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Li Y, Li Y, Wang T, Li Y, Tao N, Kong X, Zhang Y, Han Q, Liu Y, Li H. Multidrug-resistant Mycobacterium tuberculosis transmission in Shandong, China. Medicine (Baltimore) 2024; 103:e37617. [PMID: 38518003 PMCID: PMC10956945 DOI: 10.1097/md.0000000000037617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 02/23/2024] [Indexed: 03/24/2024] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) has imposed a significant economic and health burden worldwide, notably in China. Using whole genome sequence, we sought to understand the mutation and transmission of MDR-TB in Shandong. A retrospective study of patients diagnosed with pulmonary tuberculosis in Shandong from 2009 to 2018 was conducted. To explore transmission patterns, we performed whole genome sequencing on MDR-TB isolates, identified genomic clusters, and assessed the drug resistance of TB isolates. Our study analyzed 167 isolates of MDR-TB, finding that 100 were clustered. The predominant lineage among MDR-TB isolates was lineage 2, specifically with a notable 88.6% belonging to lineage 2.2.1. Lineage 4 constituted a smaller proportion, accounting for 4.2% of the isolates. We discovered that Shandong has a significant clustering percentage for MDR-TB, with Jining having the highest percentage among all Shandong cities. The clustering percentages of MDR-TB, pre-extensively drug-resistant tuberculosis, and extensively drug-resistant tuberculosis were 59.9%, 66.0%, and 71.4%, respectively, and the clustering percentages increased with the expansion of the anti-TB spectrum. Isolates from genomic clusters 1 and 3 belonged to lineage 2.2.1 and showed signs of cross-regional transmission. The distribution of rrs A1401G and katG S315T mutations in lineage 2.2.1 and 2.2.2 strains differed significantly (P < .05). MDR-TB isolates with rpoB I480V, embA-12C > T, and rrs A1401G mutations showed a higher likelihood of clustering (P < .05). Our findings indicate a significant problem of local transmission of MDR-TB in Shandong, China. Beijing lineage isolates and some drug-resistant mutations account for the MDR-TB transmission in Shandong.
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Affiliation(s)
- Yingying Li
- Department of Chinese Medicine Integrated with Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yifan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Tingting Wang
- Department of Chinese Medicine Integrated with Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yameng Li
- Department of Chinese Medicine Integrated with Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Ningning Tao
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Xianglong Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, Shandong, China
| | - Yuzhen Zhang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Qilin Han
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Huaichen Li
- Department of Chinese Medicine Integrated with Western Medicine, Shandong University of Traditional Chinese Medicine, Jinan, China
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
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Mondol SM, Islam MR, Rakhi NN, Shakil SK, Islam I, Mustary JF, Amiruzzaman, Shahjalal HM, Gomes DJ, Rahaman MM. Unveiling a high-risk epidemic clone (ST 357) of 'Difficult to Treat Extensively Drug-Resistant' (DT-XDR) Pseudomonas aeruginosa from a burn patient in Bangladesh: A resilient beast revealing coexistence of four classes of beta lactamases. J Glob Antimicrob Resist 2024; 36:83-95. [PMID: 38122983 DOI: 10.1016/j.jgar.2023.11.014] [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: 08/22/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023] Open
Abstract
OBJECTIVES Pseudomonas aeruginosa (P. aeruginosa) stands out as a key culprit in the colonization of burn wounds, instigating grave infections of heightened severity. In this study, we have performed comparative whole genome analysis of a difficult to treat extensively drug resistant P. aeruginosa isolated from a burn patient in order to elucidate genomic diversity, molecular patterns, mechanisms and genes responsible for conferring antimicrobial resistance and virulence. METHOD P. aeruginosa SHNIBPS206 was isolated from an infected burn wound of a critically injured burn patient. Whole genome sequencing was carried out and annotated with Prokka. Sequence type, serotype, antimicrobial resistance genes and mechanisms, virulence genes, metal resistance genes and CRISPR/Cas systems were investigated. Later, pangenome analysis was carried out to find out genomic diversity. RESULT P. aeruginosa SHNIBPS206 (MLST 357, Serotype O11) was resistant to 14 antibiotics including carbapenems and harboured all four classes of beta lactamase producing genes: Class A (blaPME-1, blaVEB-9), Class B (blaNDM-1), Class C (blaPDC-11) and Class D (blaOXA-846). Mutational analysis of Porin D gave valuable insights. Several efflux pump, virulence and metal resistance genes were also detected. Pangenome analysis revealed high genomic diversity among different strains of P. aeruginosa. CONCLUSION To our knowledge, this is the first report of an extensively drug resistant ST 357 P. aeruginosa from Bangladesh, which is an epidemic high-risk P. aeruginosa clone. Further research and in-depth comprehensive studies are required to investigate the prevalence of such high-risk clone of P. aeruginosa in Bangladesh.
