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Roos EO, Loubser J, Kerr TJ, Dippenaar A, Streicher E, Olea-Popelka F, Robbe-Austerman S, Stuber T, Buss P, de Klerk-Lorist LM, Warren RM, van Helden PD, Parsons SD, Miller MA. Whole genome sequencing improves the discrimination between Mycobacterium bovis strains on the southern border of Kruger National Park, South Africa. One Health 2023; 17:100654. [PMID: 38283183 PMCID: PMC10810834 DOI: 10.1016/j.onehlt.2023.100654] [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: 07/23/2023] [Accepted: 11/08/2023] [Indexed: 01/30/2024] Open
Abstract
Background Mycobacterium bovis forms part of the Mycobacterium tuberculosis complex and has an extensive host range and zoonotic potential. Various genotyping methods (e.g., spoligotyping) have been used to describe the molecular epidemiology of M. bovis. Advances in whole genome sequencing (WGS) have increased resolution to enable detection of genomic variants to the level of single nucleotide polymorphisms. This is especially relevant to One Health research on tuberculosis which benefits by being able to use WGS to identify epidemiologically linked cases, especially recent transmission. The use of WGS in molecular epidemiology has been extensively used in humans and cattle but is limited in wildlife. This approach appears to overcome the limitations of conventional genotyping methods due to lack of genetic diversity in M. bovis. Methods This pilot study investigated the spoligotype and WGS of M. bovis isolates (n = 7) from wildlife in Marloth Park (MP) and compared these with WGS data from other South African M. bovis isolates. In addition, the greater resolution of WGS was used to explore the phylogenetic relatedness of M. bovis isolates in neighbouring wildlife populations. Results The phylogenetic analyses showed the closest relatives to the seven isolates from MP were isolates from wildlife in Kruger National Park (KNP), which shares a border with MP. However, WGS data indicated that the KNP and MP isolates formed two distinct clades, even though they had similar spoligotypes and identical in silico genetic regions of difference profiles. Conclusions Mycobacterium bovis isolates from MP were hypothesized to be directly linked to KNP wildlife, based on spoligotyping. However, WGS indicated more complex epidemiology. The presence of two distinct clades which were genetically distinct (SNP distance of 19-47) and suggested multiple transmission events. Therefore, WGS provided new insight into the molecular epidemiology of the M. bovis isolates from MP and their relationship to isolates from KNP. This approach will facilitate greater understanding of M. bovis transmission at wildlife-livestock-human interfaces and advances One Health research on tuberculosis, especially across different host species.
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Affiliation(s)
- Eduard O. Roos
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Johannes Loubser
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Tanya J. Kerr
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Elizma Streicher
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Francisco Olea-Popelka
- Department of Pathology and Laboratory Medicine, Schulich Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Suelee Robbe-Austerman
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Tod Stuber
- National Veterinary Services Laboratories, Veterinary Services, Animal and Plant Health Inspection Service, United States Department of Agriculture, Ames, IA, USA
| | - Peter Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Private Bag X402, Skukuza, 1350, South Africa
| | - Lin-Mari de Klerk-Lorist
- Department of Agriculture Land Reform and Rural Development, Office of the State Veterinarian, Kruger National Park, PO Box 12, Skukuza, 1350, South Africa
| | - Robin M. Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Paul D. van Helden
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Sven D.C. Parsons
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
| | - Michele A. Miller
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa
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Kerr TJ, Goosen WJ, Gumbo R, de Klerk-Lorist LM, Pretorius O, Buss PE, Kleynhans L, Lyashchenko KP, Warren RM, van Helden PD, Miller MA. Diagnosis of Mycobacterium bovis infection in free-ranging common hippopotamus (Hippopotamus amphibius). Transbound Emerg Dis 2021; 69:378-384. [PMID: 33423384 DOI: 10.1111/tbed.13989] [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: 07/20/2020] [Revised: 09/29/2020] [Accepted: 01/07/2021] [Indexed: 11/28/2022]
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis) infection, is a multi-host disease which negatively affects the wildlife industry, with adverse consequences for conservation, ecotourism, and game/wildlife sales. Although interspecies transmission has been reported between some wildlife hosts, the risk of spread in complex ecosystems is largely unknown. As a controlled disease, tools for accurate detection of M. bovis infection are crucial for effective surveillance and management, especially in wildlife populations. There are, however, limited species-specific diagnostic tests available for wildlife. Hippopotamuses are rarely tested for M. bovis infection, and infection has not previously been confirmed in these species. In this study, blood and tissue samples collected from common hippopotamus (Hippopotamus amphibius) residing in a bTB-endemic area, the Greater Kruger Protected area (GKPA), were retrospectively screened to determine whether there was evidence for interspecies transmission of M. bovis, and identify tools for M. bovis detection in this species. Using the multi-species DPP® VetTB serological assay, a bTB seroprevalence of 8% was found in hippopotamus from GKPA. In addition, the first confirmed case of M. bovis infection in a free-ranging common hippopotamus is reported, based on the isolation in mycobacterial culture, genetic speciation and detection of DNA in tissue samples. Importantly, the M. bovis spoligotype (SB0121) isolated from this common hippopotamus is shared with other M. bovis-infected hosts in GKPA, suggesting interspecies transmission. These results support the hypothesis that M. bovis infection may be under recognized in hippopotamus. Further investigation is needed to determine the risk of interspecies transmission of M. bovis to common hippopotamus in bTB-endemic ecosystems and evaluate serological and other diagnostic tools in this species.
