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Scaltriti E, Iyad K, Boniotti MB, Menozzi I, Bolzoni L, Ippolito D, Ciarello FP, Loda D, D’Incau M, Zanoni M, Presti VDML, Mazzone P, Gavaudan S, Pacciarini ML. Inside Mycobacterium bovis SB0120 spoligotype circulating in Italy: analysis of the most frequent genotypes by whole genome sequencing. Front Microbiol 2024; 15:1416605. [PMID: 39132144 PMCID: PMC11310128 DOI: 10.3389/fmicb.2024.1416605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 07/05/2024] [Indexed: 08/13/2024] Open
Abstract
Bovine tuberculosis (bTB) is a chronic inflammatory disease primarily caused by Mycobacterium bovis. The infection affects domestic animals and wildlife, posing a zoonotic risk to humans. To understand the dynamics of transmission and genetic diversity in Italy's M. bovis population, we conducted whole-genome sequencing (WGS) analysis on two prevalent genotypes, belonging to Spoligotype SB0120, identified in different geographical and temporal contexts. By comparing these genomes with international M. bovis isolates, we identified a distinct clade within the lineage La1.2, encompassing the Italian SB0120 isolates, indicating a genomic segregation of Italian M. bovis from other European isolates. Within Italy, a significant level of genetic variability emerged across regions, while isolates within epidemiologically linked outbreaks exhibited minimal genetic diversity. Additionally, isolates derived from cattle and wild boars within a tuberculosis hotspot in Central Italy and from cattle and black pigs in Sicily formed unified clonal clusters. This indicates the presence of persistent strains circulating in the examined regions. The genetic diversity within herds was limited, as specific clones endured over time within certain herds. This research enhances our comprehension of the epidemiology and transmission patterns of bTB in Italy, thereby aiding the development of precise control strategies and disease management. Using WGS and implementing standardized protocols and databases will be pivotal in combating bTB and promoting One-Health approaches to address this noteworthy public health concern.
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Affiliation(s)
- Erika Scaltriti
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Karaman Iyad
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Maria Beatrice Boniotti
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Ilaria Menozzi
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Luca Bolzoni
- Risk Analysis and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale Della Lombardia e Dell'Emilia-Romagna (IZSLER), Parma, Italy
| | - Dorotea Ippolito
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Flavia Pruiti Ciarello
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Daniela Loda
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Mario D’Incau
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Mariagrazia Zanoni
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
| | - Vincenzo Di Marco Lo Presti
- Area Territoriale Barcellona Pozzo di Gotto, Istituto Zooprofilattico Sperimentale della Sicilia "A. Mirri", Barcellona Pozzo di Gotto, Messina, Italy
| | - Piera Mazzone
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Perugia, Italy
| | - Stefano Gavaudan
- Istituto Zooprofilattico Sperimentale dell’Umbria e delle Marche “Togo Rosati” (IZSUM), Ancona, Italy
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna – IZSLER, Brescia, Italy
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Deb S, Basu J, Choudhary M. An overview of next generation sequencing strategies and genomics tools used for tuberculosis research. J Appl Microbiol 2024; 135:lxae174. [PMID: 39003248 DOI: 10.1093/jambio/lxae174] [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: 04/15/2024] [Revised: 06/07/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Tuberculosis (TB) is a grave public health concern and is considered the foremost contributor to human mortality resulting from infectious disease. Due to the stringent clonality and extremely restricted genomic diversity, conventional methods prove inefficient for in-depth exploration of minor genomic variations and the evolutionary dynamics operating in Mycobacterium tuberculosis (M.tb) populations. Until now, the majority of reviews have primarily focused on delineating the application of whole-genome sequencing (WGS) in predicting antibiotic resistant genes, surveillance of drug resistance strains, and M.tb lineage classifications. Despite the growing use of next generation sequencing (NGS) and WGS analysis in TB research, there are limited studies that provide a comprehensive summary of there role in studying macroevolution, minor genetic variations, assessing mixed TB infections, and tracking transmission networks at an individual level. This highlights the need for systematic effort to fully explore the potential of WGS and its associated tools in advancing our understanding of TB epidemiology and disease transmission. We delve into the recent bioinformatics pipelines and NGS strategies that leverage various genetic features and simultaneous exploration of host-pathogen protein expression profile to decipher the genetic heterogeneity and host-pathogen interaction dynamics of the M.tb infections. This review highlights the potential benefits and limitations of NGS and bioinformatics tools and discusses their role in TB detection and epidemiology. Overall, this review could be a valuable resource for researchers and clinicians interested in NGS-based approaches in TB research.
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Affiliation(s)
- Sushanta Deb
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman 99164, WA, United States
- All India Institute of Medical Sciences, New Delhi 110029, India
| | - Jhinuk Basu
- Department of Clinical Immunology and Rheumatology, Kalinga Institute of Medical Sciences (KIMS), KIIT University, Bhubaneswar 751024, India
| | - Megha Choudhary
- All India Institute of Medical Sciences, New Delhi 110029, India
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Catana-Botello N, Becerril-Montes P, Castro-Garza J, González-Salazar F, Almanza-Reyes H, Del Bosque-Moncayo MDLÁ, Morales-Vargas A, Velázquez-Moreno VM. Mycobacterium tuberculosis Beijing in the State of Nuevo Leon, Mexico. Rev Argent Microbiol 2024:S0325-7541(24)00046-4. [PMID: 38942679 DOI: 10.1016/j.ram.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/16/2023] [Accepted: 12/31/2023] [Indexed: 06/30/2024] Open
Abstract
Tuberculosis remains a serious threat to human health as an infectious disease in Mexico. Data about the genotypes of circulating Mycobacterium tuberculosis isolates (MTB) in the State of Nuevo Leon, Mexico are scarce. We aimed to determine the genotypes of circulating MTB belonging to the Beijing lineage recovered from patients in the State of Nuevo Leon, Mexico. A total of 406 MTB isolates from this state were genotyped using the spoligotyping method and 18-locus MIRU-VNTR. Lineage classification and MTB transmission analysis were performed. Based on the spoligotyping analysis, we found 24 strains belonging to the Beijing genotype that were characterized phylogenetically. The MIRUs showed greater discriminatory power than the standard RFLP-IS6110 method; therefore, the greatest allelic diversity among the Beijing strains was observed with MIRU10, MIRU31, MIRU39, MRU40, and MIRU 26. MVLA analysis showed a profile variation between Beijing and non-Beijing strains. The minimum spanning tree (MST) showed that 79% (19) of the strains are related. All Beijing strains exhibited the deletion of region TbD1, which is a characteristic of modern strains. The application of spoligotyping and MIRU-VNTR-18 methods together proved to be more sensitive, discriminatory, and rapid than the standard method for the epidemiological analysis of Mycobacterium Beijing isolates. This study is one of the first to describe the genomic diversity of M. Beijing in the State of Nuevo Leon, Mexico.
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Affiliation(s)
- Nohemí Catana-Botello
- Faculty of Biological Sciences, Autonomous University of Nuevo León, Ave. Pedro de Alba S/N, Niños Héroes, Ciudad Universitaria, San Nicolás de los Garza, Nuevo León 64260, Mexico
| | - Pola Becerril-Montes
- Biomedical Research Center of the Northeast, Mexican Social Security Institute, San Luis Potosí 611, Col. Independencia, Monterrey, Nuevo León 64720, Mexico.
| | - Jorge Castro-Garza
- Secretary of Health of the State of Nuevo León, C. Mariano Matamoros 520, Nuevo León 64000, Mexico
| | - Francisco González-Salazar
- Biomedical Research Center of the Northeast, Mexican Social Security Institute, San Luis Potosí 611, Col. Independencia, Monterrey, Nuevo León 64720, Mexico; Health Sciences, University of Monterrey, Av. Ignacio Morones Prieto 4500 poniente, Col. Jesús M. Garza, San Pedro Garza García, Nuevo León 66238, Mexico.
| | - Horacio Almanza-Reyes
- Faculty of Medicine and Psychology, Autonomous University of Baja California, Universidad 14418, UABC, Parque Internacional Industrial Tijuana, Tijuana Baja California 22390, Mexico.
| | | | - Alejandro Morales-Vargas
- State Public Health Laboratory of Nuevo León, Prof. Serafín Peña 2211, Valles de La Silla, Guadalupe, Nuevo León 67180, Mexico
| | - Víctor Manuel Velázquez-Moreno
- State Public Health Laboratory of Nuevo León, Prof. Serafín Peña 2211, Valles de La Silla, Guadalupe, Nuevo León 67180, Mexico
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Byrne A, Bissonnette N, Ollier S, Tahlan K. Investigating in vivo Mycobacterium avium subsp. paratuberculosis microevolution and mixed strain infections. Microbiol Spectr 2023; 11:e0171623. [PMID: 37584606 PMCID: PMC10581078 DOI: 10.1128/spectrum.01716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's Disease (JD) in ruminants, which is responsible for significant economic loss to the global dairy industry. Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with genetically distinct strains of a pathogen, whereas within-host changes in an infecting strain leading to genetically distinguishable progeny is called microevolution. The two processes can influence host-pathogen dynamics, disease progression and outcomes, but not much is known about their prevalence and impact on JD. Therefore, we obtained up to 10 MAP isolates each from 14 high-shedding animals and subjected them to whole-genome sequencing. Twelve of the 14 animals examined showed evidence for the presence of MSIs and microevolution, while the genotypes of MAP isolates from the remaining two animals could be attributed solely to microevolution. All MAP isolates that were otherwise isogenic had differences in short sequence repeats (SSRs), of which SSR1 and SSR2 were the most diverse and homoplastic. Variations in SSR1 and SSR2, which are located in ORF1 and ORF2, respectively, affect the genetic reading frame, leading to protein products with altered sequences and computed structures. The ORF1 gene product is predicted to be a MAP surface protein with possible roles in host immune modulation, but nothing could be inferred regarding the function of ORF2. Both genes are conserved in Mycobacterium avium complex members, but SSR1-based modulation of ORF1 reading frames seems to only occur in MAP, which could have potential implications on the infectivity of this pathogen. IMPORTANCE Johne's disease (JD) is a major problem in dairy animals, and concerns have been raised regarding the association of Mycobacterium avium subsp. paratuberculosis (MAP) with Crohn's disease in humans. MAP is an extremely slow-growing bacterium with low genome evolutionary rates. Certain short sequence repeats (SSR1 and SSR2) in the MAP chromosome are highly variable and evolve at a faster rate than the rest of the chromosome. In the current study, multiple MAP isolates with genetic variations such as single-nucleotide polymorphisms, and more noticeably, diverse SSRs, could simultaneously infect animals. Variations in SSR1 and SSR2 affect the products of the respective genes containing them. Since multiple MAP isolates can infect the same animal and the possibility that the pathogen undergoes further changes within the host due to unstable SSRs, this could provide a compensative mechanism for an otherwise slow-evolving pathogen to increase phenotypic diversity for overcoming host responses.
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Affiliation(s)
- Alexander Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Séverine Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
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Shibabaw A, Gelaw B, Ghanem M, Legall N, Schooley AM, Soehnlen MK, Salvador LCM, Gebreyes W, Wang SH, Tessema B. Molecular epidemiology and transmission dynamics of multi-drug resistant tuberculosis strains using whole genome sequencing in the Amhara region, Ethiopia. BMC Genomics 2023; 24:400. [PMID: 37460951 DOI: 10.1186/s12864-023-09502-2] [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: 03/14/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
BACKGROUND Drug resistant Mycobacterium tuberculosis prevention and care is a major challenge in Ethiopia. The World health organization has designated Ethiopia as one of the 30 high burden multi-drug resistant tuberculosis (MDR-TB) countries. There is limited information regarding genetic diversity and transmission dynamics of MDR-TB in Ethiopia. OBJECTIVE To investigate the molecular epidemiology and transmission dynamics of MDR-TB strains using whole genome sequence (WGS) in the Amhara region. METHODS Forty-five MDR-TB clinical isolates from Amhara region were collected between 2016 and 2018, and characterized using WGS and 24-loci Mycobacterium Interspersed Repetitive Units Variable Number of Tandem Repeats (MIRU-VNTR) typing. Clusters were defined based on the maximum distance of 12 single nucleotide polymorphisms (SNPs) or alleles as the upper threshold of genomic relatedness. Five or less SNPs or alleles distance or identical 24-loci VNTR typing is denoted as surrogate marker for recent transmission. RESULTS Forty-one of the 45 isolates were analyzed by WGS and 44% (18/41) of the isolates were distributed into 4 clusters. Of the 41 MDR-TB isolates, 58.5% were classified as lineage 4, 36.5% lineage 3 and 5% lineage 1. Overall, TUR genotype (54%) was the predominant in MDR-TB strains. 41% (17/41) of the isolates were clustered into four WGS groups and the remaining isolates were unique strains. The predominant cluster (Cluster 1) was composed of nine isolates belonging to lineage 4 and of these, four isolates were in the recent transmission links. CONCLUSIONS Majority of MDR-TB strain cluster and predominance of TUR lineage in the Amhara region give rise to concerns for possible ongoing transmission. Efforts to strengthen TB laboratory to advance diagnosis, intensified active case finding, and expanded contact tracing activities are needed in order to improve rapid diagnosis and initiate early treatment. This would lead to the interruption of the transmission chain and stop the spread of MDR-TB in the Amhara region.
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Affiliation(s)
- Agumas Shibabaw
- Department of Medical Laboratory Sciences, College of Medicine and Health Sciences, Wollo University, Dessie, Ethiopia.
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA.
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia.
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA.