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Affiliation(s)
| | - Md Rafiul Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | | | - Shahriar Kabir Shakil
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh; Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali, Bangladesh
| | - Israt Islam
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | - Jannatul Ferdous Mustary
- Microbiology Department, Sheikh Hasina National Institute of Burn and Plastic Surgery, Dhaka, Bangladesh
| | - Amiruzzaman
- Department of Medicine, Sir Salimullah Medical College, Dhaka, Bangladesh
| | - Hussain Md Shahjalal
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka, Bangladesh
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Folliero V, Ferravante C, Iovane V, Salvati A, Crescenzo L, Perna R, Corvino G, Della Rocca MT, Panetta V, Tranfa A, Greco G, Baldoni T, Pagnini U, Finamore E, Giurato G, Nassa G, Coppola M, Atripaldi L, Greco R, D'Argenio A, Foti MG, Abate R, Del Giudice A, Sarnelli B, Weisz A, Iovane G, Pinto R, Franci G, Galdiero M. Whole Genome Sequence Dataset of Mycobacterium tuberculosis Strains from Patients of Campania Region. Sci Data 2024; 11:220. [PMID: 38374088 PMCID: PMC10876956 DOI: 10.1038/s41597-024-03032-6] [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: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/21/2024] Open
Abstract
Tuberculosis (TB) is one of the deadliest infectious disorders in the world. To effectively TB manage, an essential step is to gain insight into the lineage of Mycobacterium tuberculosis (MTB) and the distribution of drug resistance. Although the Campania region is declared a cluster area for the infection, to contribute to the effort to understand TB evolution and transmission, still poorly known, we have generated a dataset of 159 genomes of MTB strains, from Campania region collected during 2018-2021, obtained from the analysis of whole genome sequence. The results show that the most frequent MTB lineage is the 4 according for 129 strains (81.11%). Regarding drug resistance, 139 strains (87.4%) were classified as multi susceptible, while the remaining 20 (12.58%) showed drug resistance. Among the drug-resistance strains, 8 were isoniazid-resistant MTB, 4 multidrug-resistant MTB, while only one was classified as pre-extensively drug-resistant MTB. This dataset expands the existing available knowledge on drug resistance and evolution of MTB, contributing to further TB-related genomics studies to improve the management of this disease.
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Affiliation(s)
- Veronica Folliero
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Carlo Ferravante
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Valentina Iovane
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Naples, Italy
| | - Annamaria Salvati
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Laura Crescenzo
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | - Rossella Perna
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Giusy Corvino
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | - Maria T Della Rocca
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Vittorio Panetta
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Alessandro Tranfa
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Giuseppe Greco
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Teresa Baldoni
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Ugo Pagnini
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Emiliana Finamore
- UOC Virology and Microbiology - University Hospital AOU "Luigi Vanvitelli", Naples, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | - Giovanni Nassa
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
| | | | - Luigi Atripaldi
- Laboratory of Microbiology and Virology, Ospedali dei Colli, Naples, Italy
| | - Rita Greco
- UOSD Microbiology - AORN Sant 'Anna and San Sebastiano, Caserta, Italy
| | - Annamaria D'Argenio
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Maria Grazia Foti
- UOC Microbiology and Virology- San Giuseppe Moscati Hospital, Avellino, Italy
| | - Rosamaria Abate
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | | | - Bruno Sarnelli
- UOC Microbiology - Ospedale Cardinale Ascalesi, ASL NA1, Naples, Italy
| | - Alessandro Weisz
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy
- Molecular Pathology and Medical Genomics Program, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy
| | - Giuseppe Iovane
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Renato Pinto
- UOD Prevenzione e Sanità Pubblica Veterinaria, Direzione Generale Tutela della Salute - Regione Campania, Naples, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", Baronissi, SA, Italy.
- Clinical Pathology and Microbiology Unit, San Giovanni di Dio e Ruggi D'Aragona University Hospital, Salerno, Italy.
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy.
- UOC Virology and Microbiology - University Hospital AOU "Luigi Vanvitelli", Naples, Italy.
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Morey-León G, Mejía-Ponce PM, Granda Pardo JC, Muñoz-Mawyin K, Fernández-Cadena JC, García-Moreira E, Andrade-Molina D, Licona-Cassani C, Berná L. A precision overview of genomic resistance screening in Ecuadorian isolates of Mycobacterium tuberculosis using web-based bioinformatics tools. PLoS One 2023; 18:e0294670. [PMID: 38051742 DOI: 10.1371/journal.pone.0294670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
INTRODUCTION Tuberculosis (TB) is among the deadliest diseases worldwide, and its impact is mainly due to the continuous emergence of resistant isolates during treatment due to the laborious process of resistance diagnosis, nonadherence to treatment and circulation of previously resistant isolates of Mycobacterium tuberculosis. In this study, we evaluated the performance and functionalities of web-based tools, including Mykrobe, TB-profiler, PhyResSE, KvarQ, and SAM-TB, for detecting resistance in 88 Ecuadorian isolates of Mycobacterium tuberculosis drug susceptibility tested previously. Statistical analysis was used to determine the correlation between genomic and phenotypic analysis. Our results showed that with the exception of KvarQ, all tools had the highest correlation with the conventional drug susceptibility test (DST) for global resistance detection (98% agreement and 0.941 Cohen's kappa), while SAM-TB, PhyResSE, TB-profiler and Mykrobe had better correlations with DST for first-line drug analysis individually. We also identified that in our study, only 50% of mutations characterized by the web-based tools in the rpoB, katG, embB, pncA, gyrA and rrs regions were canonical and included in the World Health Organization (WHO) catalogue. Our findings suggest that SAM-TB, PhyResSE, TB-profiler and Mykrobe were efficient in determining canonical resistance-related mutations, but more analysis is needed to improve second-line detection. Improving surveillance programs using whole-genome sequencing tools for first-line drugs, MDR-TB and XDR-TB is essential to understand the molecular epidemiology of TB in Ecuador. IMPORTANCE Tuberculosis, an infectious disease caused by Mycobacterium tuberculosis, most commonly affects the lungs and is often spread through the air when infected people cough, sneeze, or spit. However, despite the existence of effective drug treatment, patient adherence, long duration of treatment, and late diagnosis have reduced the effectiveness of therapy and increased drug resistance. The increase in resistant cases, added to the impact of the COVID-19 pandemic, has highlighted the importance of implementing efficient and timely diagnostic methodologies worldwide. The significance of our research is in evaluating and identifying a more efficient and user-friendly web-based tool to characterize resistance in Mycobacterium tuberculosis by whole-genome sequencing, which will allow more routine application to improve TB strain surveillance programs locally.
