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Hodgeman R, Liu Y, Rochfort S, Rodoni B. Development and evaluation of genomics informed real-time PCR assays for the detection and strain typing of Mycobacterium avium subsp. paratuberculosis. J Appl Microbiol 2024; 135:lxae107. [PMID: 38684472 DOI: 10.1093/jambio/lxae107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/18/2024] [Accepted: 04/25/2024] [Indexed: 05/02/2024]
Abstract
AIMS This study aimed to identify specific genomic targets for the detection and strain typing of Map and analyse their sensitivity and specificity, and detect Map directly from faeces. METHODS AND RESULTS A comparative genomics approach was used to identify specific genomic targets for the detection and strain typing of Map. A Map specific qPCR using the primer pair 7132 that targets a DNA segregation ATPase protein was able to detect all strains of Map and is more sensitive than the current Johne's disease PCR assays with a sensitivity of 0.0002 fg µl-1. A strain specific qPCR using the Atsa primer pair that targets the arylsulfase gene was able to differentiate between Type S and Type C strains of Map and was more sensitive than the IS1311 PCR and REA with a sensitivity of 40 fg µl-1 and was specific for Type S Map. Both assays successfully detected Map directly from faeces. CONCLUSION This study developed and validated two genomics informed qPCR assays, 7132B Map and Atsa Type S and found both assays to be highly specific and sensitive for the detection of Map from culture and directly from faeces. This is the first time that a probe-based qPCR has been designed and developed for Map strain typing, which will greatly improve the response time during outbreak investigations.
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Affiliation(s)
- Rachel Hodgeman
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Yuhong Liu
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Simone Rochfort
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria 3083, Australia
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2
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Najafpour R, Zolfaghari MR, Mosavari N, Nazari R, Tadayon K. More insights about genomic population structure of Mycobacterium avium subspecies paratuberculosis (Map) from multiple hosts in west and central provinces of Iran using a boosted genotyping approach. Comp Immunol Microbiol Infect Dis 2023; 100:101912. [PMID: 37487314 DOI: 10.1016/j.cimid.2022.101912] [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: 08/11/2022] [Revised: 11/05/2022] [Accepted: 11/09/2022] [Indexed: 11/13/2022]
Abstract
To investigate the population genetic of Mycobacterium avium subsp. paratuberculosis (Map) in Iran, Mycobacterial Interspersed Repetitive Units (MIRUs) and Multi Locus Short Sequence Repeat (MLSSR) system were employed. Numerous genotypes by MIRU (N = 11) and MLSSR (N = 9) methods bearing discriminatory indices of 0.90 and 0.79 respectively, were obtained. Browsing the INRA-Nouzilly list (http://mac-inmv.tours.inra.fr/) detected 3 of the found patterns as new types. Some loci either MIRU-VNTR or SSR proved more polymorphic and therefore are recommended to be applied in priority for strain typing in the Iranian environment. While identical MIRU-VNTR or MLSSR patterns were detected among different conspecifics and geographical locations, dissimilar types were also observed at the same farms an indication of coexistence of Map strains within one herd. We suggest extension of the genotyping work described here to include more endogenous isolates in order to better analysis of transmission and virulence in epidemiology and control of paratuberculosis.
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Affiliation(s)
- Reza Najafpour
- Department of Microbiology, Faculty of Basic Science, Qom Branch, Islamic Azad University, Qom, Iran
| | - Mohammad Reza Zolfaghari
- Department of Microbiology, Faculty of Basic Science, Qom Branch, Islamic Azad University, Qom, Iran.
| | - Nader Mosavari
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Bovine Tuberculosis Laboratory, Tuberculin and Mallein Research & Production Department, Karaj, Iran
| | - Razieh Nazari
- Department of Microbiology, Faculty of Basic Science, Qom Branch, Islamic Azad University, Qom, Iran
| | - Keyvan Tadayon
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Veterinary, Aerobic Bacteria Vaccines Department, Karaj, Iran.
