcid":null,"position":4,"is_corresponding":false},{"id":419948,"name":"Soumitesh Chakravorty","orcid":"0000-0001-5499-0204","position":5,"is_corresponding":false},{"id":43059,"name":"Shawn Levy","orcid":"0000-0002-1369-5740","position":6,"is_corresponding":false},{"id":86840,"name":"Angela L. Jones","orcid":"0000-0002-1565-4360","position":7,"is_corresponding":false},{"id":421165,"name":"Geetika Trivedi","orcid":null,"position":8,"is_corresponding":false},{"id":421166,"name":"Sheilla Chebore","orcid":null,"position":9,"is_corresponding":false},{"id":421167,"name":"Dennis Addo","orcid":null,"position":10,"is_corresponding":false},{"id":419949,"name":"Denis K. Byarugaba","orcid":"0000-0002-4175-5659","position":11,"is_corresponding":false},{"id":421168,"name":"Panganani Njobvu","orcid":null,"position":12,"is_corresponding":false},{"id":421169,"name":"Frederick Wabwire-Mangen","orcid":null,"position":13,"is_corresponding":false},{"id":421170,"name":"Bernard Erima","orcid":null,"position":14,"is_corresponding":false},{"id":419950,"name":"Eric Ramos","orcid":"0000-0003-1236-5990","position":15,"is_corresponding":false},{"id":231902,"name":"Carlton A. Evans","orcid":"0000-0002-6873-5447","position":16,"is_corresponding":false},{"id":421171,"name":"Braden Hale","orcid":null,"position":17,"is_corresponding":false},{"id":419951,"name":"James D. Mancuso","orcid":"0000-0002-0717-8202","position":18,"is_corresponding":false},{"id":292870,"name":"David Alland","orcid":"0000-0001-5196-1571","position":19,"is_corresponding":false},{"id":421162,"name":"Mazhgan Rowneki","orcid":null,"position":0,"is_corresponding":true}],"reference_count":24,"raw_metadata":null,"created_at":"2026-07-18T21:52:34.401799Z","pmid":"32384098","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}