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA.
| | - Baye Gelaw
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Mostafa Ghanem
- Department of Veterinary Medicine, Virginia-Maryland College of Veterinary Medicine, University of Maryland, College Park, MD, USA
| | - Noah Legall
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Angie M Schooley
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Marty K Soehnlen
- Michigan Department of Health and Human Services, Infectious disease, Lansing, MI, USA
| | - Liliana C M Salvador
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and life sciences, University of Arizona, Tucson, AZ, USA
| | - Wondwossen Gebreyes
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Shu-Hua Wang
- Global One Health Initiative (GOHi), The Ohio State University, Columbus, OH, USA
- Department of Internal Medicine, Division of Infectious Diseases, College of Medicine, The Ohio State University, Columbus, OH, USA
| | - Belay Tessema
- Department of Medical Microbiology, School of Medical Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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Marianelli C, Verrubbi V, Pruiti Ciarello F, Ippolito D, Pacciarini ML, Di Marco Lo Presti V. Geo-epidemiology of animal tuberculosis and Mycobacterium bovis genotypes in livestock in a small, high-incidence area in Sicily, Italy. Front Microbiol 2023; 14:1107396. [PMID: 37007490 PMCID: PMC10063800 DOI: 10.3389/fmicb.2023.1107396] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 02/23/2023] [Indexed: 03/19/2023] Open
Abstract
IntroductionThe persistence of animal tuberculosis (TB) in livestock is a major concern in Sicily, Italy. The objective of this study was to elucidate the transmission dynamics of M. bovis infection in a highly circumscribed, and at the same time geographically diverse, high-risk area of the island through an in-depth geo-epidemiological investigation of TB in cattle and black pigs raised in small-scale extensive farms across the district of Caronia.MethodsWe used genotype analysis coupled with geographic information system (GIS) technology and phylogenetic inference to characterize the spatial distribution of TB and M. bovis genotypes in livestock and the genetic relationships between M. bovis isolates. A total of 589 M. bovis isolates collected from slaughtered cattle (n = 527) and Sicilian black pigs (n = 62) over a 5-year period (2014–2018) were included in the study.ResultsTB was widespread throughout the district and was most frequent in the north-central area of the district, especially along one of the district’s streams. We identified a total of 62 M. bovis genotypes. Identical genetic profiles were isolated from both neighboring and non-neighburing herds. The 10 most frequent genotypes, accounting for 82% of M. bovis isolates, showed geographic specificities in that they tended to cluster in specific spatial niches. The landscape structure of these niches—i.e. steep slopes, rocky ridges, meadows and streams—is likely to have had a significant influence on the distribution of TB among livestock in Caronia. Higher concentrations of TB were observed along streams and in open meadows, while rocky ridges and slopes appeared to have hampered the spread of TB.DiscussionThe geographical distribution of TB cases among livestock in Caronia is consistent with several epidemiological scenarios (e.g., high density of infected herds along the streams or in hilly plateau where livestock share pastures). Landscape structure is likely to play an important role in the transmission and persistence of M. bovis infection across the district. Additional potential risk factors, such as livestock trading and extensive breeding methods, are also discussed. Our results will contribute to the improvement of surveillance, control and eradication activities of TB in Sicily by the implementation of ad hoc TB control measures, especially in farms located along streams, sharing common pastures or with mixed animal species.
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Affiliation(s)
- Cinzia Marianelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
- *Correspondence: Cinzia Marianelli,
| | - Vladimiro Verrubbi
- Agenzia nazionale per le nuove tecnologie, l’energia e lo sviluppo economico sostenibile, Rome, Italy
| | - Flavia Pruiti Ciarello
- Istituto Zooprofilattico Sperimentale della Sicilia, Sezione Diagnostica Barcellona Pozzo di Gotto, Barcellona Pozzo di Gotto, Italy
| | - Dorotea Ippolito
- Istituto Zooprofilattico Sperimentale della Sicilia, Sezione Diagnostica Barcellona Pozzo di Gotto, Barcellona Pozzo di Gotto, Italy
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Vincenzo Di Marco Lo Presti
- Istituto Zooprofilattico Sperimentale della Sicilia, Sezione Diagnostica Barcellona Pozzo di Gotto, Barcellona Pozzo di Gotto, Italy
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Gürer Giray B, Aslantürk A, Şimşek H, Özgür D, Kılıç S, Aslan G. Determination of genetic diversity of multidrug-resistant Mycobacterium tuberculosis strains in Turkey using 15 locus MIRU-VNTR and spoligotyping methods. Pathog Glob Health 2023; 117:85-91. [PMID: 35642888 PMCID: PMC9848327 DOI: 10.1080/20477724.2022.2084807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Tuberculosis (TB) remains the leading cause of deaths from infectious disease worldwide. Nowadays, the tendency of Mycobacterium tuberculosis complex (MTBC) to spread between continents due to uncontrolled migration movements shows that TB is a global health problem. The number of studies for the detection of MTBC strains' epidemiological features in areas with TB spread risk using molecular-based methods such as spoligotyping and Mycobacterial Interspersed Repetitive Unit (MIRU) Variable Number Tandem Repeats (VNTR) at the clonal level is insufficient. In this study, it was aimed to determine the phylogenetic relationships of MTBC strains at the species level by spoligotyping and 15 locus MIRU-VNTR (MIRU-VNTR15) molecular methods of 96 multidrug-resistant (MDR) MTBC strains isolated from sputum samples of patients with a preliminary diagnosis of pulmonary TB or suspected contact history those sent to National Tuberculosis Reference Laboratory from the centers that are members of the Tuberculosis Laboratory Surveillance Network. The phylogenetic relationship between 96 MDR-TB strains was investigated with the combination of bead-based spoligotyping and MIRU-VNTR15 methods on the MAGPIX® Milliplex Map device. In this study, it was determined that the T1 family is more common in our country and LAM7-TUR family is less common than the Beijing family unlike other studies. It was determined that the strains in the same cluster had different locus profiles, and there was no transmission from the same clone in the clonal typing we performed with spoligotyping and MIRU-VNTR15.
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Affiliation(s)
- Burcu Gürer Giray
- Ankara Provincial Health Directorate Public Health Molecular Diagnosis Laboratory, Ankara, Turkey,CONTACT Burcu Gürer Giray Molecular Diagnosis Laboratory, Public Health Institution of Ankara, Turkey
| | - Ahmet Aslantürk
- National Tuberculosis Reference Laboratory, Public Health Institution of Turkey (PHIT), Ankara, Turkey
| | - Hülya Şimşek
- Faculty of Medicine, Department of Medical Microbiology, Yozgat Bozok University, Yozgat, Turkey
| | - Didem Özgür
- Department of Medical Microbiology, Kafkas University, Kars, Turkey
| | - Selçuk Kılıç
- Department of Medical CBRN, University of Health Sciences, Institute of Dedenxe Health Sciences, Ankara, Turkey
| | - Gönül Aslan
- Mersin University Faculty of Medicine, Department of Medical Microbiology, Mersin, Turkey
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Kashi P, Pakdel F, Barhaghi MHS, Rezaee MA, Taghizadeh S, Sadeghi J, Yousefi M, Ghotaslou R, Asgharzadeh M, Gholizadeh P, Kafil HS. Genetic diversity of Mycobacterium tuberculosis isolates from northwest of Iran during COVID-19 era. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023; 24:3. [PMID: 37519898 PMCID: PMC9829222 DOI: 10.1186/s43042-023-00383-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 12/31/2022] [Indexed: 01/11/2023] Open
Abstract
Background Tuberculosis (TB) is considered one of the most infectious diseases in the world. In this study, we intended to examine the epidemiology of tuberculosis by MIRU-VNTR to define the changes that occur in the transmission of tuberculosis in the region during the COVID-19 era. A total of 120 Mycobacterium tuberculosis isolates were collected from sputum samples of patients referred to East Azerbaijan Center TB from December 2020 to August 2021. Demographic information such as age, sex, place of birth, previous TB history, and relevant medical data was collected. The proportion method was performed for drug susceptibility testing, and the PCR-based MIRU-VNTR method was applied to identify molecular epidemiology relationships. Results The isolates were collected from 78 male (65%) and 39 female (32.5%) Iranian patients and 3 (2.5%) Azerbaijani patients. Ninety-three distinct patterns were identified including 15 clustered patterns and 36 unique patterns. The largest cluster was composed of seven isolates. Furthermore, one cluster with 5 members, four clusters with 3 members, and nine clusters with 2 members. In MIRU-VNTR typing, 75 clusters belonged to the Tabriz region and just 3 to the Republic of Azerbaijan. All isolates were sensitive to rifampin, isoniazid, and ethambutol. Conclusions Results of the current study showed COVID-19 pandemic had a direct effect on the transmission and diagnosis of tuberculosis. Less diagnosis and less clustering can indicate public controls and hygiene, and the use of masks had a direct effect on the transmission and diagnosis of tuberculosis. However, misidentification and less focus on other respiratory infections are expected during the pandemic. Studies on the co-infection of COVID-19 and tuberculosis and the role of mask and sanitization against TB are strongly recommended.
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Affiliation(s)
- Peyvand Kashi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farzaneh Pakdel
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Sepehr Taghizadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Javid Sadeghi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Yousefi
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Reza Ghotaslou
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Asgharzadeh
- Biotechnology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Rache L, Blondin L, Diaz Tatis P, Flores C, Camargo A, Kante M, Wonni I, López C, Szurek B, Dupas S, Pruvost O, Koebnik R, Restrepo S, Bernal A, Vernière C. A minisatellite-based MLVA for deciphering the global epidemiology of the bacterial cassava pathogen Xanthomonas phaseoli pv. manihotis. PLoS One 2023; 18:e0285491. [PMID: 37167330 PMCID: PMC10174486 DOI: 10.1371/journal.pone.0285491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 04/25/2023] [Indexed: 05/13/2023] Open
Abstract
Cassava Bacterial Blight (CBB) is a destructive disease widely distributed in the different areas where this crop is grown. Populations studies have been performed at local and national scales revealing a geographical genetic structure with temporal variations. A global epidemiology analysis of its causal agent Xanthomonas phaseoli pv. manihotis (Xpm) is needed to better understand the expansion of the disease for improving the monitoring of CBB. We targeted new tandem repeat (TR) loci with large repeat units, i.e. minisatellites, that we multiplexed in a scheme of Multi-Locus Variable number of TR Analysis (MLVA-8). This genotyping scheme separated 31 multilocus haplotypes in three clusters of single-locus variants and a singleton within a worldwide collection of 93 Xpm strains isolated over a period of fifty years. The major MLVA-8 cluster 1 grouped strains originating from all countries, except the unique Chinese strain. On the contrary, all the Xpm strains genotyped using the previously developed MLVA-14 microsatellite scheme were separated as unique haplotypes. We further propose an MLVA-12 scheme which takes advantage of combining TR loci with different mutation rates: the eight minisatellites and four faster evolving microsatellite markers, for global epidemiological surveillance. This MLVA-12 scheme identified 78 haplotypes and separated most of the strains in groups of double-locus variants (DLV) supporting some phylogenetic relationships. DLV groups were subdivided into closely related clusters of strains most often sharing the same geographical origin and isolated over a short period, supporting epidemiological relationships. The main MLVA-12 DLV group#1 was composed by strains from South America and all the African strains. The MLVA-12 scheme combining both minisatellite and microsatellite loci with different discriminatory power is expected to increase the accuracy of the phylogenetic signal and to minimize the homoplasy effects. Further investigation of the global epidemiology of Xpm will be helpful for a better control of CBB worldwide.
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Affiliation(s)
- Leidy Rache
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C., Colombia
| | - Laurence Blondin
- CIRAD, UMR PHIM, Montpellier, France
- Plant Health Institute of Montpellier (PHIM), Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Paula Diaz Tatis
- Facultad de Ciencias, Universidad Antonio Nariño, Bogotá, Colombia
| | - Carolina Flores
- Plant Health Institute of Montpellier (PHIM), Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Andrea Camargo
- Facultad de Ciencias, Universidad Antonio Nariño, Bogotá, Colombia
| | - Moussa Kante
- Plant Health Institute of Montpellier (PHIM), Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Issa Wonni
- INERA, LMI Pathobios, Bobo Dioulasso, Burkina Faso
| | - Camilo López
- Departamento de Biología, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Boris Szurek
- Plant Health Institute of Montpellier (PHIM), Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Stephane Dupas
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C., Colombia
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Silvia Restrepo
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C., Colombia
| | - Adriana Bernal
- Department of Biological Sciences, Universidad de los Andes, Bogotá D.C., Colombia
| | - Christian Vernière
- Plant Health Institute of Montpellier (PHIM), Université Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
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10
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Gaballah A, Ghazal A, Almiry R, Hussein S, Emad R, El-Sherbini E. Fingerprinting of Mycobacterium tuberculosis isolates by MIRU-VNTR genotyping and detection of isoniazid resistance by real-time PCR. J Med Microbiol 2022; 71. [DOI: 10.1099/jmm.0.001603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Tuberculosis (TB) is a great public health problem in developing countries such as Egypt. Genotyping of
Mycobacterium tuberculosis
isolates has a prominent role in the field of TB prevention.
Aim. This study aimed to evaluate real-time PCR using Minor Groove Binder (MGB) probes and to identify circulating lineages/sub-lineages of
M. tuberculosis
and their transmission patterns.
Hypothesis. We hypothesize that MIRU-VNTR technique is efficient in identifying circulating
M. tuberculosis
lineages in Egypt.