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3
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Fawzy A, Zschöck M, Ewers C, Eisenberg T. Development of a hierarchical typing approach for Mycobacterium avium subsp. paratuberculosis (MAP) and characterization of MAP field cultures from Central Germany. J Appl Microbiol 2020; 129:1193-1206. [PMID: 32426861 DOI: 10.1111/jam.14722] [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: 10/29/2019] [Revised: 04/30/2020] [Accepted: 05/13/2020] [Indexed: 11/29/2022]
Abstract
AIMS Development of a novel hierarchical Mycobacterium avium subsp. paratuberculosis (MAP) typing approach and characterization of MAP field cultures in Central Germany. METHODS AND RESULTS By combining single nucleotide polymorphisms (SNPs) and mycobacterial interspersed repetitive unit-variable number tandem repeat, we developed a highly discriminating and phylogenetically accurate hierarchical MAP typing approach. Moreover, a novel stepwise workflow was employed to reduce the number of SNP reactions required making the typing approach more affordable. MAP field cultures (n = 142) from dairy herds in Central Germany were classified as cattle type and showed a high level of heterogeneity. Intra-herd multiple genotypes were evident in (13-25%) of the investigated herds. CONCLUSIONS The hierarchical MAP typing approach proved to be useful in fine discrimination between MAP cultures within limited geographical regions. This could potentially be used in unravelling MAP transmission chains in the respective regions. The observed heterogeneity in some herds is assumed to be due to either multiple introductions through inter-herd trade or intra-herd evolution over time. SIGNIFICANCE AND IMPACT OF THE STUDY Future MAP epidemiological studies will benefit from the advantages of the novel hierarchical typing approach. The SNP number reduction approach employed here could be extrapolated for other analogous pathogens.
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Affiliation(s)
- A Fawzy
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, Cairo University, Giza Square, Egypt.,Institute for Hygiene and Infectious Diseases of Animals, Justus-Liebig-University, Giessen, Germany.,Hessian State Laboratory, Giessen, Germany
| | - M Zschöck
- Hessian State Laboratory, Giessen, Germany
| | - C Ewers
- Institute for Hygiene and Infectious Diseases of Animals, Justus-Liebig-University, Giessen, Germany
| | - T Eisenberg
- Institute for Hygiene and Infectious Diseases of Animals, Justus-Liebig-University, Giessen, Germany.,Hessian State Laboratory, Giessen, Germany
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4
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Volpe R, Fett T, Cassart D, Godfroid J, Linden A. Mixed
Mycobacterium avium
subspecies
avium
and
M avium
subspecies
paratuberculosis
infection in a wild red deer (
Cervus elaphus
) in Belgium. VETERINARY RECORD CASE REPORTS 2020. [DOI: 10.1136/vetreccr-2020-001130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Rosario Volpe
- Department of Infectious and Parasitic DiseasesUniversity of LiegeLiegeBelgium
| | - Thomas Fett
- Department of Infectious and Parasitic DiseasesUniversity of LiegeLiegeBelgium
| | - Dominique Cassart
- Department of Infectious and Parasitic DiseasesUniversity of LiegeLiegeBelgium
| | - Jacques Godfroid
- Biosciences, Fisheries and EconomicsUiT The Arctic University of NorwayTromsøNorway
- Department of Arctic and Marine BiologyThe Arctic University of NorwayTromsøNorway
| | - Annick Linden
- Department of Infectious and Parasitic DiseasesUniversity of LiegeLiegeBelgium
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5
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Differential Genotyping of Mycobacterium avium Complex and Its Implications in Clinical and Environmental Epidemiology. Microorganisms 2020; 8:microorganisms8010098. [PMID: 31936743 PMCID: PMC7022546 DOI: 10.3390/microorganisms8010098] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 01/03/2020] [Accepted: 01/07/2020] [Indexed: 11/16/2022] Open
Abstract
In recent decades, the incidence and prevalence of nontuberculous mycobacteria (NTM) have greatly increased, becoming a major worldwide public health problem. Among numerous NTM species, the Mycobacterium avium complex (MAC) is the most predominant species, causing disease in humans. MAC is recognized as a ubiquitous microorganism, with contaminated water and soil being established sources of infection. However, the reason for the recent increase in MAC-associated disease has not yet been fully elucidated. Furthermore, human MAC infections are associated with a variety of infection sources. To improve the determination of infection sources and epidemiology of MAC, feasible and reliable genotyping methods are required to allow for the characterization of the epidemiology and biology of MAC. In this review, we discuss genotyping methods, such as pulsed-field gel electrophoresis, a variable number of tandem repeats, mycobacterial interspersed repetitive-unit-variable number of tandem repeats, and repetitive element sequence-based PCR that have been applied to elucidate the association between the MAC genotypes and epidemiological dominance, clinical phenotypes, evolutionary process, and control measures of infection. Characterizing the association between infection sources and the epidemiology of MAC will allow for the development of novel preventive strategies for the effective control of MAC infection.