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Affiliation(s)
- Tanya J Kerr
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wynand J Goosen
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Rachiel Gumbo
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Lin-Mari de Klerk-Lorist
- Skukuza State Veterinary Office, Department of Agriculture, Land Reform and Rural Development, Skukuza, South Africa
| | - Oonagh Pretorius
- Bushbuckridge South State Veterinary Office, Department of Agriculture, Rural Development, Land and Environmental Affairs, Mkhuhlu, South Africa
| | - Peter E Buss
- Veterinary Wildlife Services, South African National Parks, Skukuza, South Africa
| | - Léanie Kleynhans
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Paul D van Helden
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Michele A Miller
- Department of Science and Innovation-National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Pourahmad F, Adams A, Thompson KD, Richards RH. Identification of aquatic mycobacteria based on sequence analysis of the 16S–23S rRNA internal transcribed spacer region. J Med Microbiol 2019; 68:221-229. [DOI: 10.1099/jmm.0.000891] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- F. Pourahmad
- 1School of Veterinary Sciences, Ilam University, PO Box 69315516, Ilam, Iran
| | - A. Adams
- 2Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
| | - K. D. Thompson
- 3Aquaculture Research Group, Moredun Research Institute, Pentlands Science Park Bush Loan, Penicuik, Midlothian, UK
| | - R. H. Richards
- 2Institute of Aquaculture, University of Stirling, Stirling FK9 4LA, UK
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Roos EO, Olea-Popelka F, Buss P, Hausler GA, Warren R, van Helden PD, Parsons SDC, de Klerk-Lorist LM, Miller MA. Measuring antigen-specific responses in Mycobacterium bovis-infected warthogs (Phacochoerus africanus) using the intradermal tuberculin test. BMC Vet Res 2018; 14:360. [PMID: 30458774 PMCID: PMC6247514 DOI: 10.1186/s12917-018-1685-8] [Citation(s) in RCA: 9] [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: 05/24/2018] [Accepted: 11/02/2018] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND Bovine tuberculosis (bTB) caused by Mycobacterium bovis has previously been diagnosed in warthogs and infection can be highly prevalent (> 30%) in endemic areas. Thus, warthogs could potentially be an important species to consider as sentinels for disease surveillance. However, disease surveillance is dependent on availability of accurate diagnostic assays and only a few diagnostic tests have been investigated for warthogs. Furthermore, the tests that have been used in this species require laboratory equipment and trained personnel to obtain results. Therefore, this study investigated the use of the intradermal tuberculin test (ITT) to screen warthogs for bTB, which can be done with minimal equipment and under field conditions by most veterinarians and other qualified professionals. Changes in skin fold thickness measurements at the bovine purified protein derivative (PPD) administration site, between 0 and 72 h, were compared with differential changes between the bovine and avian PPD sites, for 34 warthogs, to evaluate the performance when different interpretation criteria for the ITT was used. RESULTS Using an increase of 1.8 mm or more at the bovine PPD site as a cut-off for positive responders, 69% of 16 M. bovis culture-positive warthogs had a positive test result, with 100% of the 18 culture-negative warthogs considered as test negative. When a differential of 1.2 mm or more in skin fold thickness at the bovine PPD compared to the avian PPD site was used as a cut-off for the comparative ITT, 81% of culture-positive warthogs were considered as test positive, with 100% of culture-negative warthogs considered as test negative. CONCLUSION The findings in this study suggest that the ITT is a promising tool to use when screening warthogs for M. bovis infection.