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Affiliation(s)
- Gabriel Morey-León
- Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
- Universidad de la República, Montevideo, Uruguay
- University of Guayaquil, Guayaquil, Ecuador
| | - Paulina M Mejía-Ponce
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Monterrey, Nuevo León, México
| | - Juan Carlos Granda Pardo
- Centro de Referencia Nacional de Micobacterias, Instituto Nacional de Investigación en Salud Pública Dr Leopoldo Izquieta Perez, INSPI-LIP, Guayaquil, Ecuador
| | - Karen Muñoz-Mawyin
- Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | | | | | - Derly Andrade-Molina
- Facultad de Ciencias de la Salud, Universidad Espíritu Santo, Samborondón, Ecuador
- Laboratorio de Ciencias Ómicas, Universidad Espíritu Santo, Samborondón, Ecuador
| | | | - Luisa Berná
- Laboratorio de Interacciones Hospedero-Patógeno, Unidad de Biología Molecular, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Unidad de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Wang Z, Tang Z, Heidari H, Molaeipour L, Ghanavati R, Kazemian H, Koohsar F, Kouhsari E. Global status of phenotypic pyrazinamide resistance in Mycobacterium tuberculosis clinical isolates: an updated systematic review and meta-analysis. J Chemother 2023; 35:583-595. [PMID: 37211822 DOI: 10.1080/1120009x.2023.2214473] [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: 01/19/2023] [Revised: 05/01/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
Pyrazinamide (PZA) is an essential first-line tuberculosis drug for its unique mechanism of action active against multidrug-resistant-TB (MDR-TB). Thus, the aim of updated meta-analysis was to estimate the PZA weighted pooled resistance (WPR) rate in M. tuberculosis isolates based on publication date and WHO regions. We systematically searched the related reports in PubMed, Scopus, and Embase (from January 2015 to July 2022). Statistical analyses were performed using STATA software. The 115 final reports in the analysis investigated phenotypic PZA resistance data. The WPR of PZA was 57% (95% CI 48-65%) in MDR-TB cases. According to the WHO regions, the higher WPRs of PZA were reported in the Western Pacific (32%; 95% CI 18-46%), South East Asian region (37%; 95% CI 31-43%), and the Eastern Mediterranean (78%; 95% CI 54-95%) among any-TB patients, high risk of MDR-TB patients, and MDR-TB patients, respectively. A negligible increase in the rate of PZA resistance were showed in MDR-TB cases (55% to 58%). The rate of PZA resistance has been rising in recent years among MDR-TB cases, underlines the essential for both standard and novel drug regimens development.
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Affiliation(s)
- Zheming Wang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Zhihua Tang
- Department of Pharmacy, Shaoxing People's Hospital, Shaoxing, China
| | - Hamid Heidari
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Leila Molaeipour
- Department of Epidemiology, School of Public Health, University of Medical Sciences, Tehran, Iran
| | | | - Hossein Kazemian
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Faramarz Koohsar
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
- Department of Laboratory Sciences, Faculty of Paramedicine, Golestan University of Medical Sciences, Gorgan, Iran
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Mejía-Ponce PM, Ramos-González EJ, Ramos-García AA, Lara-Ramírez EE, Soriano-Herrera AR, Medellín-Luna MF, Valdez-Salazar F, Castro-Garay CY, Núñez-Contreras JJ, De Donato-Capote M, Sharma A, Castañeda-Delgado JE, Zenteno-Cuevas R, Enciso-Moreno JA, Licona-Cassani C. Genomic epidemiology analysis of drug-resistant Mycobacterium tuberculosis distributed in Mexico. PLoS One 2023; 18:e0292965. [PMID: 37831695 PMCID: PMC10575498 DOI: 10.1371/journal.pone.0292965] [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: 05/03/2023] [Accepted: 09/29/2023] [Indexed: 10/15/2023] Open
Abstract
Genomics has significantly revolutionized pathogen surveillance, particularly in epidemiological studies, the detection of drug-resistant strains, and disease control. Despite its potential, the representation of Latin American countries in the genomic catalogues of Mycobacterium tuberculosis (Mtb), the bacteria responsible for Tuberculosis (TB), remains limited. In this study, we present a whole genome sequencing (WGS)-based analysis of 85 Mtb clinical strains from 17 Mexican states, providing insights into local adaptations and drug resistance signatures in the region. Our results reveal that the Euro-American lineage (L4) accounts for 94% of our dataset, showing 4.1.2.1 (Haarlem, n = 32), and 4.1.1.3 (X-type, n = 34) sublineages as the most prevalent. We report the presence of the 4.1.1.3 sublineage, which is endemic to Mexico, in six additional locations beyond previous reports. Phenotypic drug resistance tests showed that 34 out of 85 Mtb samples were resistant, exhibiting a variety of resistance profiles to the first-line antibiotics tested. We observed high levels of discrepancy between phenotype and genotype associated with drug resistance in our dataset, including pyrazinamide-monoresistant Mtb strains lacking canonical variants of drug resistance. Expanding the Latin American Mtb genome databases will enhance our understanding of TB epidemiology and potentially provide new avenues for controlling the disease in the region.