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Cochard T, Branger M, Supply P, Sreevatsan S, Biet F. MAC-INMV-SSR: a web application dedicated to genotyping members of Mycobacterium avium complex (MAC) including Mycobacterium avium subsp. paratuberculosis strains. INFECTION GENETICS AND EVOLUTION 2019; 77:104075. [PMID: 31634642 DOI: 10.1016/j.meegid.2019.104075] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/11/2019] [Accepted: 10/16/2019] [Indexed: 01/27/2023]
Abstract
Genotyping of Mycobacterium avium subsp. paratuberculosis (Map) is an indispensable tool for surveillance of this significant veterinary pathogen. For Map, multi-locus variable number tandem repeat analysis (MLVA) targeting mycobacterial interspersed repetitive units (MIRUs) and other variable number variable-number tandem repeats (VNTRs) was established using 8 markers. In the recent past this standard, portable, reproducible and discriminatory typing method has been frequently applied alone or in combinations with multi-locus short-sequence-repeat (MLSSR) sequencing. With the widespread use of these genotyping methods, standardization between laboratories needs to be managed, and knowledge of existing profiles and newly defined genotypes should be indexed and shared. To meet this need, a web application called "MAC-INMV-SSR database" was developed. This freely accessible service allows users to compare MLVA and MLSSR subtype data of their strains with those of existing reference strains analyzed with the same genotyping methods.
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Affiliation(s)
- Thierry Cochard
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Maxime Branger
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France
| | - Philip Supply
- INSERM U1019, F-59019 Lille Cedex, France; CNRS UMR 8204, F-59019, Lille Cedex, France; Institut Pasteur de Lille, France; Univ Lille Nord de France, F-59019 Lille Cedex, France
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing 48824, USA
| | - Franck Biet
- ISP, INRA, Université de Tours, UMR 1282, 37380 Nouzilly, France.
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7
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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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8
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Fawzy A, Zschöck M, Ewers C, Eisenberg T. Genotyping methods and molecular epidemiology of Mycobacterium avium subsp. paratuberculosis (MAP). Int J Vet Sci Med 2018; 6:258-264. [PMID: 30564606 PMCID: PMC6286618 DOI: 10.1016/j.ijvsm.2018.08.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 08/02/2018] [Accepted: 08/02/2018] [Indexed: 12/22/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease (JD) which affects mainly ruminants and is characterized by chronic diarrhea and emaciation. Johne’s disease is highly prevalent in many countries around the world and leads to high economic losses associated with decreased production. Genotyping of the involved pathogen could be used in the study of population genetics, pathogenesis and molecular epidemiology including disease surveillance and outbreak investigation. Principally, researchers have first assumed the presence of two different MAP strains that are associated with the animal host species (cattle and sheep). However, nowadays MAP characterization depends mainly upon genetic testing using genetic markers such as insertion elements, repetitive sequences and single nucleotide polymorphisms. This work aims to provide an overview of the advances in molecular biological tools used for MAP typing in the last two decades, discuss how these methods have been used to address interesting epidemiological questions, and explore the future prospects of MAP molecular epidemiology given the ever decreasing costs of the high throughput sequencing technology.
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Affiliation(s)
- Ahmad Fawzy
- Faculty of Veterinary Medicine, Department of Medicine and Infectious Diseases, Cairo University, Egypt
- Hessian State Laboratory (LHL), Giessen, Germany
- Institute of Hygiene and Animal Infectious Diseases, Justus-Liebig University, Giessen, Germany
- Corresponding author at: Institute of Hygiene and Animal Infectious Diseases, Justus-Liebig University, Giessen, Germany.