Methodology. Fifty sputum specimens positive for acid-fast bacilli were included. Isoniazid (INH) resistance was detected using the 1 % proportion method. Real-time PCR using MGB-probes was used for simultaneous detection of TB infection and INH resistance. Partial sequencing of the katG gene was used to confirm INH resistance results. A standard 15 Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (15-MIRU-VNTR) approach was used for genotyping through the MIRU-VNTRplus online platform.
Results. Only seven specimens showed phenotypic resistance to INH.
M. tuberculosis
was detected in all samples, while a mutation in the katG gene codon 315 was detected only in five samples, which were also phenotypically INH-resistant. Sequencing of the katG gene showed codon 315 mutation genotypically and phenotypically in the five INH-resistant isolates. Molecular genotyping of
M. tuberculosis
isolates revealed that the majority of isolates (26/50, 52 %) belonged to the S family of lineage_4. A low clustering rate (2 %) was observed among our isolates. According to the Hunter-Gaston Discriminatory Index (HGDI), 11 MIRU-VNTR loci were highly or moderately discriminative, while four loci were less polymorphic.
Conclusion. MIRU-VNTR genotyping revealed a low clustering rate with a low recent transmission rate of
M. tuberculosis
strains in Alexandria, Egypt.
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Affiliation(s)
- Ahmed Gaballah
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Abeer Ghazal
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
| | - Reda Almiry
- Department of Clinical Pathology, Alexandria Armed Forces Hospital, Alexandria, Egypt
| | - Somaya Hussein
- Elmamoura Chest Hospital, Egyptian Ministry of Health, Alexandria, Egypt
| | - Rasha Emad
- Alexandria Main University Hospital, Alexandria University, Alexandria, Egypt
| | - Eglal El-Sherbini
- Department of Microbiology, Medical Research Institute, Alexandria University, Egypt
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11
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Sousa EDO, Carneiro RTDO, Montes FCOF, Conceição EC, Bartholomay P, Marinho JM, Lima KVB, Natividade MSD, Araújo WND, Matos ED, Barbosa T. Laboratory-based study of drug resistance and genotypic profile of multidrug-resistant tuberculosis isolates in Salvador, Bahia, Brazil. Rev Soc Bras Med Trop 2022; 55:e00132022. [PMID: 35894395 PMCID: PMC9359346 DOI: 10.1590/0037-8682-0013-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 05/20/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Surveillance of multidrug resistant/extensively drug-resistant tuberculosis (MDR/XDR-TB) is essential to guide disease dissemination control measures. Brazil contributes to a significant fraction of tuberculosis (TB) cases worldwide, but only few reports addressed MDR/XDR-TB in the country. Methods: This cross-sectional, laboratory-based study describes the phenotypic resistance profiles of isolates obtained between January 2008 and December 2011 in Bahia, Brazil, and sociodemographic, epidemiological, and clinical characteristics (obtained from mandatory national registries) of the corresponding 204 MDR/XDR-TB patients. We analyzed the mycobacterial spoligotyping and variable number of tandem repeats of mycobacterial interspersed repetitive units in 12-loci profiles obtained from Salvador. Results: MDR/XDR-TB patients were predominantly male, had a median age of 43 years, belonged to black ethnicity, and failed treatment before MDR-TB diagnosis. Nearly one-third of the isolates had phenotypic resistance (evaluated by mycobacteria growth indicator tube assay) to second-line anti-TB drugs (64/204, 31%), of which 22% cases (14/64) were diagnosed as XDR-TB. Death was a frequent outcome among these individuals and was associated with resistance to second-line anti-TB drugs. Most isolates successfully genotyped belonged to the Latin-American Mediterranean (LAM) Family, with an unprecedented high proportion of LAM10-Cameroon subfamily bacilli. More than half of these isolates were assigned to a unique cluster by the genotyping methods performed. Large clusters of identical genotypes were also observed among LAM SIT42 and SIT376 strains. Conclusions: We highlight the need for strengthening local and national efforts to perform early detection of TB drug resistance and to prevent treatment discontinuation to limit the emergence of drug-resistant strains.
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Affiliation(s)
- Erivelton de Oliveira Sousa
- Laboratório Central de Saúde Pública Professor Gonçalo Moniz (LACEN-BA), Salvador, BA, Brasil.,Fundação Oswaldo Cruz, Instituto de Pesquisa Gonçalo Moniz, Salvador, BA, Brasil
| | | | | | - Emilyn Costa Conceição
- Universidade Federal do Rio de Janeiro, Instituto de Microbiologia Paulo de Góes, Rio de Janeiro, RJ, Brasil
| | | | - Jamocyr Moura Marinho
- Escola Baiana de Medicina e Saúde Pública, Faculdade de Medicina, Salvador, Bahia, Brasil
| | | | | | | | - Eliana Dias Matos
- Escola Baiana de Medicina e Saúde Pública, Faculdade de Medicina, Salvador, Bahia, Brasil
| | - Theolis Barbosa
- Fundação Oswaldo Cruz, Instituto de Pesquisa Gonçalo Moniz, Salvador, BA, Brasil.,Rede Brasileira de Pesquisa em Tuberculose, Rio de Janeiro, RJ, Brasil
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12
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Kashi P, Pakdel F, Barhaghi MHS, Rezaee MA, Taghizadeh S, Sadeghi J, Yousefi M, Ghotaslou R, Asgharzadeh M, Gholizadeh P, Kafil HS. Genetic diversity of Mycobacterium tuberculosis isolates from northwest of Iran during Covid-19 era. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2022.101572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Genetic Diversity and Transmission of Multidrug Resistant Mycobacterium tuberculosis strains in Lusaka, Zambia. Int J Infect Dis 2021; 114:142-150. [PMID: 34718155 DOI: 10.1016/j.ijid.2021.10.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVE Zambia is among the 30 high tuberculosis burden countries in the world. Despite increasing reports of multidrug resistant tuberculosis (MDR-TB) in routine surveillance, information on the transmission of MDR Mycobacterium tuberculosis strains is largely unknown. This study elucidated genetic diversity and transmission of MDR M. tuberculosis strains in Lusaka, Zambia. METHODS Eighty-five MDR M. tuberculosis samples collected from the year 2013 to 2017 at the University Teaching Hospital were used. Drug-resistance associated gene sequencing, spoligotyping, 24-loci mycobacterial interspersed repetitive units-variable number of tandem repeats, and multiplex PCR for RD-Rio sub-lineage identification were applied. RESULTS Clades identified were LAM (48%), CAS (29%), T (14%), X (6%) and Harlem (2%). Strains belonging to SITs 21/CAS1-Kili and 20/LAM1 formed the largest clonal complexes. Combined spoligotyping and 24 loci-MIRU-VNTR revealed 47 genotypic patterns with clustering rate of 63%. Ninety five percent of LAM strains belonged to RD-Rio sub-lineage. CONCLUSION The high clustering rate suggested that a large proportion of MDR-TB was due to recent transmission rather than independent acquisition of MDR. This spread was attributed to clonal expansion of SIT21/CAS1-Kili and SIT20/LAM1 strains. Therefore, TB control programs recommending genotyping coupled with conventional epidemiological methods can guide measures for stopping the spread of MDR-TB.
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14
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Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, Robène I, Studholme DJ, Tavares F, Vicente JG, Koebnik R, Costa J. Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms 2021; 9:862. [PMID: 33923763 PMCID: PMC8073235 DOI: 10.3390/microorganisms9040862] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 11/17/2022] Open
Abstract
Bacteria in the genus Xanthomonas infect a wide range of crops and wild plants, with most species responsible for plant diseases that have a global economic and environmental impact on the seed, plant, and food trade. Infections by Xanthomonas spp. cause a wide variety of non-specific symptoms, making their identification difficult. The coexistence of phylogenetically close strains, but drastically different in their phenotype, poses an added challenge to diagnosis. Data on future climate change scenarios predict an increase in the severity of epidemics and a geographical expansion of pathogens, increasing pressure on plant health services. In this context, the effectiveness of integrated disease management strategies strongly depends on the availability of rapid, sensitive, and specific diagnostic methods. The accumulation of genomic information in recent years has facilitated the identification of new DNA markers, a cornerstone for the development of more sensitive and specific methods. Nevertheless, the challenges that the taxonomic complexity of this genus represents in terms of diagnosis together with the fact that within the same bacterial species, groups of strains may interact with distinct host species demonstrate that there is still a long way to go. In this review, we describe and discuss the current molecular-based methods for the diagnosis and detection of regulated Xanthomonas, taxonomic and diversity studies in Xanthomonas and genomic approaches for molecular diagnosis.
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Affiliation(s)
- Vittoria Catara
- Department of Agriculture, Food and Environment, University of Catania, 95125 Catania, Italy
| | - Jaime Cubero
- National Institute for Agricultural and Food Research and Technology (INIA), 28002 Madrid, Spain;
| | - Joël F. Pothier
- Environmental Genomics and Systems Biology Research Group, Institute for Natural Resource Sciences, Zurich University of Applied Sciences (ZHAW), 8820 Wädenswil, Switzerland;
| | - Eran Bosis
- Department of Biotechnology Engineering, ORT Braude College of Engineering, Karmiel 2161002, Israel;
| | - Claude Bragard
- UCLouvain, Earth & Life Institute, Applied Microbiology, 1348 Louvain-la-Neuve, Belgium;
| | - Edyta Đermić
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
| | - Maria C. Holeva
- Benaki Phytopathological Institute, Scientific Directorate of Phytopathology, Laboratory of Bacteriology, GR-14561 Kifissia, Greece;
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS-Ouest, Univ Angers, SFR 4207 QUASAV, 49071 Beaucouzé, France;
| | - Francoise Petter
- European and Mediterranean Plant Protection Organization (EPPO/OEPP), 75011 Paris, France;
| | - Olivier Pruvost
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | - Isabelle Robène
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, La Réunion, France; (O.P.); (I.R.)
| | | | - Fernando Tavares
- CIBIO—Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal; or
- FCUP-Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
| | | | - Ralf Koebnik
- Plant Health Institute of Montpellier (PHIM), Univ Montpellier, Cirad, INRAe, Institut Agro, IRD, 34398 Montpellier, France;
| | - Joana Costa
- Centre for Functional Ecology-Science for People & the Planet, Department of Life Sciences, University of Coimbra, 300-456 Coimbra, Portugal
- Laboratory for Phytopathology, Instituto Pedro Nunes, 3030-199 Coimbra, Portugal
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15
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Ordaz-Vázquez A, Soberanis-Ramos O, Cruz-Huerta E, Retis-Sanchez-de-la-Barquera S, Chávez-Mazari B, Gudiño-Enriquez T, Santacruz-Aguilar M, Ponce-De-León-Garduño A, Sifuentes-Osornio J, Bobadilla-Del-Valle M. Genetic diversity of Mycobacterium bovis evaluated by spoligotyping and MIRU-VNTR in an intensive dairy cattle breeding area in Mexico. Transbound Emerg Dis 2021; 69:1144-1154. [PMID: 33725428 DOI: 10.1111/tbed.14074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 01/22/2021] [Accepted: 03/12/2021] [Indexed: 11/29/2022]
Abstract
Bovine tuberculosis (bTB) is mainly caused by Mycobacterium bovis. In Mexico, dairy cattle play an important role in the persistence and spread of the bacillus. In order to describe M. bovis genetic diversity, we genotyped a total of 132 strains isolated from slaughtered cattle with bTB suggestive lesions between 2009 and 2010 in Hidalgo, Mexico, using a panel of 9-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) and spoligotyping. We found 21 spoligotypes, and 124 isolates were grouped in 13 clusters. The most frequent spoligotypes were SB0121 (49, 37.1%) and SB0673 (27, 20.5%); three new spoligotypes were reported SB02703, SB02704 and SB02705. We observed 37 MIRU-VNTR patterns, 107 isolates were grouped in 12 clusters and 25 isolates were unique. Spoligotypes SB0121, SB0673, SB0140, SB0145 and SB0120 showed marked subdivision applying MIRU-VNTR method; meanwhile, spoligotypes SB0971 and SB0327 showed single MIRU-VNTR profiles. The Hunter-Gaston discriminatory index (HGDI) was 0.88, 0.78 and 0.90 for 9-loci MIRU-VNTR, spoligotyping and both methods, respectively. Additionally, allelic diversity (h) analysis showed high diversity for QUB3232, QUB26 and QUB11b with h = 0.79, 0.66 and 0.63, respectively. Overall, high genetic variability was observed among M. bovis isolates. Thus, the use of 9-loci MIRU-VNTR panel is enough to describe genetic diversity, evolution and distribution of M. bovis. This study supports the use of these tools for subsequent epidemiological studies in high incidence areas.