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Affiliation(s)
- Paulina M. Mejía-Ponce
- Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, México
| | - Elsy J. Ramos-González
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Axel A. Ramos-García
- Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, México
| | - Edgar E. Lara-Ramírez
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Alma R. Soriano-Herrera
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Mitzy F. Medellín-Luna
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
- Posgrado en Ciencias Farmacobiológicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Fernando Valdez-Salazar
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - Claudia Y. Castro-Garay
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | - José J. Núñez-Contreras
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
| | | | - Ashutosh Sharma
- Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Querétaro, México
| | - Julio E. Castañeda-Delgado
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
- Consejo Nacional de Ciencia y Tecnología, CONACYT, Ciudad de México, México
| | - Roberto Zenteno-Cuevas
- Instituto de Salud Pública, Universidad Veracruzana, Veracruz, México
- Red Multidisciplinaria de Investigación en Tuberculosis, Ciudad de México, México
| | - Jose Antonio Enciso-Moreno
- Unidad de Investigación Biomédica de Zacatecas, Instituto Mexicano Del Seguro Social, Zacatecas, México
- Facultad de Química, Universidad Autónoma de Querétaro, Querétaro, México
| | - Cuauhtémoc Licona-Cassani
- Centro de Biotecnología FEMSA, Escuela de Ingeniería y Ciencias, Tecnológico de Monterrey, Nuevo León, México
- Red Multidisciplinaria de Investigación en Tuberculosis, Ciudad de México, México
- Division of Integrative Biology, The Institute for Obesity Research, Tecnológico de Monterrey, Nuevo León, México
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7
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Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiol Spectr 2022; 10:e0125222. [PMID: 36102651 PMCID: PMC9602270 DOI: 10.1128/spectrum.01252-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) remains one of the most important infectious diseases globally. Establishing a resistance profile from the initial TB diagnosis is a priority. Rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, and Whole Genome Sequencing (WGS) needs culture prior to next-generation sequencing (NGS), limiting their clinical value. Targeted sequencing (TS) from clinical samples avoids these drawbacks, providing a signature of genetic markers that can be associated with drug resistance and phylogeny. In this study, a proof-of-concept protocol was developed for detecting genomic variants associated with drug resistance and for the phylogenetic classification of Mycobacterium Tuberculosis (Mtb) in sputum samples. Initially, a set of Mtb reference strains from the WHO were sequenced (WGS and TS). The results from the protocol agreed >95% with WHO reported data and phenotypic drug susceptibility testing (pDST). Lineage genetics results were 100% concordant with those derived from WGS. After that, the TS protocol was applied to sputum samples from TB patients to detect resistance to first- and second-line drugs and derive phylogeny. The accuracy was >90% for all evaluated drugs, except Eto/Pto (77.8%), and 100% were phylogenetically classified. The results indicate that the described protocol, which affords the complete drug resistance profile and phylogeny of Mtb from sputum, could be useful in the clinical area, advancing toward more personalized and more effective treatments in the near future. IMPORTANCE The COVID-19 pandemic negatively affected the progress in accessing essential Tuberculosis (TB) services and reducing the burden of TB disease, resulting in a decreased detection of new cases and increased deaths. Generating molecular diagnostic tests with faster results without losing reliability is considered a priority. Specifically, developing an antimicrobial resistance profile from the initial stages of TB diagnosis is essential to ensure appropriate treatment. Currently available rapid molecular tests evaluate only the most common genetic variants responsible for resistance to certain drugs, limiting their clinical value. In this work, targeted sequencing on sputum samples from TB patients was used to identify Mycobacterium tuberculosis mutations in genes associated with drug resistance and to derive a phylogeny of the infecting strain. This protocol constitutes a proof-of-concept toward the goal of helping clinicians select a timely and appropriate treatment by providing them with actionable information beyond current molecular approaches.