| | | | - Christa Ewers
- Institute of Hygiene and Animal Infectious Diseases, Justus-Liebig University, Giessen, Germany
| | - Tobias Eisenberg
- Hessian State Laboratory (LHL), Giessen, Germany
- Institute of Hygiene and Animal Infectious Diseases, Justus-Liebig University, Giessen, Germany
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9
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Rani M, Narang D, Kumar D, Chandra M, Singh ST, Filia G. ISMap 02 element targeted nested polymerase chain in the detection of Mycobacterium avium subsp. paratuberculosis in fecal samples of cattle and buffaloes. Vet World 2018; 11:397-401. [PMID: 29657435 PMCID: PMC5891858 DOI: 10.14202/vetworld.2018.397-401] [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] [Received: 09/29/2017] [Accepted: 02/21/2018] [Indexed: 11/16/2022] Open
Abstract
Background and Aim Johne's disease is chronic granulomatous enteritis which affects ruminants. There are many diagnostic approaches for the detection of Mycobacterium avium subsp. paratuberculosis (MAP) of which molecular detection methods using various elements are less time consuming and more accurate. The present study was conducted using ISMap02 element for nested polymerase chain reaction (nPCR) based detection of MAP in fecal samples. The aim was to test the sensitivity and specificity of the ISMap02 element and also to use this element for the detection of MAP in fecal samples of cattle and buffaloes. Materials and Methods A total of 211 fecal samples of cattle and buffaloes from different herds around Ludhiana aged between 2 and 13 years were collected, and DNA extraction was done from these samples. The nPCR was carried out for the detection of MAP in fecal samples. Results The ISMap02 element was specific for the detection of MAP only and showed a sensitivity of detection of 7.6 fg/µL of the standard genomic DNA. Among the 211 fecal samples of cattle and buffaloes tested for the ISMap02 element, 18 samples (8.5%) were positive for MAP. Conclusion The ISMap02 element is specific and sensitive for the detection of MAP in various samples, and when used in nPCR format, it can increase the sensitivity of detection.
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Affiliation(s)
- Mamta Rani
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Deepti Narang
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Dinesh Kumar
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Mudit Chandra
- Department of Veterinary Microbiology, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - Sikh Tejinder Singh
- Directorate of Livestock Farms, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
| | - G Filia
- Animal Disease Research Centre, College of Veterinary Science, Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, India
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10
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Bakuła Z, Brzostek A, Borówka P, Żaczek A, Szulc-Kiełbik I, Podpora A, Parniewski P, Strapagiel D, Dziadek J, Proboszcz M, Bielecki J, van Ingen J, Jagielski T. Molecular typing of Mycobacterium kansasii using pulsed-field gel electrophoresis and a newly designed variable-number tandem repeat analysis. Sci Rep 2018; 8:4462. [PMID: 29535391 PMCID: PMC5849605 DOI: 10.1038/s41598-018-21562-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Accepted: 02/06/2018] [Indexed: 11/09/2022] Open
Abstract
Molecular epidemiological studies of Mycobacterium kansasii are hampered by the lack of highly-discriminatory genotyping modalities. The purpose of this study was to design a new, high-resolution fingerprinting method for M. kansasii. Complete genome sequence of the M. kansasii ATCC 12478 reference strain was searched for satellite-like repetitive DNA elements comprising tandem repeats. A total of 24 variable-number tandem repeat (VNTR) loci were identified with potential discriminatory capacity. Of these, 17 were used to study polymorphism among 67 M. kansasii strains representing six subtypes (I-VI). The results of VNTR typing were compared with those of pulsed-field gel electrophoresis (PFGE) with AsnI digestion. Six VNTRs i.e. (VNTR 1, 2, 8, 14, 20 and 23) allow to differentiate analyzed strains with the same discriminatory capacities as use of a 17-loci panel. VNTR typing and PFGE in conjunction revealed 45 distinct patterns, including 11 clusters with 33 isolates and 34 unique patterns. The Hunter-Gaston's discriminatory index was 0.95 and 0.66 for PFGE and VNTR typing respectively, and 0.97 for the two methods combined. In conclusion, this study delivers a new typing scheme, based on VNTR polymorphism, and recommends it as a first-line test prior to PFGE analysis in a two-step typing strategy for M. kansasii.