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Affiliation(s)
- Anabel Ordaz-Vázquez
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Orbelin Soberanis-Ramos
- Department of Preventive Medicine and Public Health, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Edith Cruz-Huerta
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Sandra Retis-Sanchez-de-la-Barquera
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Bárbara Chávez-Mazari
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Tomasa Gudiño-Enriquez
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | | | - Alfredo Ponce-De-León-Garduño
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - José Sifuentes-Osornio
- Department of Medicine, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Miriam Bobadilla-Del-Valle
- Laboratory of Clinical Microbiology, Department of Infectious Diseases, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
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16
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Hassan WMM, Tawab AAAE, El-Shannat SM. Current advances in molecular subtyping using multilocus variable number of tandem repeat analysis of Salmonella Enteritidis and Salmonella Typhimurium in Egyptian chickens. Vet World 2020; 13:2252-2259. [PMID: 33281364 PMCID: PMC7704301 DOI: 10.14202/vetworld.2020.2252-2259] [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: 06/08/2020] [Accepted: 09/21/2020] [Indexed: 11/23/2022] Open
Abstract
Aim: This study aimed to characterize the genetic diversity, evolutionary level, and prevalence of genotypes of common isolates of Salmonella (Salmonella Enteritidis and Salmonella Typhimurium). Using one of the most advanced molecular recognition techniques, multilocus variable number of tandem repeat analysis (MLVA), we characterized the genotype and prevalence of S. Enteritidis and S. Typhimurium. Materials and Methods: One hundred and twenty-five internal organ samples were collected from the major chicken slaughterhouses in Egypt, and Salmonella species were isolated. PCR was utilized to amplify the IE-1 and Flic-C genes to identify S. Enteritidis and S. Typhimurium DNA, respectively, from Salmonella isolates. MLVA was applied on nine samples of S. Enteritidis DNA and three samples of S. Typhimurium DNA. Six variable number tandem repeat (VNTR) loci (Sal02, Sal04, Sal06, Sal10, Sal20, and Sal23) were amplified. Results: Of the examined samples (n=125), a total of 12 isolates (9.6%) were either identified as Enteritidis or Typhimurium. PCR-mediated amplification of IE-1 and Flic-C revealed that 75% (n=9) of the 12 Salmonella isolates were S. Enteritidis and 25% (n=3) were S. Typhimurium. The six loci amplified through MLVA had allelic diversity. The most discriminatory heterogenic locus for S. Enteritidis was Sal20. Sal04 and Sal23 were the most discriminatory heterogenic loci for S. Typhimurium. VNTR allelic profile analysis revealed nine unique genotypes for S. Enteritidis and three for S. Typhimurium. Conclusion: This study was the first to use MLVA analysis to identify S. Enteritidis and S. Typhimurium strains isolated from chickens in Egypt. The molecular typing data reported herein allowed us to characterize the genotypes of S. Enteritidis and S. Typhimurium that are most prevalent in Egyptian chickens. Moreover, this epidemiological information provides valuable insight on how to prevent disease transmission. Moreover, our methods provide an alternative to traditional serotyping techniques that may produce inaccurate strain identifications for organisms with rough lipopolysaccharide structures.
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Affiliation(s)
- Wafaa M M Hassan
- Reference Laboratory for Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza, Egypt
| | - Ashraf A Abd El Tawab
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Sara M El-Shannat
- Department of Microbiology, Animal Health Research Institute, Marsa Matruh, Egypt
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17
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Outhred AC, Gurjav U, Jelfs P, McCallum N, Wang Q, Hill-Cawthorne GA, Marais BJ, Sintchenko V. Extensive Homoplasy but No Evidence of Convergent Evolution of Repeat Numbers at MIRU Loci in Modern Mycobacterium tuberculosis Lineages. Front Public Health 2020; 8:455. [PMID: 32974265 PMCID: PMC7481465 DOI: 10.3389/fpubh.2020.00455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
More human deaths have been attributable to Mycobacterium tuberculosis than any other pathogen, and the epidemic is sustained by ongoing transmission. Various typing schemes have been developed to identify strain-specific differences and track transmission dynamics in affected communities, with recent introduction of whole genome sequencing providing the most accurate assessment. Mycobacterial interspersed repetitive unit (MIRU) typing is a family of variable number tandem repeat schemes that have been widely used to study the molecular epidemiology of M. tuberculosis. MIRU typing was used in most well-resourced settings to perform routine molecular epidemiology. Instances of MIRU homoplasy have been observed in comparison with sequence-based phylogenies, limiting its discriminatory value. A fundamental question is whether the observed homoplasy arises purely through stochastic processes, or whether there is evidence of natural selection. We compared repeat numbers at 24 MIRU loci with a whole genome sequence-based phylogeny of 245 isolates representing three modern M. tuberculosis lineages. This analysis demonstrated extensive homoplasy of repeat numbers, but did not detect any evidence of natural selection of repeat numbers, at least since the ancestral branching of the three modern lineages of M. tuberculosis. In addition, we observed good sensitivity but poor specificity and positive predictive values of MIRU-24 to detect clusters of recent transmission, as defined by whole-genome single nucleotide polymorphism analysis. These findings provide mechanistic insight, and support a transition away from VNTR-based typing toward sequence-based typing schemes for both research and public health purposes.
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Affiliation(s)
- Alexander C. Outhred
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Children's Hospital at Westmead, Sydney, NSW, Australia
- Center for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Ulziijargal Gurjav
- Department of Microbiology and Immunology, Mongolian National University of Medical Sciences, Ulaanbaatar, Mongolia
| | - Peter Jelfs
- Center for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research—NSW Health Pathology, Sydney, NSW, Australia
| | - Nadine McCallum
- Deep Seq Lab, Queen's Medical Center, University of Nottingham, Nottingham, United Kingdom
| | - Qinning Wang
- Center for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Grant A. Hill-Cawthorne
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Ben J. Marais
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Children's Hospital at Westmead, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- Center for Infectious Diseases and Microbiology—Public Health, Westmead Hospital, Sydney, NSW, Australia
- NSW Mycobacterium Reference Laboratory, Center for Infectious Diseases and Microbiology Laboratory Services, Institute of Clinical Pathology and Medical Research—NSW Health Pathology, Sydney, NSW, Australia
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18
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Méndez MV, Abadía E, Sequera M, de Waard JH, Takiff HE. Most LAM Mycobacterium tuberculosis strains in Venezuela, but not SIT605, belong to the RD Rio subfamily. INFECTION GENETICS AND EVOLUTION 2020; 84:104380. [PMID: 32470631 DOI: 10.1016/j.meegid.2020.104380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 05/21/2020] [Accepted: 05/24/2020] [Indexed: 11/27/2022]
Abstract
Tuberculosis is a global public health problem that is resurgent in Venezuela, with 13 thousand estimated new cases in 2018. Strains of the Mycobacterium tuberculosis RDRio, subfamily belong to the Latín American Mediterranean (LAM) family and are a major cause of TB in Rio de Janeiro, Brazil. LAM strains predominate in Venezuela, where spoligotype SIT605 is common, but surprisingly not found elsewhere. We sought to assess the presence of RDRio strains in tuberculosis patients in different regions of Venezuela and determine whether SIT605 also belongs to the RDRio subfamily. Using spoligotyping and MIRU-VNTR 24 loci, we identified 86 clinical LAM and SIT605 isolates from the Venezuelan capital Caracas and several Venezuelan states. Region of difference deletion loci RD174 and RDRio, and also IS1561 were used to identify strains of the RDRio subfamily, while IS6110 at position 932,204 and the Ag85C103 polymorphism were used to validate SIT 605 as a LAM family strain. We found that 69.8% of the isolates were RDRío, including 94.3% of strains isolated in Caracas, 17.9% isolated in the state of Carabobo, the two strains analyzed from Delta Amacuro, and one each from Sucre, Apure and Aragua states. RDRio was in 100% of: SIT17 (LAM 2); SIT20 (LAM 1); SITs 93, 1694, 1696, 960, 1367 (LAM 5); and SITs 216 (LAM 9); but only 75% of SIT42 (LAM 9) strains. Thus, most of the LAM strains in Venezuela belong to the RDRío subfamily. SIT 605 strains, although LAM, are not in the RDRío subfamily.
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Affiliation(s)
- María Victoria Méndez
- Universidad de Carabobo-Escuela de Bioanálisis-Sede Aragua, Venezuela; Laboratorio de Genética Molecular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela.
| | - Edgar Abadía
- Laboratorio de Genética Molecular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela
| | - Mónica Sequera
- Universidad de Carabobo-Escuela de Ciencias Biomédicas-Sede Carabobo, Venezuela
| | - Jacobus H de Waard
- Instituto de Biomedicina-Universidad Central de Venezuela (UCV), Venezuela; One Health Research Group, Facultad de Ciencias de la Salud, Universidad de Las Américas, Sede Queri, Quito, Ecuador
| | - Howard Eugene Takiff
- Laboratorio de Genética Molecular, Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas 1020A, Venezuela; Pathogenomique Mycobacterienne Integree, Institut Pasteur, Paris, France; Department of Tuberculosis Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
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19
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Molecular characterisation of multidrug-resistant Mycobacterium tuberculosis isolates from a high-burden tuberculosis state in Brazil. Epidemiol Infect 2020; 147:e216. [PMID: 31364547 PMCID: PMC6624858 DOI: 10.1017/s0950268819001006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death among infectious diseases worldwide. Among the estimated cases of drug-resistant TB, approximately 60% occur in the BRICS countries (Brazil, Russia, India, China and South Africa). Among Brazilian states, primary and acquired multidrug-resistant TB (MDR-TB) rates were the highest in Rio Grande do Sul (RS). This study aimed to perform molecular characterisation of MDR-TB in the State of RS, a high-burden Brazilian state. We performed molecular characterisation of MDR-TB cases in RS, defined by drug susceptibility testing, using 131 Mycobacterium tuberculosis (M.tb) DNA samples from the Central Laboratory. We carried out MIRU-VNTR 24loci, spoligotyping, sequencing of the katG, inhA and rpoB genes and RDRio sublineage identification. The most frequent families found were LAM (65.6%) and Haarlem (22.1%). RDRio deletion was observed in 42 (32%) of the M.tb isolates. Among MDR-TB cases, eight (6.1%) did not present mutations in the studied genes. In 116 (88.5%) M.tb isolates, we found mutations associated with rifampicin (RIF) resistance in rpoB gene, and in 112 isolates (85.5%), we observed mutations related to isoniazid resistance in katG and inhA genes. An insertion of 12 nucleotides (CCAGAACAACCC) at the 516 codon in the rpoB gene, possibly responsible for a decreased interaction of RIF and RNA polymerase, was found in 19/131 of the isolates, belonging mostly to LAM and Haarlem families. These results enable a better understanding of the dynamics of transmission and evolution of MDR-TB in the region.
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20
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Tatara MB, Perdigão J, Viveiros M, Kritski A, Silva KED, Sacchi FPC, de Lima CC, Dos Santos PCP, Diniz JDLDCG, Almeida Silva PE, Gomes P, Gomes MMQ, Cunha EAT, Lapa E Silva JR, Portugal I, Croda J, Andrade MKDN. Genetic Diversity and Molecular Epidemiology of Mycobacterium tuberculosis in Roraima State, Brazil. Am J Trop Med Hyg 2020; 101:774-779. [PMID: 31392954 DOI: 10.4269/ajtmh.19-0324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
National border areas are special places for the spread of Mycobacterium tuberculosis (MTB). These regions concentrate vulnerable populations and constant population movements. Understanding the dynamics of the transmission of MTB is fundamental to propose control measures and to monitor drug resistance. We conducted a population-based prospective study of tuberculosis (TB) to evaluate molecular characteristics of MTB isolates circulating in Roraima, a state on the border of Venezuela and Guyana. Eighty isolates were genotyped by IS6110-RFLP (restriction fragment length polymorphism), spoligotyping, and 24-locus mycobacterial interspersed repetitive unit-variable number of repeats tandem (MIRU-VNTR). Drug susceptibility tests were performed by using the proportion method and GeneXpert® MTB/RIF (Cepheid, Sunnyvale, CA). Isolates showing a phenotypic resistance profile were submitted to polymerase chain reaction (PCR) and sequencing. Spoligotyping showed 40 distinct patterns with a high prevalence of Latin-American and Mediterranean (LAM), Haarlem (H), and the "ill-defined" T clades. Mycobacterial interspersed repetitive unit -VNTR and IS6110-RFLP showed clustering rates of 21.3% and 30%, respectively. Drug resistance was detected in 11 (15.1%) isolates, and all were found to have primary resistance; among these, six (8.2%) isolates were streptomycin mono-resistant, four (5.4%) isoniazid mono-resistant, and one (1.3%) multidrug resistant. This is the first study on the molecular epidemiology and drug resistance profile of MTB from Roraima. Herein, we describe high diversity of genetic profiles circulating in this region that may be driven by the introduction of new strain types because of large population flow in this region. In summary, our results showed that analyses of these circulating strains can contribute to a better understanding of TB epidemiology in the northern Brazilian border and be useful to establish public health policies on TB prevention.