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Mohammed KAS, Khudhair GS, Al-Rabeai DB. Prevalence and Drug Resistance Pattern of Mycobacterium tuberculosis Isolated from Tuberculosis Patients in Basra, Iraq. Pol J Microbiol 2022; 71:205-215. [PMID: 35675816 PMCID: PMC9252138 DOI: 10.33073/pjm-2022-018] [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: 01/17/2022] [Accepted: 03/12/2022] [Indexed: 12/03/2022] Open
Abstract
Drug-resistant Mycobacterium tuberculosis (DR-MTB) is a major health threat to human beings. This study aimed to evaluate the prevalence and drug resistance profile of MTB. Data were collected from 2,296 newly diagnosed, and 246 retreated tuberculosis (TB) patients who attended the Advisory Clinic for Chest Diseases and Respiratory in Basra province from January 2016 to December 2020. Both new diagnostic and retreated TB cases showed that DR-MTB cases were significantly higher at age 15–34 years, pulmonary TB, and urban residents but with no significant difference regarding gender. The drugs resistance was significantly higher among the retreated cases compared with the new diagnostic patients (20.3% vs. 2.4%, p < 0.0001), with the percentage of the resistance to first-line drugs in primary and secondary cases including isoniazid (1% and 17.1%), rifampicin (0.78% and 15.8%), ethambutol (0.56% and 8.5%), streptomycin (1.3% and 9.75%). Notice that the most common drug resistance was against streptomycin with 1.3% in new patients and against isoniazid (17.1%) in retreated patients. The rate of total drug-resistant TB, multi-drug resistant TB, mono-drug resistant TB, and rifampicin-resistant TB among new tuberculosis cases increased in this period from 2.2 to 6.7%, 0.17 to 1.6%, 0.85 to 4%, and 0.17 to 4%, with a percentage change of 204.54, 841.17, 370.58, 22.5%, respectively. The rates of poly drug-resistant TB and ethambutol-resistant-TB dropped in this period by 15.96%, and 0.7%, with a decrease from 1.19 to 1% and from 1 to 0.3%, respectively. Similarly, the increase of drug-resistant TB among secondary cases has also occurred. In conclusion, the temporal trend showed an increase in the rate of drug resistance of M. tuberculosis since 2016, with a predominant multi-drug-resistant TB and isoniazid-resistant TB. ![]()
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Affiliation(s)
- Khairallah A S Mohammed
- Department of Medical Lab Technology, College of Health and Medical Technology, Southern Technical University, Basra, Iraq
| | - Ghorob S Khudhair
- Department of Medical Lab Technology, College of Health and Medical Technology, Southern Technical University, Basra, Iraq
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Fernández-Morales EA, Bermudez G, Montero H, Luzania-Valerio M, Zenteno-Cuevas R. Whole genome characterization, and geographical distribution of M. tuberculosis in central region of Veracruz, Mexico. Braz J Infect Dis 2022; 26:102357. [PMID: 35533727 PMCID: PMC9387445 DOI: 10.1016/j.bjid.2022.102357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/06/2022] [Accepted: 04/14/2022] [Indexed: 11/17/2022] Open
Abstract
The purpose of this work was to perform by Whole Genomic Sequencing (WGS) a characterization of tuberculosis isolates circulating in the central region of Veracruz, Mexico, and to determine its geographical distribution. The genome of 25 clinical isolates of tuberculosis patients, recovered from central zone of Veracruz, Mexico, were sequenced and the information obtained was used to characterize lineage, prediction of drug resistance, identification of clonal complexes, and finally correlated with the geolocalization data. Isolates analyzed were included into seven L4 sublineages, most frequent was X3; X1 (4.1.1.3) in 35%. rpoBSer450Leu polymorphism was the most frequently found variant. Sublineage Haarlem (4.1.2) had the widest distribution, found in five municipalities. Of the of two clonal complexes found, the most abundant included eight isolates, with X3/X1 lineage, placed in two municipalities. Combination of WGS and geographic information system was very useful for the identification of sublineages, clonal complexes, and their geographical dispersion with important implications in the epidemiological surveillance and clinical control of TB.
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Affiliation(s)
- Esdras Antonio Fernández-Morales
- University of Veracruz, Health Sciences Institute, Health Sciences Master Program, Mexico; University of Veracruz, Public Health Institute, Mexico
| | - Gustavo Bermudez
- University of Veracruz, Health Sciences Institute, Health Sciences Doctoral Program, Mexico
| | - Hilda Montero
- University of Veracruz, Public Health Institute, Mexico
| | | | - Roberto Zenteno-Cuevas
- University of Veracruz, Public Health Institute, Mexico; Multidisciplinary Network of Tuberculosis Research, Mexico.
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Shrestha A, Picoy J, Torres A, Moore DA, Gilman RH, Coronel J, Grandjean L. A case report of transmission and disease caused by Mycobacterium caprae and Mycobacterium bovis in Lima, Peru. BMC Infect Dis 2021; 21:1265. [PMID: 34930187 PMCID: PMC8686613 DOI: 10.1186/s12879-021-06944-5] [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] [Received: 09/30/2021] [Accepted: 12/03/2021] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The Tuberculosis (TB) burden in Peru is significant with respect to both disease morbidity and mortality. Furthermore the recent diversification of farming enterprise to include a wide range of animal species has necessitated the consideration of members of the Mycobacterium Tuberculosis Complex (MTBC) with the potential for zoonotic transmission. M. bovis and M. caprae, a lesser known member of the MTBC exhibit an exceptionally wide host spectrum in animals and are capable of causing disease in humans. M. bovis has a predictable resistance profile which includes resistance to pyrazinamide. Thus, failure to identify M. bovis as the causative agent in reported TB cases leads to higher levels of treatment failure and contributes to the transmission of drug-resistant TB. CASE PRESENTATION Reported here are the clinical presentations, investigations and treatment histories of two patients identified from a population level genotyping study in Lima, Peru that were at the time of treatment thought to be M. tuberculosis patients but in retrospect were spectated using whole genome sequencing as M. caprae and M. Bovis. CONCLUSIONS The cases reported here constitute convincing evidence that M. caprae and M. bovis are causative agents of TB infection in humans in Peru and underscore the importance of species-level MTBC member identification to effectively control and treat zoonotic TB. Furthermore these cases highlight the challenges of using clinical risk factors to identify cases of zoonotic TB in humans as their clinical presentation and transmission history is often difficult to distinguish from anthroponotic TB.