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Affiliation(s)
- Zofia Bakuła
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Anna Brzostek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Paulina Borówka
- Department of Anthropology, University of Łódź, Łódź, Poland
| | - Anna Żaczek
- Department of Biochemistry and Cell Biology, University of Rzeszów, Rzeszów, Poland
| | | | - Agata Podpora
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Paweł Parniewski
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland
| | - Jarosław Dziadek
- Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Małgorzata Proboszcz
- Department of Internal Medicine, Pulmonary Diseases and Allergy, Medical University of Warsaw, Warsaw, Poland
| | - Jacek Bielecki
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Jakko van Ingen
- Department of Medical Microbiology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Tomasz Jagielski
- Department of Applied Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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11
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Yue R, Liu C, Barrow P, Liu F, Cui Y, Yang L, Zhao D, Zhou X. The isolation and molecular characterization of Mycobacterium avium subsp. paratuberculosis in Shandong province, China. Gut Pathog 2016; 8:9. [PMID: 27006704 PMCID: PMC4802609 DOI: 10.1186/s13099-016-0092-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 02/29/2016] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Mycobacterium avium subspecies paratuberculosis (Map) causes Johne's disease in domestic and wild ruminants. It has been a debate that whether Map can cause Crohn's disease in human. To our knowledge there is no report about molecular characterization of Map in China, although several Map strains have been reported in other country. The objectives of this study was to know the recent prevalence of Johne's disease in dairy farms in Shandong province, and have a better understanding of genotypic distribution of Map in China. METHODS Johne's disease was detected from 1038 individuals in 19 dairy farms by ELISA. Map in fecal and milk specimens was identified by Ziehl-Neelsen staining and confirmed using PCR-REA. In addition, frozen sections of ileum and mesenteric lymph nodes from two Map shedding cows were performed to observe the histopathological changes. Next-generation sequencing technology was performed to get whole genome sequences. RESULT A total of 121 (11.7 %) animals were positive for Map antibody from 1038 sera tested, and 11 (57.9 %) dairy herds were positive for Map antibody. Typically histopathologic changes were observed in mesenteric lymph nodes. We have successfully isolated two Map strains, which both were Map-C. The current genome-wide analysis showed that the genome size of our isolates are respectively 4,750,273 and 4,727,050 bp with a same G + C content of 69.3 %, and the numbers of single nucleotide polymorphisms (SNPs) against Map K-10 are respectively 292 and 296. CONCLUSION Map is a prevalent pathogen among dairy cattle in China. This study successfully isolated two Map strains from one Chinese dairy herd with signs of diarrhoea, and identified that the two isolates were both Map-C. Furthermore, these isolates were most closely related to Map K-10.
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Affiliation(s)
- Ruichao Yue
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Chunfa Liu
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Paul Barrow
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD UK
| | - Fei Liu
- Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101 China
| | - Yongyong Cui
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Lifeng Yang
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Deming Zhao
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
| | - Xiangmei Zhou
- State Key Laboratories for Agrobiotechnology, Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193 China
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12
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Rónai Z, Csivincsik Á, Dán Á, Gyuranecz M. Molecular analysis and MIRU-VNTR typing of Mycobacterium avium subsp. avium, 'hominissuis' and silvaticum strains of veterinary origin. INFECTION GENETICS AND EVOLUTION 2016; 40:192-199. [PMID: 26964909 DOI: 10.1016/j.meegid.2016.03.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 03/02/2016] [Accepted: 03/05/2016] [Indexed: 10/22/2022]
Abstract
Besides Mycobacterium avium subsp. paratuberculosis (MAP), M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS), and 'M. avium subsp. hominissuis' (MAH) are equally important members of M. avium complex, with worldwide distribution and zoonotic potential. Genotypic discrimination is a prerequisite to epidemiological studies which can facilitate disease prevention through revealing infection sources and transmission routes. The primary aim of this study was to identify the genetic diversity within 135 MAA, 62 MAS, and 84 MAH strains isolated from wild and domestic mammals, reptiles and birds. Strains were tested for the presence of large sequence polymorphism LSP(A)17 and were submitted to Mycobacterial interspersed repetitive units-variable-number tandem repeat (MIRU-VNTR) analysis at 8 loci, including MIRU1, 2, 3, and 4, VNTR25, 32, and 259, and MATR9. In 12 strains hsp65 sequence code type was also determined. LSP(A)17 was present only in 19.9% of the strains. All LSP(A)17 positive strains belonged to subspecies MAH. The discriminatory power of the MIRU-VNTR loci set used reached 0.9228. Altogether 54 different genotypes were detected. Within MAH, MAA, and MAS strains 33, 16, and 5 different genotypes were observed. The described genotypes were not restricted to geographic regions or host species, but proved to be subspecies specific. Our knowledge about MAS is limited due to isolation and identification difficulties. This is the first study including a large number of MAS field strains. Our results demonstrate the high diversity of MAH and MAA strains and the relative uniformity of MAS strains.
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Affiliation(s)
- Zsuzsanna Rónai
- Veterinary Diagnostic Directorate, National Food Chain Safety Office (NFCSO), P.O. Box 2, 1581 Budapest, Hungary.
| | - Ágnes Csivincsik
- University of Kaposvar, Diagnostic Imaging and Radiation Oncology, Guba Sándor u. 40., 7400 Kaposvár, Hungary
| | - Ádám Dán
- Veterinary Diagnostic Directorate, National Food Chain Safety Office (NFCSO), P.O. Box 2, 1581 Budapest, Hungary
| | - Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungarian Academy of Sciences, Hungária krt. 21., 1143 Budapest, Hungary
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