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Affiliation(s)
- Mariana Bento Tatara
- Laboratory of Research in Health Science, Faculty of Health Science, Federal University of Grande Dourados, Dourados, Brazil
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Miguel Viveiros
- Institute of Hygiene and Tropical Medicine (IHMT), Global Health and Tropical Medicine (GHTM), University NOVA of Lisbon, Lisbon, Portugal
| | - Afrânio Kritski
- School of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Kesia Esther da Silva
- Laboratory of Research in Health Science, Faculty of Health Science, Federal University of Grande Dourados, Dourados, Brazil
| | | | - Camila Camioli de Lima
- Laboratory of Research in Health Science, Faculty of Health Science, Federal University of Grande Dourados, Dourados, Brazil
| | - Paulo César Pereira Dos Santos
- Laboratory of Research in Health Science, Faculty of Health Science, Federal University of Grande Dourados, Dourados, Brazil
| | | | - Pedro Eduardo Almeida Silva
- Nucleus of Research in Medical Microbiology, Faculty of Medicine, Federal University of Rio Grande, Rio Grande, Brazil
| | - Pedro Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | | | | | | | - Isabel Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, University of Lisbon, Lisbon, Portugal
| | - Julio Croda
- School of Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Brazil.,Oswaldo Cruz Foundation, Campo Grande, Brazil
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21
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Salvato RS, Costa ERD, Reis AJ, Schiefelbein SH, Halon ML, Barcellos RB, Unis G, Dias CF, Viveiros M, Portugal I, da Silva PEA, Kritski AL, Perdigão J, Rossetti MLR. First insights into circulating XDR and pre-XDR Mycobacterium tuberculosis in Southern Brazil. INFECTION GENETICS AND EVOLUTION 2020; 78:104127. [DOI: 10.1016/j.meegid.2019.104127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2019] [Revised: 11/20/2019] [Accepted: 11/24/2019] [Indexed: 11/30/2022]
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22
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Trends in Mycobacterium tuberculosis Transmission During a 10-year Period (2006-2016) in the Northwest of Iran by MIRU-VNTR Molecular Typing. Jundishapur J Microbiol 2020. [DOI: 10.5812/jjm.95891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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23
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Ami VKG, Balasubramanian R, Hegde SR. Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis. BMC Genomics 2020; 21:167. [PMID: 32070281 PMCID: PMC7029489 DOI: 10.1186/s12864-020-6573-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 02/10/2020] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Tuberculosis remains one of the leading causes of morbidity and mortality worldwide. Therefore, understanding the pathophysiology of Mycobacterium tuberculosis is imperative for developing new drugs. Post-transcriptional regulation plays a significant role in microbial adaptation to different growth conditions. While the proteins associated with gene expression regulation have been extensively studied in the pathogenic strain M. tuberculosis H37Rv, post-transcriptional regulation involving small RNAs (sRNAs) remains poorly understood. RESULTS We developed a novel moving-window based approach to detect sRNA expression using RNA-Seq data. Overlaying ChIP-seq data of RNAP (RNA Polymerase) and NusA suggest that these putative sRNA coding regions are significantly bound by the transcription machinery. Besides capturing many experimentally validated sRNAs, we observe the context-dependent expression of novel sRNAs in the intergenic regions of M. tuberculosis genome. For example, ncRv11806 shows expression only in the stationary phase, suggesting its role in mycobacterial latency which is a key attribute to long term pathogenicity. Also, ncRv11875C showed expression in the iron-limited condition, which is prevalent inside the macrophages of the host cells. CONCLUSION The systems level analysis of sRNA highlights the condition-specific expression of sRNAs which might enable the pathogen survival by rewiring regulatory circuits.
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Affiliation(s)
- Vimla Kany G Ami
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India
| | - Rami Balasubramanian
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India
| | - Shubhada R Hegde
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, 560 100, India.
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24
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Phylogenetic diversity of Mycobacterium tuberculosis in two geographically distinct locations in Botswana - The Kopanyo Study. INFECTION GENETICS AND EVOLUTION 2020; 81:104232. [PMID: 32028055 DOI: 10.1016/j.meegid.2020.104232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 01/28/2020] [Accepted: 02/01/2020] [Indexed: 12/18/2022]
Abstract
Mycobacterium tuberculosis complex (MTBC) is divided into several major phylogenetic lineages, with differential distribution globally. Using population-based data collected over a three year period, we performed 24-locus Mycobacterial Interspersed Repeat Unit - Variable Number Tandem Repeat (MIRU-VNTR) genotyping on all culture isolates from two districts of the country that differ in tuberculosis (TB) incidence (Gaborone, the capital, and Ghanzi in the Western Kalahari). The study objective was to characterize the molecular epidemiology of TB in these districts. Overall phylogenetic diversity mirrored that reported from neighboring Republic of South Africa, but differences in the two districts were marked. All four major lineages of M. tuberculosis were found in Gaborone, but only three of the four major lineages were found in Ghanzi. Strain diversity was lower in Ghanzi, with a large proportion (38%) of all isolates having an identical MIRU-VNTR result, compared to 6% of all isolates in Gaborone with the same MIRU-VNTR result. This study demonstrates localized differences in strain diversity by two districts in Botswana, and contributes to a growing characterization of MTBC diversity globally.
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25
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Pole I, Trofimova J, Norvaisa I, Supply P, Skenders G, Nodieva A, Ozere I, Riekstina V, Igumnova V, Storozenko J, Jansone I, Viksna L, Ranka R. Analysis of Mycobacterium tuberculosis genetic lineages circulating in Riga and Riga region, Latvia, isolated between 2008 and 2012. INFECTION GENETICS AND EVOLUTION 2019; 78:104126. [PMID: 31783188 DOI: 10.1016/j.meegid.2019.104126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 11/17/2022]
Abstract
Although the number of new tuberculosis (TB) cases registered per year has decreased by 3-fold between 2001 and 2017 in Latvia, the TB incidence and rates of multidrug resistant TB in this Baltic country remain substantially higher than in most other European countries. Molecular typing methods of Mycobacterium tuberculosis (MTB) play an important role both in clinical studies of the disease and the epidemiological investigations, allowing to describe and characterize the pathogen's population structure and spread of particular genotypes. Aim of this study was to examine the prevalence of MTB lineages in Riga and Riga region of Latvia within a five-year period (2008-2012), and to evaluate the discriminatory power (DP) of spoligotyping, standard 24-locus MIRU-VNTR and IS6110-RFLP methods in this setting. The results showed that the main MTB spoligotype families were Beijing (25.3%) and LAM (24.3%), followed by T (22.1%), Ural (11.2%), Haarlem (6.6%) and X superfamily (3.4%). This distribution remained stable over the five consecutive years. 67.6% of MTB isolates were pan-susceptible, and 32.4% were resistant to any drug; multi-drug resistance was found in 5.8% of MTB strains, and 7.6% of MTB isolates were extensively drug-resistant. Drug resistance was associated with SIT1, SIT283 and SIT42 genotypes, while SIT1 and SIT42 were overrepresented among multi drug-resistant MTB strains. Overall, DP of spoligotyping method alone was 0.8953, while DP of both 24-locus MIRU-VNTR analysis and IS6110 RFLP was higher (DP = 0.9846 and 0.9927, respectively), mainly due to the improvement of the resolution for the Beijing strains. In conclusion, this work represents the first comprehensive molecular epidemiological description of TB in Latvia, highlighting the high genetic diversity of MTB strains circulating in Riga and Riga region. In combination with detailed epidemiological data this approach was helpful for the in-depth understanding of epidemiological processes in settings where the Next-Gen sequencing is not available as a routine method.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antitubercular Agents/pharmacology
- Child
- Child, Preschool
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Female
- Genetic Variation
- Genotyping Techniques
- Humans
- Infant
- Infant, Newborn
- Latvia/epidemiology
- Male
- Microbial Sensitivity Tests
- Middle Aged
- Minisatellite Repeats
- Molecular Epidemiology
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Polymorphism, Restriction Fragment Length
- Prevalence
- Tuberculosis/epidemiology
- Tuberculosis/microbiology
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/microbiology
- Young Adult
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Affiliation(s)
- Ilva Pole
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia; Latvian Biomedical Research and Study Centre, Latvia
| | - Julija Trofimova
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia
| | - Inga Norvaisa
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, CIIL - Center for Infection and Immunity of Lille, U1019 - UMR 8204, Lille F-59000, France
| | - Girts Skenders
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia
| | | | - Iveta Ozere
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia; Riga Stradiņš University, Latvia
| | - Vija Riekstina
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia
| | - Viktorija Igumnova
- Latvian Biomedical Research and Study Centre, Latvia; Riga Stradiņš University, Latvia
| | - Jelena Storozenko
- Riga Stradiņš University, Latvia; Riga East University Hospital, Latvian Centre of Infectious Diseases, Latvia
| | - Inta Jansone
- Latvian Biomedical Research and Study Centre, Latvia
| | - Ludmila Viksna
- Riga Stradiņš University, Latvia; Riga East University Hospital, Latvian Centre of Infectious Diseases, Latvia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Latvia; Riga Stradiņš University, Latvia.
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Genotyping of Mycobacterium tuberculosis spreading in Hanoi, Vietnam using conventional and whole genome sequencing methods. INFECTION GENETICS AND EVOLUTION 2019; 78:104107. [PMID: 31706080 DOI: 10.1016/j.meegid.2019.104107] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/24/2019] [Accepted: 11/04/2019] [Indexed: 12/22/2022]
Abstract
Hanoi is the capital of Vietnam, one of the 30 countries with a high tuberculosis (TB) burden. Fundamental data on the molecular epidemiology of the disease is required for future TB management. To identify lineages and genotypes of Mycobacterium tuberculosis (Mtb), conventional genotyping data from clinical isolates of the Hanoi area was compared with whole genome sequencing (WGS) analysis from 332 of 470 samples. It was obtained from lineage-specific single nucleotide variants (SNVs), large sequence polymorphisms, spoligotyping, and variable number of tandem repeats (VNTR) analysis using mycobacterial interspersed repetitive unit (MIRU) and Japan anti-tuberculosis association (JATA) locus sets. This information was directly compared with results obtained from WGS. Mini-satellite repeat unit variants were identified using BLAST search against concatenated short read sequences, the RepUnitTyping tool. WGS analysis revealed that the Mtb strains tested are diverse and classified into lineage (L) 1, 2 and 4 (24.7, 57.2 and 18.1% respectively). The majority of the L2 strains were further divided into ancient and modern Beijing genotypes, and most of the L1 group were EAI4_VNM strains. Although conventional PCR-based genotyping results were mostly consistent with information obtained through WGS analysis, in-depth analysis identified aberrant deletions and spacers that may cause discordance. JATA-VNTR sets, including hypervariable loci, separated large Beijing genotypic clusters generated by MIRU15 into smaller groups. The distribution of repeat unit variants observed within 33 VNTR loci showed clear variation depending on the three lineages. WGS-based pairwise-SNV differences within VNTR-defined genotypic clusters were greater in L1 than in L2 and L4 (P = .001). Direct comparisons between results of PCR-based genotyping and in silico analysis of WGS data would bridge a gap between classical and modern technologies during this transition period, and provide further information on Mtb genotypes in specific geographical areas.
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Elsayed MSAE. Applicability of using 15 MIRU-VNTR loci for genotyping of Mycobacterium avium subsp. paratuberculosis from two cattle farms in Egypt. Mol Biol Rep 2019; 46:6253-6262. [PMID: 31520269 DOI: 10.1007/s11033-019-05065-2] [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: 07/13/2019] [Accepted: 09/04/2019] [Indexed: 11/26/2022]
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is a notorious infectious agent that causes Johne's disease which leads to serious economic losses in cattle farms all over the world. The Lack of accurate epidemiological and molecular data is a major barrier to the implementation of disease control strategies. Basically, the tracing of infections requires rapid detection of the widely spreading genotypes with the ability to determine isolates from common and different sources. This study aimed to evaluate the applicability and discriminatory power of 15 mycobacterial interspersed repetitive unit (MIRU)-variable number tandem repeat (VNTR) loci of M. tuberculosis for MAP genotyping. Additionally, detection of the most efficient loci combinations for molecular epidemiological investigations of MAP isolates. The discriminatory capacity and applicability of 15 known loci [2 exact tandem repeat (ETR) loci, 6 MIRU loci, 4 Mtub loci, and 3 Queen's University of Belfast (QUB) group loci] were assessed using 26 isolates from two cattle herds (Holstein Frisian) in El buhaira and Giza Governorates at north of Egypt. The results proved the presence of 12 different genotypes. All the used loci gave Hunter-Gaston discrimination index of DI = 0.963 while the ten loci (Mtub04, MIRU10, QUB11b, MIRU26, QUB26, QUB4156, MIRU04, ETRC, Mtub30, and Mtub39) were highly discriminating with DI = 0.956. Moreover, the five loci (Mtub21, MIRU31, MIRU16, MIRU40, and ETRA) gave moderate discriminatory power with DI = 0.839. The MIRU31 locus expressed no polymorphism among strains. MIRU-VNTR typing generally proved applicability and high discriminatory power with DI = 0.963. The ten highly discriminating DI = 0.956 proved to be the most suitable for the first-line genotyping of MAP from cattle, with nearly similar resolving ability as all the 15 loci. MIRU-VNTR proved fastness, efficiency, and feasibility in genotyping of MAP from cattle in Egypt.
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Genomic Polymorphism Associated with the Emergence of Virulent Isolates of Mycobacterium bovis in the Nile Delta. Sci Rep 2019; 9:11657. [PMID: 31406159 PMCID: PMC6690966 DOI: 10.1038/s41598-019-48106-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 07/30/2019] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium bovis is responsible for bovine tuberculosis in both animals and humans. Despite being one of the most important global zoonotic disease, data related to the ecology and pathogenicity of bovine tuberculosis is scarce, especially in developing countries. In this report, we examined the dynamics of M. bovis transmission among dairy cattle in the Nile Delta of Egypt. Animals belonging to 27 herds from 7 governorates were tested by the Single Intradermal Comparative Skin Tuberculin (SICST), as a preliminary screen for the presence of bovine tuberculosis. Positive SICST reactors were identified in 3% of the animals spread among 40% of the examined herds. Post-mortem examination of slaughtered reactors confirmed the presence of both pulmonary and/or digestive forms of tuberculosis in > 50% of the examined animals. Targeted and whole-genome analysis of M. bovis isolates indicated the emergences of a predominant spoligotype (SB0268) between 2013–2015, suggesting a recent clonal spread of this isolate within the Nile Delta. Surprisingly, 2 isolates belonged to M. bovis BCG group, which are not allowed for animal vaccination in Egypt, while the rest of isolates belonged to the virulent M. bovis clonal complex European 2 present in Latin America and several European countries. Analysis of strain virulence in the murine model of tuberculosis indicated the emergence of a more virulent strain (MBE4) with a specific genotype. More analysis is needed to understand the molecular basis for successful spread of virulent isolates of bovine tuberculosis among animals and to establish genotype/phenotype association.