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Affiliation(s)
- Amber Shrestha
- grid.420468.cDepartment of Infectious Disease, Great Ormond Street Hospital for Children, London, WC1N 3JH UK
| | - Janeth Picoy
- Department of Infectious Disease, Diresa Callao Jr, Colina #879, Bellavista, 07016 Lima, Peru
| | - Arturo Torres
- grid.7445.20000 0001 2113 8111Department of Infectious Disease, Imperial College London, South Kensington, London, SW7 2AZ UK
| | - David A. Moore
- grid.8991.90000 0004 0425 469XTB Centre, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Robert H. Gilman
- grid.11100.310000 0001 0673 9488Laboratorio de Tuberculosis, Laboratorios de Investigación Y Desarrollo, Facultad de Ciencias Y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru ,grid.21107.350000 0001 2171 9311Department of International Health, School of Public Health, Johns Hopkins University, Baltimore, MD USA
| | - Jorge Coronel
- grid.11100.310000 0001 0673 9488Laboratorio de Investigación de Enfermedades Infecciosas, Universidad Peruana Cayetano Heredia: Lima, Lima, Peru
| | - Louis Grandjean
- Department of Infectious Disease, Great Ormond Street Hospital for Children, London, WC1N 3JH, UK. .,University College London, Gower St, Bloomsbury, London, WC1E 6BT, UK.
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The Neglected Contribution of Streptomycin to the Tuberculosis Drug Resistance Problem. Genes (Basel) 2021; 12:genes12122003. [PMID: 34946952 PMCID: PMC8701281 DOI: 10.3390/genes12122003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/22/2022] Open
Abstract
The airborne pathogen Mycobacterium tuberculosis is responsible for a present major public health problem worsened by the emergence of drug resistance. M. tuberculosis has acquired and developed streptomycin (STR) resistance mechanisms that have been maintained and transmitted in the population over the last decades. Indeed, STR resistant mutations are frequently identified across the main M. tuberculosis lineages that cause tuberculosis outbreaks worldwide. The spread of STR resistance is likely related to the low impact of the most frequent underlying mutations on the fitness of the bacteria. The withdrawal of STR from the first-line treatment of tuberculosis potentially lowered the importance of studying STR resistance. However, the prevalence of STR resistance remains very high, could be underestimated by current genotypic methods, and was found in outbreaks of multi-drug (MDR) and extensively drug (XDR) strains in different geographic regions. Therefore, the contribution of STR resistance to the problem of tuberculosis drug resistance should not be neglected. Here, we review the impact of STR resistance and detail well-known and novel candidate STR resistance mechanisms, genes, and mutations. In addition, we aim to provide insights into the possible role of STR resistance in the development of multi-drug resistant tuberculosis.
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Anwaierjiang A, Wang Q, Liu H, Yin C, Xu M, Li M, Liu M, Liu Y, Zhao X, Liu J, Li G, Mijiti X, Wan K. Prevalence and Molecular Characteristics Based on Whole Genome Sequencing of Mycobacterium tuberculosis Resistant to Four Anti-Tuberculosis Drugs from Southern Xinjiang, China. Infect Drug Resist 2021; 14:3379-3391. [PMID: 34466004 PMCID: PMC8402983 DOI: 10.2147/idr.s320024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 08/07/2021] [Indexed: 12/25/2022] Open
Abstract
Objective Drug-resistant tuberculosis is a major public health problem, especially in the southern region of Xinjiang, China; however, there is little information regarding drug resistance profiles and mechanism of Mycobacterium tuberculosis in this area. The aim of this study was to determine the prevalence and molecular characteristics of M. tuberculosis resistant to four anti-tuberculosis drugs from this area. Methods Three hundred and forty-six isolates from the southern region of Xinjiang, China were included and used to perform phenotypic drug susceptibility testing and whole genome sequencing (WGS). Mutations in seven loci associated with drug resistance, including rpoB for rifampicin (RMP), katG, inhA promoter and oxyR-ahpC for isoniazid (INH), rrs 530 and 912 loops and rpsL for streptomycin (STR), and embB for ethambutol (EMB), were characterized. Results Among 346 isolates, 106, 60, 70 and 29 were resistant to INH, RMP, STR and EMB, respectively; 132 were resistant to at least one of the four anti-tuberculosis drugs and 51 were multi-drug resistant (MDR). Beijing genotype and retreated patients showed a significantly increased risk for developing MDR tuberculosis. Compared with the phenotypic data, the sensitivity and specificity for WGS to predict resistance were 96.7% and 98.6% for RMP, 75.5% and 97.1% for INH, 68.6% and 99.6% for STR, 93.1% and 93.7% for EMB, respectively. The most common mutations conferring RMP, INH, STR and EMB resistance were Ser450Leu (51.7%) in rpoB, Ser315Thr (44.3%) in katG, Lys43Arg (35.7%) in rpsL and Met306Val (24.1%) in embB. Conclusion This study provides the first information on the prevalence and molecular characters of drug resistant M. tuberculosis in the southern region of Xinjiang, China, which will be helpful for choosing early detection methods for drug resistance (ig, molecular methods) and subsequently initiation of proper therapy of tuberculosis in this area.