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29
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Marianelli C, Amato B, Boniotti MB, Vitale M, Pruiti Ciarello F, Pacciarini ML, Di Marco Lo Presti V. Genotype diversity and distribution of Mycobacterium bovis from livestock in a small, high-risk area in northeastern Sicily, Italy. PLoS Negl Trop Dis 2019; 13:e0007546. [PMID: 31306431 PMCID: PMC6658142 DOI: 10.1371/journal.pntd.0007546] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 07/25/2019] [Accepted: 06/11/2019] [Indexed: 11/18/2022] Open
Abstract
Bovine tuberculosis (bTB) caused by Mycobacterium bovis is an important re-emerging disease affecting livestock, wildlife and humans. Epidemiological studies are crucial to identifying the source of bTB infection, and its transmission dynamics and host preference, and thus to the implementation of effective strategies to contain it. In this study, we typed M. bovis isolates from livestock, and investigated their genetic diversity and distribution. A total of 204 M. bovis isolates were collected from cattle (n = 164) and Sicilian black pigs (n = 40) reared in a limited area of the province of Messina, northeastern Sicily, an area that had previously been identified as having the highest incidence of bTB in livestock on the island. All M. bovis isolates were typed by both spoligotyping and 12-loci MIRU-VNTR analysis. Results from both methods were then combined in order to improve the discriminatory power of M. bovis typing. We identified 73 combined genetic profiles. Thirty-five point six percent of the profiles were common to at least two animals, whereas 64.4% of profiles occurred in only one animal. A number of genetic profiles were predominant in either cattle or black pigs. We identified common genetic patterns in M. bovis isolates originating not only from neighboring districts, but also from non-neighboring districts. Our findings suggest that bTB is widespread in our setting, and is caused by a large number of genetically diverse M. bovis strains. The ecology and farming practices characteristic of the area may explain the substantial M. bovis heterogeneity observed, and could represent obstacles to bTB eradication. Bovine tuberculosis is a widespread infectious disease affecting both domestic and wild animals, as well as humans. In addition to being of public health concern, the disease, caused mainly by Mycobacterium bovis, has a significant economic impact on the farming industry due to the costs of eradication efforts. In Sicily, the largest of the Italian islands, bovine tuberculosis in livestock is of great concern, and targeted control strategies are needed. Molecular epidemiology is an essential tool for determining the distribution of a disease, so as to control it and minimize its threat to the population. We typed M. bovis isolates isolated from cattle and pigs reared in a limited area of Sicily. An in-depth comparison of the genetic makeup of these isolates allowed us a better understanding of the genetic diversity and distribution of the pathogen in our population of animals. We found that the disease is widespread in the area and caused by a large variety of M. bovis strains, which are in several cases common to different species of livestock. The paper concludes with a discussion of the findings in light of the environmental and ecological setting, and of farming practices in the area. The results are expected to contribute to the improvement of surveillance and control programs of bovine tuberculosis in the region.
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Affiliation(s)
- Cinzia Marianelli
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
- * E-mail:
| | - Benedetta Amato
- Sezione Diagnostica Barcellona P.G., Istituto Zooprofilattico Sperimentale della Sicilia, Barcellona Pozzo di Gotto, Italy
| | - Maria Beatrice Boniotti
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Maria Vitale
- Sezione Diagnostica Barcellona P.G., Istituto Zooprofilattico Sperimentale della Sicilia, Barcellona Pozzo di Gotto, Italy
| | - Flavia Pruiti Ciarello
- Sezione Diagnostica Barcellona P.G., Istituto Zooprofilattico Sperimentale della Sicilia, Barcellona Pozzo di Gotto, Italy
| | - Maria Lodovica Pacciarini
- National Reference Centre for Bovine Tuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna, Brescia, Italy
| | - Vincenzo Di Marco Lo Presti
- Sezione Diagnostica Barcellona P.G., Istituto Zooprofilattico Sperimentale della Sicilia, Barcellona Pozzo di Gotto, Italy
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Kyi MS, Palittapongarnpim P, Chaiprasert A, Ajawatanawong P, GarcIa HCG, Chongsuvivatwong V. Infection of multiple Mycobacterium tuberculosis strains among tuberculosis/human immunodeficiency virus co-infected patients: A molecular study in Myanmar. Int J Mycobacteriol 2019; 7:375-379. [PMID: 30531038 PMCID: PMC6341994 DOI: 10.4103/ijmy.ijmy_108_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Appearance of Mycobacterium tuberculosis (MTB) in the sputum of a tuberculosis (TB)/human
immunodeficiency virus (HIV) co-infected patient under treatment may indicate either failure or new infection. This study aims
to evaluate whether TB treatment failure among TB/HIV co-infected patients is a real failure. Methods: A prospective cohort study was conducted among 566 TB/HIV co-infected patients who started TB treatment in 12 townships
in the upper Myanmar. Among the 566 participants, 16 (2.8%) resulted in treatment failure. We performed a molecular study
using mycobacterial interspersed repetitive-unit-variable number of tandem repeat (MIRU-VNTR) genotyping for them. The
MIRU-VNTR profiles were analyzed using the web server, MIRU-VNTRplus. All data were entered into EpiData version 3.1 and
analyzed using R version 3.4.3. Results: Among 16 failure patients, seven had incomplete laboratory results. Of the nine remaining patients, nobody had exactly
the same MIRU-VNTR pattern between the initial and final isolates. Four patients had persistent East-African Indian (EAI)
lineages and one each had persistent Beijing lineage, changing from EAI to Beijing, from Beijing to EAI, NEW-1 to Beijing, and
NEW-1 to X strains. Female patients have significantly larger genetic difference between MTB of the paired isolates than male
patients (t-test, P = 0.04). Conclusion: Thus, in our study patients, infection of multiple MTB strains is a possible cause of TB treatment failure. Explanation
for the association between gender and distance of genotypes from the initial to subsequent MTB infection needs further
studies.
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Affiliation(s)
- Myo Su Kyi
- Department of Regional Public Health, Nay Pyi Taw Union Territory, Ministry of Health and Sports, Myanmar; Department of Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
| | | | - Angkana Chaiprasert
- Department of Research and Development Affairs, Faculty of Medicine, Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pravech Ajawatanawong
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - H Ctor Guzmán GarcIa
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Virasakdi Chongsuvivatwong
- Department of Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla, Thailand
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A case of Mycobacterium tuberculosis laboratory cross-contamination. J Infect Chemother 2019; 25:610-614. [PMID: 30982725 DOI: 10.1016/j.jiac.2019.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/08/2019] [Accepted: 03/13/2019] [Indexed: 11/23/2022]
Abstract
SETTING A laboratory cross-contamination event was suspected because Mycobacterium tuberculosis was unexpectedly detected at a high incidence in the cultures of several clinical specimens at the National Hospital Organization, Tokyo National Hospital, Japan. OBJECTIVE To describe a case of Mycobacterium tuberculosis laboratory cross-contamination. DESIGN We reviewed the medical records of 20 patients whose clinical specimens were suspected to have been contaminated by Mycobacterium tuberculosis. Variable number of tandem repeat analysis with 15 loci, the Japan Anti-Tuberculosis Association-12, and three additional hyper-variable loci, was performed to identify the cross-contamination event. RESULTS The clinical, laboratory, and variable number of tandem repeat data revealed that the cross-contamination had possibly originated from one strongly positive specimen, resulting in false-positive results in 11 other specimens, including a case treated with anti-tuberculosis drugs. CONCLUSION Clinical and laboratory data must be re-evaluated when cross-contamination is suspected and variable number of tandem repeat analysis should be used to confirm cross-contamination. Furthermore, original isolates should be stored appropriately, without sub-culturing and genotyping should be performed at the earliest possible for better utilization of variable number of tandem repeat for the identification of cross-contamination.
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Deciphering Within-Host Microevolution of Mycobacterium tuberculosis through Whole-Genome Sequencing: the Phenotypic Impact and Way Forward. Microbiol Mol Biol Rev 2019; 83:83/2/e00062-18. [PMID: 30918049 DOI: 10.1128/mmbr.00062-18] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The Mycobacterium tuberculosis genome is more heterogenous and less genetically stable within the host than previously thought. Currently, only limited data exist on the within-host microevolution, diversity, and genetic stability of M. tuberculosis As a direct consequence, our ability to infer M. tuberculosis transmission chains and to understand the full complexity of drug resistance profiles in individual patients is limited. Furthermore, apart from the acquisition of certain drug resistance-conferring mutations, our knowledge on the function of genetic variants that emerge within a host and their phenotypic impact remains scarce. We performed a systematic literature review of whole-genome sequencing studies of serial and parallel isolates to summarize the knowledge on genetic diversity and within-host microevolution of M. tuberculosis We identified genomic loci of within-host emerged variants found across multiple studies and determined their functional relevance. We discuss important remaining knowledge gaps and finally make suggestions on the way forward.
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Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden. Sci Rep 2019; 9:4931. [PMID: 30894568 PMCID: PMC6426893 DOI: 10.1038/s41598-019-39971-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/06/2019] [Indexed: 11/17/2022] Open
Abstract
Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.
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Abstract
In infectious disease epidemiology, the laboratory plays a critical role in diagnosis, outbreak investigations, surveillance, and characterizing biologic properties of microbes associated with their transmissibility, resistance to anti-infectives, and pathogenesis. The laboratory can inform and refine epidemiologic study design and data analyses. In public health, the laboratory functions to assess effect of an intervention. In addition to research laboratories, the new-generation molecular microbiology technology has been adapted into clinical and public health laboratories to simplify, accelerate, and make precise detection and identification of infectious disease pathogens. This technology is also being applied to subtype microbes to conduct investigations that advance our knowledge of epidemiology of old and emerging infectious diseases. Because of the recent explosive progress in molecular microbiology technology and the vast amount of data generated from the applications of this technology, this Microbiology Spectrum Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases describes these methods separately for bacteria, viruses, and parasites. This review discusses past and current advancements made in laboratory methods used to conduct epidemiologic studies of bacterial infections. It describes methods used to subtype bacterial organisms based on molecular microbiology techniques, following a discussion on what is meant by bacterial "species" and "clones." Discussions on past and new genotyping tests applied to epidemiologic investigations focus on tests that compare electrophoretic band patterns, hybridization matrices, and nucleic acid sequences. Applications of these genotyping tests to address epidemiologic issues are detailed elsewhere in other reviews of this series. *This article is part of a curated collection.
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The Evolution of Genotyping Strategies To Detect, Analyze, and Control Transmission of Tuberculosis. Microbiol Spectr 2019; 6. [PMID: 30338753 DOI: 10.1128/microbiolspec.mtbp-0002-2016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The introduction of genotypic tools to analyze Mycobacterium tuberculosis isolates has transformed our knowledge of the transmission dynamics of this pathogen. We discuss the development of the laboratory methods that have been applied in recent years to study the epidemiology of M. tuberculosis. This review integrates two approaches: on the one hand, it considers how genotyping techniques have evolved over the years; and on the other, it looks at how the way we think these techniques should be applied has changed. We begin by examining the application of fingerprinting tools to suspected outbreaks only, before moving on to universal genotyping schemes, and finally we describe the latest real-time strategies used in molecular epidemiology. We also analyze refined approaches to obtaining epidemiological data from patients and to increasing the discriminatory power of genotyping by techniques based on genomic characterization. Finally, we review the development of integrative solutions to reconcile the speed of PCR-based methods with the high discriminatory power of whole-genome sequencing in easily implemented formats adapted to low-resource settings. Our analysis of future considerations highlights the need to bring together the three key elements of high-quality surveillance of transmission in tuberculosis, namely, speed, precision, and ease of implementation.
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Weerasekera D, Pathirane H, Madegedara D, Dissanayake N, Thevanesam V, Magana-Arachchi DN. Evaluation of the 15 and 24-loci MIRU-VNTR genotyping tools with spoligotyping in the identification of Mycobacterium tuberculosis strains and their genetic diversity in molecular epidemiology studies. Infect Dis (Lond) 2019; 51:206-215. [PMID: 30689510 DOI: 10.1080/23744235.2018.1551619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND The transmission dynamics of Mycobacterium tuberculosis (Mtb) using various genotyping tools has been studied globally and a particular tool for genotyping Mtb is the mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR). Tuberculosis (TB) remains an important public health problem worldwide and Sri Lanka being a country of tourist destination; because of major development projects undergoing, it has a high proportion of tourists and immigrants from Asia and Europe that are characterized with highest TB incidences and drug-resistant clinical isolates. Hence, in order to address the question of Mtb genetic diversity, we investigated the discriminatory power of both MIRU-VNTR typing of 15 and 24 loci with spoligotyping to differentiate Mtb isolates. METHOD Acid-fast bacilli positive sputum samples (n = 150) from first visit patients were collected. Decontamination of sputum and extraction of genomic DNA were carried out using standard techniques. The isolates were characterized by MIRU-VNTR for both the 15 and 24 loci and spoligotyping. RESULTS In our study population, MIRU-VNTR 15 and 24 loci did not show a significant difference among the identified M. tuberculosis strains. However, MIRU 24 loci yielded an additional strain LAM, which is of T1 origin. 15 loci strain grouping had more clusters of strains grouped together while 24 loci differentiated the same cluster of strains into distinct strain types. CONCLUSION We conclude that the use of 15-locus MIRU-VNTR typing is sufficient for a first-line epidemiological study to genotype M. tuberculosis, but the additional discriminatory power of 24 loci MIRU-VNTR has been able to differentiate samples within highly homologous groups.