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Affiliation(s)
- Aiketaguli Anwaierjiang
- College of Public Health, Xinjiang Medical University, Wulumuqi, 830011, People's Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Wulumuqi, 830001, People's Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Chunjie Yin
- College of Public Health, Xinjiang Medical University, Wulumuqi, 830011, People's Republic of China
| | - Miao Xu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Wulumuqi, 830001, People's Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Mengwen Liu
- College of Public Health, Xinjiang Medical University, Wulumuqi, 830011, People's Republic of China
| | - Yan Liu
- The Eighth Affiliated Hospital of Xinjiang Medical University, Wulumuqi, 830001, People's Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Jinbao Liu
- College of Public Health, Xinjiang Medical University, Wulumuqi, 830011, People's Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Wulumuqi, 830001, People's Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People's Republic of China
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13
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Prasanna A, Niranjan V. MutVis: Automated framework for analysis and visualization of mutational signatures in pathogenic bacterial strains. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 91:104805. [PMID: 33689914 DOI: 10.1016/j.meegid.2021.104805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 12/17/2020] [Accepted: 03/04/2021] [Indexed: 12/01/2022]
Abstract
In recent years, mutational signature analysis has become a routine practice in cancer genomics for classification and diagnosis. Characterizing mutational signatures across species or within genomes of a bacteria helps in understanding their evolution and adaptation. However, an integrated framework for analysis and visualization of mutational signatures in bacterial genome is lacking. Hence, we aim to develop an integrated, automated, open-source and user-friendly framework called MutVis to analyze mutational signatures from bacterial whole genome next generation sequencing data. The current framework integrates various publicly available packages using Snakemake workflow management software, Python and R scripting. MutVis supports variant calling, transition (Ti) and transversion (Tv) graphical representation, generation of mutational count matrix, graphical visualization of base-pair substitution spectrum (BPSs) and mutation signatures extraction. TvTi plots provide the 6 base substitution classification for both genome and gene level. Further resolution of base pair substitution classification is provided as 96-profile BPSs plot. Mutation signatures is derived based on the characteristic pattern observed in BPSs using non-negative matrix factorization. Relative contribution of signatures is given as hierarchically clustered heatmap. This provides information on active signatures in the individual given sample and classify samples according to signature contributions. We demonstrated the MutVis framework using geographically different strains of Mycobacterium tuberculosis, downloaded from PATRIC TB-ARC Antibiotic Resistance Catalog (n = 963). The current framework can be used to study mutation biases and characteristic mutational signatures in bacterial genomes and is freely available at https://github.com/AkshathaPrasanna/MutVis.
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Affiliation(s)
- Akshatha Prasanna
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka 560059, India
| | - Vidya Niranjan
- Department of Biotechnology, RV College of Engineering, Bengaluru, Karnataka 560059, India..
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Cheng B, Behr MA, Howden BP, Cohen T, Lee RS. Reporting practices for genomic epidemiology of tuberculosis: a systematic review of the literature using STROME-ID guidelines as a benchmark. THE LANCET. MICROBE 2021; 2:e115-e129. [PMID: 33842904 PMCID: PMC8034592 DOI: 10.1016/s2666-5247(20)30201-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Pathogen genomics have become increasingly important in infectious disease epidemiology and public health. The Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID) guidelines were developed to outline a minimum set of criteria that should be reported in genomic epidemiology studies to facilitate assessment of study quality. We evaluate such reporting practices, using tuberculosis as an example. METHODS For this systematic review, we initially searched MEDLINE, Embase Classic, and Embase on May 3, 2017, using the search terms "tuberculosis" and "genom* sequencing". We updated this initial search on April 23, 2019, and also included a search of bioRxiv at this time. We included studies in English, French, or Spanish that recruited patients with microbiologically confirmed tuberculosis and used whole genome sequencing for typing of strains. Non-human studies, conference abstracts, and literature reviews were excluded. For each included study, the number and proportion of fulfilled STROME-ID criteria were recorded by two reviewers. A comparison of the mean proportion of fulfilled STROME-ID criteria before and after publication of the STROME-ID guidelines (in 2014) was done using a two-tailed t test. Quasi-Poisson regression and tobit regression were used to examine associations between study characteristics and the number and proportion of fulfilled STROME-ID criteria. This study was registered with PROSPERO, CRD42017064395. FINDINGS 976 titles and abstracts were identified by our primary search, with an additional 16 studies identified in bioRxiv. 114 full texts (published between 2009 and 2019) were eligible for inclusion. The mean proportion of STROME-ID criteria fulfilled was 50% (SD 12; range 16-75). The proportion of criteria fulfilled was similar before and after STROME-ID publication (51% [SD 11] vs 46% [14], p=0·26). The number of criteria reported (among those applicable to all studies) was not associated with impact factor, h-index, country of affiliation of senior author, or sample size of isolates. Similarly, the proportion of criteria fulfilled was not associated with these characteristics, with the exception of a sample size of isolates of 277 or more (the highest quartile). In terms of reproducibility, 100 (88%) studies reported which bioinformatic tools were used, but only 33 (33%) reported corresponding version numbers. Sequencing data were available for 86 (75%) studies. INTERPRETATION The reporting of STROME-ID criteria in genomic epidemiology studies of tuberculosis between 2009 and 2019 was low, with implications for assessment of study quality. The considerable proportion of studies without bioinformatics version numbers or sequencing data available highlights a key concern for reproducibility.