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Affiliation(s)
| | | | | | - Neranjan Dissanayake
- c Consultant Respiratory Unit , District General Hospital , Nuwara-Eliya , Sri Lanka
| | - Vasanthi Thevanesam
- d Department of Microbiology, Faculty of Medicine , University of Peradeniya , Peradeniya , Sri Lanka
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Caleffi-Ferracioli KR, Baldin VP, Noguti ÉN, Siqueira VLD, Scodro RBL, Pavan FR, Hirata MH, Cardoso RF. Molecular characterization of Mycobacterium tuberculosis and Mycobacterium bovis isolates by Enterobacterial Repetitive Intergenic Consensus-PCR. BRAZ J PHARM SCI 2018. [DOI: 10.1590/s2175-97902018000317554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Molecular characterization and drug susceptibility profile of Mycobacterium tuberculosis isolates from Northeast Bangladesh. INFECTION GENETICS AND EVOLUTION 2018; 65:136-143. [PMID: 30048809 DOI: 10.1016/j.meegid.2018.07.027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/24/2018] [Accepted: 07/22/2018] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) remains a major public health problem worldwide including in Bangladesh. Molecular epidemiological tools provide genotyping profiles of Mycobacterium tuberculosis (M. tuberculosis) strains that can give insight into the transmission of TB in a specific region. The objective of the study was to identify the genetic diversity and drug susceptibility profile of M. tuberculosis strains circulating in the northeast Bangladesh. A total of 244 smear-positive sputum specimens were collected from two referral hospitals in Mymensingh and Netrakona districts. The isolated strains were genotyped by deletion analysis, spoligotyping, and MIRU-VNTR typing. We also analyzed the distributions of drug susceptibility pattern and demographic data among different genotypes. All isolates were identified as M. tuberculosis and among them 167 strains (68.44%) were 'ancestral' and the remaining 77 (31.56%) were 'modern' type. Spoligotyping analysis yielded 119 distinct patterns, among them, 86 isolates had unique patterns and the remaining 158 were grouped into 33 distinct clusters containing 2 to 18 isolates. The predominant spoligotypes belong to the EAI lineage strains, comprising 66 (27.04%) isolates followed by Beijing (7.38%), T1 (6.15%), CAS1-Delhi (5.33), LAM9 (3.28%), MANU-2 and X2. MIRU-VNTR analysis revealed 167 isolates (68%) had unique patterns, whereas 77 (32%) were grouped into 26 clusters and the rate of recent transmission was 20.9%, suggesting that the majority of TB cases in this region are caused by the reactivation of previous TB infections rather than recent transmission. About 136 (55.7%) isolates were sensitive to four anti-TB drugs, 69 (28.3%) were resistant to one or more (except rifampicin and isoniazid combination) drugs and 39 (15.9%) were MDR. In conclusion, our study provides a first insight into molecular characterization and drug resistance profile of M. tuberculosis strains in northeast Bangladesh which will ultimately contribute to the national TB control program.
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Cannas A, Camassa S, Sali M, Butera O, Mazzarelli A, Sanguinetti M, Di Caro A, Delogu G, Girardi E. Genetic Diversity of Mycobacterium tuberculosis Isolates in the Metropolitan Area of Rome. Chemotherapy 2018; 63:148-154. [PMID: 29902788 DOI: 10.1159/000489860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/05/2018] [Indexed: 11/19/2022]
Abstract
BACKGROUND The presence in a geographic area of Mycobacterium tuberculosis (Mtb) strains belonging to different phylogeographic lineages and showing different drug susceptibility patterns may suggest recent transmission, with implications in terms of patient clinical management and disease control. The aim of this study was to carry out a preliminary epidemiological investigation of tuberculosis (TB) cases in Rome. METHODS A total of 232 Mtb isolates, collected from new or previously treated patients, admitted between 2008 and 2014 at 2 hospital settings in Rome with a diagnosis of TB, were analyzed by spoligotyping and analyzing 24 variable-number tandem repeats (VNTR) mycobacterial interspersed repetitive-unit (MIRU) loci. The SITVIT2 database and the MIRU-VNTRplus web applications were used to identify the strain genotypes and to generate phylogenetic trees. RESULTS Based on the position on the phylogenetic tree, 97.4% of the strains were associated with 1 of the 7 main lineages. The Euro-American lineage was the most commonly represented (81.9%) within both Italian and foreign-born populations, although all main lineages were present. The highest frequency of drug-resistant strains was found among the East-Asian lineage (Beijing genotype) isolated from foreign-born patients. CONCLUSIONS Dynamics of TB transmission in Rome indicate recent spread of Mtb strains belonging to phylogeographic lineages and clades usually found in countries and geographic areas with a high incidence of TB, similarly to what is observed in most metropolitan areas in Western Europe. Knowledge from molecular and classical epidemiology provides an important tool for disease control.
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Affiliation(s)
- Angela Cannas
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Serena Camassa
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Gemelli, Rome, Italy
| | - Michela Sali
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Gemelli, Rome, Italy
| | - Ornella Butera
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Antonio Mazzarelli
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Gemelli, Rome, Italy
| | - Antonino Di Caro
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
| | - Giovanni Delogu
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario Gemelli, Rome, Italy
| | - Enrico Girardi
- Department of Epidemiology, Preclinical Research, and Advanced Diagnostics, National Institute for Infectious Diseases Lazzaro Spallanzani - IRCCS, Rome, Italy
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A molecular epidemiological analysis of tuberculosis trends in South Korea. Tuberculosis (Edinb) 2018; 111:127-134. [PMID: 30029897 DOI: 10.1016/j.tube.2018.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/25/2018] [Accepted: 06/05/2018] [Indexed: 11/24/2022]
Abstract
Molecular epidemiological data are needed to assess tuberculosis (TB)-management policy outcomes in South Korea. IS6110 restriction fragment-length polymorphism (IS6110-RFLP) and mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) analyses are major molecular epidemiological tools for investigating the transmission or reactivation of active TB. Here, we determined trends in the clustering rate (i.e., the prevalence of Mycobacterium tuberculosis isolates with identical genotype patterns) of active TB and related differences between the 1990s and 2000s in Korea. M. tuberculosis isolates (1,007) of nationwide origins were analyzed by IS6110-RFLP and 24-locus standardized MIRU-VNTR genotyping. The clustering rate was measured by IS6110-RFLP, 24-locus MIRU-VNTR, and both analytical methods in combination. IS6110-RFLP, 24-locus MIRU-VNTR typing, and the combined method revealed 882, 754, and 983 distinct profiles; 809, 651, and 961 unique isolates; and 198, 356, and 46 clustered isolates grouped into 73, 103, and 22 clusters, respectively. In addition, we confirmed that the clustering rates in the 2000s decreased by 11.2%, 2.1%, and 3.1% relative to that in the 1990s using the three methods, respectively. Furthermore, in multivariate analysis, the younger-age group (<30) clustered more frequently than the older-age group (>50), based on all the three methods. Our study is the first report to provide nationwide molecular epidemiological information on TB in Korea.
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de Almeida AL, Scodro RBDL, de Carvalho HC, Costacurta GF, Baldin VP, Santos NCS, Ghiraldi-Lopes LD, Campanerut-Sá PAZ, Siqueira VLD, Caleffi-Ferracioli KR, Shibata FK, Sprada A, Cardoso RF. RD RioMycobacterium tuberculosis lineage in the Brazil/Paraguay/Argentina triple border. Tuberculosis (Edinb) 2018; 110:68-78. [PMID: 29779776 DOI: 10.1016/j.tube.2018.03.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 03/22/2018] [Accepted: 03/24/2018] [Indexed: 10/17/2022]
Abstract
The high tuberculosis (TB) incidence rates, the closeness of the cities and the high migration flux on the Brazil/Paraguay/Argentina border deserves an in-depth study, using Mycobacterial Interspersed Repetitive Unit (MIRU) and Spoligotyping genetic markers to explore the impact of the Mycobacterium tuberculosis RDRio lineage on disease transmission and resistance to anti-TB drugs in this setting. Although without the totality of M. tuberculosis isolates causing TB in this studied setting, a number of 97 isolates obtained from sputa samples culture of patients with confirmed TB, from 2013 to 2015, were submitted to 24 loci MIRU, Spoligotyping, detection of RDRio lineage and detection of mutation related to isoniazid and rifampicin resistance by MTBDRplus/DNA STRIP. In this sample, it was observed high clonal variability of circulating M. tuberculosis isolates causing TB in Brazilian cities bordering Paraguay and Argentina. The percentage of RDRio lineage causing TB in this setting was 15.46%, and lower than the detected in different areas of Brazil. According to 24 loci MIRU, the major MIRU International Type (MIT) related with RDRio lineage were MIT 26, MIT 738, MIT 601 with four, two and one isolates, respectively. Eight isolates with RDRio marker were classified as orphans. The mainly Spoligofamily related with RDRio lineage was LAM1 and LAM9 and no relationship between RDRio lineage and resistance in M. tuberculosis isolates circulating in this setting could be established. This work is pioneer in studying the dynamics of RDRio lineage transmission on the Brazil/Paraguay/Argentina border and deserves further studies to analyze the real contribution of the RDRio lineage in outbreaks and the risk of significant development of MDR-TB in the setting studied.
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Affiliation(s)
- Aryadne Larissa de Almeida
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil.
| | - Regiane Bertin de Lima Scodro
- Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Universidade Estadual de Maringá, PR, Brazil.
| | - Hayalla Corrêa de Carvalho
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil.
| | | | - Vanessa Pietrowski Baldin
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil.
| | | | | | | | - Vera Lucia Dias Siqueira
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil; Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil.
| | | | | | | | - Rosilene Fressatti Cardoso
- Programa de Pós-Graduação em Biociências e Fisiopatologia, Universidade Estadual de Maringá, PR, Brazil; Departamento de Análises Clínicas e Biomedicina, Universidade Estadual de Maringá, PR, Brazil; Programa de Pós-Graduação em Ciências da Saúde, Universidade Estadual de Maringá, PR, Brazil.
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Xu G, Mao X, Wang J, Pan H. Clustering and recent transmission of Mycobacterium tuberculosis in a Chinese population. Infect Drug Resist 2018; 11:323-330. [PMID: 29563813 PMCID: PMC5846054 DOI: 10.2147/idr.s156534] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Purpose The objectives of the present study were to characterize the clinical isolates prevailing in the northeast of Jiangsu and to investigate the mode of transmission. The study also aimed to explore the extent to which Mycobacterium tuberculosis strains contributed to drug resistance and the possible factors related to the recent transmission. Patients and methods We consecutively enrolled 912 culture-confirmed pulmonary tuberculosis (TB) cases from 1 January 2013 to 31 December 2014 in Lianyungang City, which is located in the center of China’s vast ocean area and the northeast of Jiangsu province. Isolates were genotyped using 15-locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing. The Hunter–Gaston discrimination index (HGDI) was used to estimate the discriminatory power and diversity of molecular markers. Results Among 741 successfully genotyped isolates, 144 (19.43%) strains formed 46 clusters, while 597 (80.57%) isolates had the unique MIRU pattern. The total HGDI for all 15 loci was 0.999. The average cluster size was 3 (2–13) patients. The estimated proportion of recent transmission was 13.34%. Patients with unfavorable treatment outcomes were infected with clustered strains at a higher proportion than were those with favorable treatment outcomes (adjusted OR: 1.78, 95% CI: 1.14–2.85, P=0.012). Conclusion The probability of recent TB transmission was relatively low in the study site, while the cases mainly arose from the activation of previous infection. Spatial analysis showed that strains forming larger clusters had the characteristics of regional aggregation.
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Affiliation(s)
- Guisheng Xu
- Department of Epidemiology, Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Xuhua Mao
- Department of Clinical Laboratory, Yixing People's Hospital, Wuxi, China
| | - Jianming Wang
- Department of Epidemiology, Key Laboratory of Infectious Diseases, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongqiu Pan
- Department of Tuberculosis, The Third Hospital of Zhenjiang, Zhenjiang, China
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Medeiros TF, Nogueira CL, Prim RI, Scheffer MC, Alves EV, Rovaris DB, Zozio T, Rastogi N, Bazzo ML. Molecular epidemiology of Mycobacterium tuberculosis strains from prison populations in Santa Catarina, Southern Brazil. INFECTION GENETICS AND EVOLUTION 2017; 58:34-39. [PMID: 29248797 DOI: 10.1016/j.meegid.2017.12.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 11/24/2017] [Accepted: 12/13/2017] [Indexed: 11/19/2022]
Abstract
The Tuberculosis (TB) notification rates are 5 to 81 times higher in prisons worldwide when compared to the general population. The state of Santa Catarina (SC) has few epidemiological data regarding TB in prisons. The aim of this study was to evaluate the molecular epidemiology of circulating strains in prisons of SC. The study comprised 95 clinical samples from six prisons. Among the cases included, all subjects were male, predominantly caucasians, and young adults, with low education level. The positive smear in the TB diagnosis comprised 62.0% of cases. About 50% of subjects had some condition associated with TB. The Spoligotyping results showed that the most frequent lineages were LAM (50.7%), T (22.2%) and S (11.6%). The 12-loci MIRU generated 62 different genotypes. The MSTs showed evolutionary relationships between Mycobacterium tuberculosis spoligotypes from SC and evolutionary relationships between the prison isolates and studied parameters. This first study on TB in prison units of SC highlighted the predominance of SIT216/LAM5, and SIT34/S. Interestingly, his profile was found to be different from that observed in a previous study performed with the state's general population. This data shows the need for continued surveillance of episodes of TB occurring among prison inmates in an emerging country like Brazil.