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Affiliation(s)
- Brianna Cheng
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Marcel A Behr
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Benjamin P Howden
- The 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, VIC, Australia
| | | | - Robyn S Lee
- Epidemiology Division, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
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15
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Jiménez-Ruano AC, Madrazo-Moya CF, Cancino-Muñoz I, Mejía-Ponce PM, Licona-Cassani C, Comas I, Muñiz-Salazar R, Zenteno-Cuevas R. Whole genomic sequencing based genotyping reveals a specific X3 sublineage restricted to Mexico and related with multidrug resistance. Sci Rep 2021; 11:1870. [PMID: 33479318 PMCID: PMC7820219 DOI: 10.1038/s41598-020-80919-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 12/08/2020] [Indexed: 01/26/2023] Open
Abstract
Whole genome sequencing (WGS) has been shown to be superior to traditional procedures of genotyping in tuberculosis (TB), nevertheless, reports of its use in drug resistant TB (DR-TB) isolates circulating in Mexico, are practically unknown. Considering the above the main of this work was to identify and characterize the lineages and genomic transmission clusters present in 67 DR-TB isolates circulating in southeastern Mexico. The results show the presence of three major lineages: L1 (3%), L2 (3%) and L4 (94%), the last one included 16 sublineages. Sublineage 4.1.1.3 (X3) was predominant in 18 (27%) of the isolates, including one genomic cluster, formed by eleven multidrug resistant isolates and sharing the SIT 3278, which seems to be restricted to Mexico. By the use of WGS, it was possible to identify the high prevalence of L4 and a high number of sublineages circulating in the region, also was recognized the presence of a novel X3 sublineage, formed exclusively by multidrug resistant isolates and with restrictive circulation in Mexico for at least the past 17 years.
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Affiliation(s)
- Ana Cristina Jiménez-Ruano
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México
- Instituto de Salud Pública, Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Animas, 91190, Xalapa, Veracruz, México
| | - Carlos Francisco Madrazo-Moya
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México
- Biomedical Institute of Valencia IBV-CSIC, Valencia, Spain
| | | | - Paulina M Mejía-Ponce
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Nuevo Leon, Mexico
| | | | - Iñaki Comas
- Biomedical Institute of Valencia IBV-CSIC, Valencia, Spain
- CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Raquel Muñiz-Salazar
- Laboratorio de Epidemiología y Ecología y Molecular, Escuela de Ciencias de la Salud, Universidad Autónoma de Baja California, Ensenada, Baja California, México
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City, Mexico
| | - Roberto Zenteno-Cuevas
- Programa de Maestría en Ciencias de la Salud, Instituto de Ciencias de la Salud, Universidad Veracruzana, Xalapa, Veracruz, México.
- Instituto de Salud Pública, Universidad Veracruzana, Av. Luis Castelazo Ayala S/N, A.P. 57, Col. Industrial Animas, 91190, Xalapa, Veracruz, México.
- Red Multidisciplinaria de Investigación en Tuberculosis, Mexico City, Mexico.
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Supo-Escalante RR, Médico A, Gushiken E, Olivos-Ramírez GE, Quispe Y, Torres F, Zamudio M, Antiparra R, Amzel LM, Gilman RH, Sheen P, Zimic M. Prediction of Mycobacterium tuberculosis pyrazinamidase function based on structural stability, physicochemical and geometrical descriptors. PLoS One 2020; 15:e0235643. [PMID: 32735615 PMCID: PMC7394417 DOI: 10.1371/journal.pone.0235643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/19/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Pyrazinamide is an important drug against the latent stage of tuberculosis and is used in both first- and second-line treatment regimens. Pyrazinamide-susceptibility test usually takes a week to have a diagnosis to guide initial therapy, implying a delay in receiving appropriate therapy. The continued increase in multi-drug resistant tuberculosis and the prevalence of pyrazinamide resistance in several countries makes the development of assays for prompt identification of resistance necessary. The main cause of pyrazinamide resistance is the impairment of pyrazinamidase function attributed to mutations in the promoter and/or pncA coding gene. However, not all pncA mutations necessarily affect the pyrazinamidase function. OBJECTIVE To develop a methodology to predict pyrazinamidase function from detected mutations in the pncA gene. METHODS We measured the catalytic constant (kcat), KM, enzymatic efficiency, and enzymatic activity of 35 recombinant mutated pyrazinamidase and the wild type (Protein Data Bank ID = 3pl1). From all the 3D modeled structures, we extracted several predictors based on three categories: structural stability (estimated by normal mode analysis and molecular dynamics), physicochemical, and geometrical characteristics. We used a stepwise Akaike's information criterion forward multiple log-linear regression to model each kinetic parameter with each category of predictors. We also developed weighted models combining the three categories of predictive models for each kinetic parameter. We tested the robustness of the predictive ability of each model by 6-fold cross-validation against random models. RESULTS The stability, physicochemical, and geometrical descriptors explained most of the variability (R2) of the kinetic parameters. Our models are best suited to predict kcat, efficiency, and activity based on the root-mean-square error of prediction of the 6-fold cross-validation. CONCLUSIONS This study shows a quick approach to predict the pyrazinamidase function only from the pncA sequence when point mutations are present. This can be an important tool to detect pyrazinamide resistance.
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Affiliation(s)
- Rydberg Roman Supo-Escalante
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Aldhair Médico
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Gustavo E. Olivos-Ramírez
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Yaneth Quispe
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Fiorella Torres
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Melissa Zamudio
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Ricardo Antiparra
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - L. Mario Amzel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, United States of America
| | - Robert H. Gilman
- International Health Department, Johns Hopkins School of Public Health, Baltimore, MD, United States of America
| | - Patricia Sheen
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mirko Zimic
- Laboratorio de Bioinformática, Biología Molecular y Desarrollos Tecnológicos, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
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