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Affiliation(s)
- Taiane Freitas Medeiros
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil
| | - Christiane Lourenço Nogueira
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil
| | - Rodrigo Ivan Prim
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil.
| | - Mara Cristina Scheffer
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil
| | - Eduardo Venâncio Alves
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil
| | - Darcita Büerger Rovaris
- Laboratório Central do Estado de Santa Catarina (LACEN/SC), Florianópolis, Santa Catarina, Brazil
| | - Thierry Zozio
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France.
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France.
| | - Maria Luiza Bazzo
- Universidade Federal de Santa Catarina - UFSC, Campus Universitário, s/n., Florianópolis, Santa Catarina, Brazil.
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Djemal SE, Siala M, Smaoui S, Kammoun S, Marouane C, Bezos J, Messadi-Akrout F, Romero B, Gdoura R. Genetic diversity assessment of Tunisian Mycobacterium bovis population isolated from cattle. BMC Vet Res 2017; 13:393. [PMID: 29246228 PMCID: PMC5732386 DOI: 10.1186/s12917-017-1314-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 12/06/2017] [Indexed: 12/16/2022] Open
Abstract
Background The genetic diversity of M. bovis in Tunisia is still underestimated despite the implementation of an eradication program. The lack of data about spatial distribution of the M. bovis population hinders the control of bovine tuberculosis (bTB) progress. This study represents the largest molecular analysis of M. bovis isolates in Tunisia. It is aimed to upgrade the understanding of bTB epidemiology and the geographical distribution of the infection. Tuberculosis research was performed in cattle (n = 149) with TB-compatible lesions collected over 5 months from a slaughterhouse located in Sfax, Tunisia. Results Ninety-four animals were found to be infected by M. bovis and two others by M. caprae. Spoligotyping revealed twenty-five patterns, SB0120, SB0134, and SB0121 being the most prevalent profiles (36.4%, 11.4%, and 7.2%, respectively). Three new spoligotypes were detected: SB2345, SB2344 and SB2343. MIRU-VNTR analysis classified the isolates in seventy-three profiles and showed a large genotypic variety observed within the main spoligotype which was split into several MIRU-VNTR types: 29 in SB0120 (h = 0.983), 10 in SB0134 (h = 0.981) and 7 in SB0121 (h = 1). Genotyping revealed a common pattern in different geographic regions. It also showed that Sfax, located in southern-Tunisia, represents a high-risk area with an elevated genetic diversity. Conclusions Spatial analysis may provide insights into disease transmission, which affects the effectiveness of eradication campaigns in cattle. Electronic supplementary material The online version of this article (10.1186/s12917-017-1314-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Saif Eddine Djemal
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax-Tunisia, Sfax, Tunisia.
| | - Mariam Siala
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax-Tunisia, Sfax, Tunisia.,Department of Biology, Preparatory Institute for Engineering Studies, University of Sfax-Tunisia, Sfax, Tunisia
| | - Salma Smaoui
- Department of Microbiology, Regional Hygiene Care Mycobacteriology Laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology, Faculty of Pharmacy, University of Monastir-Tunisia, Monastir, Tunisia.,Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A, Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Sana Kammoun
- Department of Microbiology, Regional Hygiene Care Mycobacteriology Laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology, Faculty of Pharmacy, University of Monastir-Tunisia, Monastir, Tunisia.,Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A, Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Chema Marouane
- Department of Microbiology, Regional Hygiene Care Mycobacteriology Laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology, Faculty of Pharmacy, University of Monastir-Tunisia, Monastir, Tunisia.,Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A, Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Javier Bezos
- , MAEVA SERVET SL. C/ de la Fragua 3, 28749, Alameda del Valle, Madrid, Spain.,Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Feriele Messadi-Akrout
- Department of Microbiology, Regional Hygiene Care Mycobacteriology Laboratory, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology, Faculty of Pharmacy, University of Monastir-Tunisia, Monastir, Tunisia.,Department of Microbiology, National Reference Laboratory of Mycobacteria, Research Unit (UR12SP18), A, Mami University Hospital of Pneumology, Ariana, Tunisia
| | - Beatriz Romero
- Centro de Vigilancia Sanitaria Veterinaria (VISAVET), Universidad Complutense, Avda. Puerta de Hierro s/n, 28040, Madrid, Spain
| | - Radhouane Gdoura
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences, University of Sfax-Tunisia, Sfax, Tunisia
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Augusto CJ, Carvalho WDS, Almeida IND, Figueiredo LJDA, Dantas NGT, Suffys PN, Miranda SSD. Comparative study of RFLP-IS6110 and MIRU-VNTR from Mycobacterium tuberculosis isolated in the state of Minas Gerais, Brazil. Braz J Microbiol 2017; 49:641-646. [PMID: 29249565 PMCID: PMC6112052 DOI: 10.1016/j.bjm.2017.04.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 02/08/2017] [Accepted: 04/06/2017] [Indexed: 11/16/2022] Open
Abstract
DNA genotyping of Mycobacterium tuberculosis has been widely applied in the understanding of disease transmission in many countries. The purpose of this study was to genotype the strains of M. tuberculosis isolated in patients with new tuberculosis (TB) cases in Minas Gerais, as well as to compare the similarity, discriminatory power, and agreement of the clusters between the IS6110 Restriction Fragment Length Polymorfism (RFLP) and 12 loci Variable Number Tandem Repeat – Mycobacterial Interspersed Repetitive Units (MIRU-VNTR) techniques. It was observed that 32% (66/204) of the isolated strains in the RFLP-IS6110 and 50.9% (104/204) of the isolated strains in the MIRU-VNTR presented a similarity of equal to or above 85%. The RFLP-IS6110 and MIRU-VNTR proved to contain a high discriminatory power. The similarity index resulting from the RFLP showed no recent transmission. Good agreement was observed between the techniques when clusters were detected; however, the best epidemiological relationship was found when using the RFLP-IS6110.
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Affiliation(s)
- Cláudio José Augusto
- Fundação Ezequiel Dias, Belo Horizonte, MG, Brazil; Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | | | | | | | | | - Philip Noel Suffys
- Fundação Oswaldo Cruz Foundation (FIOCRUZ), Instituto Oswaldo Cruz, Laboratório de Biologia Molecular Aplicada a Micobactérias, Rio de Janeiro, RJ, Brazil
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Varma-Basil M, Nair D. Molecular epidemiology of tuberculosis: Opportunities & challenges in disease control. Indian J Med Res 2017; 146:11-14. [PMID: 29168455 PMCID: PMC5719594 DOI: 10.4103/ijmr.ijmr_941_17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi 110 007, India
| | - Deepthi Nair
- Department of Microbiology, Vardhman Mahavir Medical College & Safdarjung Hospital, New Delhi 110 007, India
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Rasoahanitralisoa R, Rakotosamimanana N, Stucki D, Sola C, Gagneux S, Rasolofo Razanamparany V. Evaluation of spoligotyping, SNPs and customised MIRU-VNTR combination for genotyping Mycobacterium tuberculosis clinical isolates in Madagascar. PLoS One 2017; 12:e0186088. [PMID: 29053711 PMCID: PMC5650158 DOI: 10.1371/journal.pone.0186088] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 09/25/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Combining different molecular typing methods for Mycobacterium tuberculosis complex (MTBC) can be a powerful tool for molecular epidemiology-based investigation of TB. However, the current standard method that provides high discriminatory power for such a combination, mycobacterial interspersed repetitive units-variable numbers of tandem repeats typing (MIRU-VNTR), is laborious, time-consuming and often too costly for many resource-limited laboratories. We aimed to evaluate a reduced set of loci for MIRU-VNTR typing in combination with spoligotyping and SNP-typing for routine molecular epidemiology of TB. METHOD Spoligotyping and SNP-typing, in combination with the 15 loci MIRU-VNTR typing, were first used to type clinical MTBC isolates (n = 158) from Madagascar. A step by step reduction of MIRU-VNTR loci number was then performed according to the Hunter and Gaston Discriminatory Index (HGDI) and to the Principal component analysis (PCA) correlation with the spoligotype profiles to evaluate the discrimination power inside the generated spoligotype clusters. The 15 MIRU-VNTR was used as reference and SNP-typing was used to determine the main MTBC lineages. RESULTS Of the 158 clinical isolates studied, the SNP-typing classified 23 into Lineage 1 (14.6%), 31 into Lineage 2 (19.6%), 23 into Lineage 3 (14.6%) and 81 into Lineage 4 strains (51.3%). 37 different spoligotypes profiles were obtained, 15 of which were unique and 20 in clusters. 15-loci MIRU-VNTR typing revealed 144 different genotypes: 132 isolates had a unique MIRU-VNTR profile and 27 isolates were grouped into 12 clusters. After a stepwise reduction of the MIRU-VNTR loci number within each main spoligotype families, three different sets composed of 5 customised MIRU-VNTR loci had a similar discrimination level to the reference 15 loci MIRU-VNTR in lineage 1, lineage 2 and lineage 3. For lineage 4, a set of 4 and 3 MIRU-VNTR loci were proposed to subtype the Harleem and LAM spoligotype families, respectively. For the T spoligotype family, a set of 5 MIRU-VNTR loci was proposed. CONCLUSION According to the lineages and the spoligotype families, the number of MIRU-VNTR loci can be reduced to get an optimal classification of MTBC. These customized sets of MIRU-VNTR loci reduce workload and save resources while maintaining optimal discriminatory power.
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Affiliation(s)
- Rondroarivelo Rasoahanitralisoa
- Mycobacteria Unit, Institut Pasteur of Madagascar, Antananarivo, Madagascar, Ecole Doctorale Science de la Vie et de l'Environnement, Faculté des Sciences, Université d'Antananarivo, Antananarivo, Madagascar
| | | | - David Stucki
- Department of Medical Parasitology and infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Sebastien Gagneux
- Department of Medical Parasitology and infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,Institut for Integrative Cell Biology, I2BC, UMR9198 CEA-CNRS-UP Saclay, Orsay, France
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Tarazona D, Jaramillo L, Borda V, Levano K, Galarza M, Guio H. A Genomic Signature for Genotyping Mycobacterium tuberculosis. Bioinformation 2017; 13:224-230. [PMID: 28943727 PMCID: PMC5602289 DOI: 10.6026/97320630013224] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/13/2017] [Accepted: 07/23/2017] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has a vast diversity of genotypes including Beijing, CAS,
EAI, Haarlem, LAM, X, Ural, T, AFRI1 and AFRI2. However, genotyping can be expensive, time consuming and in some cases, results
may vary depending on methodology used. Here, we proposed a new set of 10 SNPs using a total of 249 MTB genomes, and selected
by first the inclusion/ exclusion (IE) criteria using spoligotyping and phylogenies, followed by the selection of the nonsynonymous
SNPs present in the most conserved cluster of orthologous groups (COG) of each genotype of MTB. Genotype assignment of the new
set of 10 SNPs was validated using an additional of 34 MTB genomes and results showed 100% correlation with their known
genotypes. Our set of 10 SNPs have not been previously reported and cover the MTB genotypes that are prevalent worldwide. This set
of SNPs could be used for molecular epidemiology with drug resistant markers.
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Affiliation(s)
- David Tarazona
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Luis Jaramillo
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Victor Borda
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Kelly Levano
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Marco Galarza
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
| | - Heinner Guio
- Laboratorio de Biotecnología y Biología Molecular, Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Perú
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Abstract
Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
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50
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Barandiaran S, Martínez Vivot M, Falzoni E, Marfil MJ, Pérez Tort G, Rovatti P, Fernández M, Iachini R, Satek F, Duchene A, Zumárraga MJ. Mycobacterioses in dogs and cats from Buenos Aires, Argentina. J Vet Diagn Invest 2017; 29:729-732. [PMID: 28599612 DOI: 10.1177/1040638717713795] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Mycobacterioses can produce nonspecific clinical signs in dogs and cats that make diagnosis difficult. Furthermore, the full characterization of mycobacterial agents is not always possible or practical. We characterized mycobacteria detected through cytology in 12 dogs and 7 cats with generalized clinical signs from the province of Buenos Aires in Argentina. In dogs, molecular testing confirmed the presence of Mycobacterium avium subsp. hominissuis (MAH) in 8 cases and M. fortuitum in 1 case. All dogs were Miniature Schnauzers, suggesting that this breed may be more susceptible to M. avium than other dog breeds. The cat isolates were 2 M. bovis, 1 M. fortuitum, and 1 MAH. Mycobacterial interspersed repetitive unit-variable-number tandem repeat patterns suggested possible links with cattle, swine, and humans studied previously in Argentina. The results show that pets may act as susceptible hosts with the potential risk of transmitting the infection to humans and other animals.
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Affiliation(s)
- Soledad Barandiaran
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Marcela Martínez Vivot
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Elvira Falzoni
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - María J Marfil
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Gabriela Pérez Tort
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Paula Rovatti
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Mónica Fernández
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Ricardo Iachini
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Fernanda Satek
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Adriana Duchene
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
| | - Martín J Zumárraga
- Department of Infectious Diseases, School of Veterinary Medicine, University of Buenos Aires, Buenos Aires, Argentina (Barandiaran, Martínez Vivot, Falzoni, Marfil, Pérez Tort, Duchene).,Biotechnology Institute, National Institute of Agricultural Technology, Hurlingham, Buenos Aires, Argentina (Marfil, Zumárraga).,Virreyes Veterinary Hospital, San Fernando, Buenos Aires, Argentina (Pérez Tort).,Private Veterinary Clinic, San Isidro, Argentina (Rovatti).,Zoonosis Luis Pasteur Institute, Buenos Aires, Argentina (Fernández, Iachini).,Surgical Veterinary Clinic (EQVET), Buenos Aires, Argentina (Satek)
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