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Affiliation(s)
- Eduard O. Roos
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000 South Africa
| | - Francisco Olea-Popelka
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 300 W. Drake Rd, Fort Collins, CO 80523 USA
| | - Peter Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Private Bag X402, Skukuza, 1350 South Africa
| | - Guy A. Hausler
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000 South Africa
| | - Robin Warren
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000 South Africa
| | - Paul D. van Helden
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000 South Africa
| | - Sven D. C. Parsons
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000 South Africa
| | - Lin-Mari de Klerk-Lorist
- Office of the State Veterinarian, Kruger National Park, Department of Agriculture, Forestries and Fisheries, PO Box 12, Skukuza, 1350 South Africa
| | - Michele A. Miller
- NRF-DST Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town, 8000 South Africa
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Roos EO, Olea-Popelka F, Buss P, de Klerk-Lorist LM, Cooper D, Warren RM, van Helden PD, Parsons SDC, Miller MA. IP-10: A potential biomarker for detection of Mycobacterium bovis infection in warthogs (Phacochoerus africanus). Vet Immunol Immunopathol 2018; 201:43-48. [PMID: 29914681 DOI: 10.1016/j.vetimm.2018.05.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/30/2018] [Accepted: 05/14/2018] [Indexed: 10/16/2022]
Abstract
Bovine tuberculosis (bTB) is endemic in several areas of South Africa and has been reported in multiple species, including common warthogs (Phacochoerus africanus). Limited diagnostic tests and disease control programs exist for African wildlife. Thus, there is a need to develop techniques for bTB detection in species such as warthogs to assess their role in disease maintenance and spread in multi-host ecosystems. In this study, we obtained blood samples from warthogs in bTB endemic areas to investigate biomarkers for detection of Mycobacterium bovis infection. Warthog whole blood was incubated in QuantiFERON® TB Gold In-Tube tubes and pathogen specific release of interferon gamma (IFN-γ) and interferon gamma induced protein 10 (IP-10) was measured by a sandwich enzyme-linked immunosorbent assay. Although we were unable to measure IFN-γ, we could successfully measure IP-10. The IP-10 assay was able to distinguish between M. bovis-infected and M. bovis-culture negative warthogs, within bTB endemic areas, with an assay specific sensitivity of 68% and specificity of 84%. Of the 88 M. bovis-exposed warthogs screened, 42% were IP-10 test positive. These results indicate warthogs develop a measurable cell-mediated immune response after antigen stimulation of whole blood, which can distinguish between M. bovis-infected and M. bovis-culture negative animals. Thus, the IP-10 assay shows promise as an ante-mortem test to diagnose bTB in warthogs.
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Affiliation(s)
- Eduard O Roos
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa.
| | - Francisco Olea-Popelka
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 300 W. Drake Rd, Fort Collins, CO 80523, USA.
| | - Peter Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Private Bag X402, Skukuza, 1350, South Africa.
| | - Lin-Mari de Klerk-Lorist
- Office of the State Veterinarian, Kruger National Park, PO Box 12, Skukuza 1350, Department of Agriculture, Forestry and Fisheries, South Africa.
| | - David Cooper
- Ezemvelo KwaZulu Natal Wildlife, PO Box 25, Mtubatuba 3935, South Africa.
| | - Robin M Warren
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa.
| | - Paul D van Helden
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa.
| | - Sven D C Parsons
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa.
| | - Michele A Miller
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, PO Box 241, Cape Town 8000, South Africa.
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Roos EO, Olea-Popelka F, Buss P, de Klerk-Lorist LM, Cooper D, van Helden PD, Parsons SDC, Miller MA. Seroprevalence of Mycobacterium bovis infection in warthogs (Phacochoerus africanus) in bovine tuberculosis-endemic regions of South Africa. Transbound Emerg Dis 2018. [PMID: 29520985 DOI: 10.1111/tbed.12856] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis), has been reported in many species including suids. Wild boar are important maintenance hosts of the infection with other suids, that is domestic and feral pigs, being important spillover hosts in the Eurasian ecosystem and in South Africa, warthogs (Phacochoerus africanus) may play a similar role in M. bovis-endemic areas. However, novel diagnostic tests for warthogs are required to investigate the epidemiology of bTB in this species. Recent studies have demonstrated that serological assays are capable of discriminating between M. bovis-infected and uninfected warthogs (Roos et al., ). In this study, an indirect ELISA utilizing M. bovis purified protein derivative (PPD) as a test antigen was used to measure the prevalence and investigate risk factors associated with infection in warthogs from uMhkuze Nature Reserve and the southern region of the Greater Kruger National Park (GKNP). There was a high overall seroprevalence of 38%, with adult warthogs having a higher risk of infection (46%). Seroprevalence also varied by geographic location with warthogs from Marloth Park in the GKNP having the greatest percentage of positive animals (63%). This study indicates that warthogs in M. bovis-endemic areas are at high risk of becoming infected with mycobacteria. Warthogs might present an under-recognized disease threat in multi-species systems. They might also serve as convenient sentinels for M. bovis in endemic areas. These findings highlight the importance of epidemiological studies in wildlife to understand the role each species plays in disease ecology.
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Affiliation(s)
- E O Roos
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - F Olea-Popelka
- Department of Clinical Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, CO, USA
| | - P Buss
- Veterinary Wildlife Services, South African National Parks, Kruger National Park, Skukuza, South Africa
| | - L-M de Klerk-Lorist
- Office of the State Veterinarian, Kruger National Park, Department of Agriculture, Forestry and Fisheries, Skukuza, South Africa
| | - D Cooper
- Ezemvelo KZN Wildlife, Mtubatuba, South Africa
| | - P D van Helden
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - S D C Parsons
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - M A Miller
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical TB Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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Fatahi-Bafghi M. Nocardiosis from 1888 to 2017. Microb Pathog 2017; 114:369-384. [PMID: 29146497 DOI: 10.1016/j.micpath.2017.11.012] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 11/06/2017] [Accepted: 11/09/2017] [Indexed: 01/11/2023]
Abstract
The genus Nocardia is an aerobic bacterium, Gram-positive and catalase positive that is in Nocardiaceae family. This bacterium first described by Edmond Nocard in 1888 and is not in human commensal bacteria. To date, nocardiosis incidence is increasing due to increase population growth rate, increase in patients with immune disorder diseases and immunocompromised patients. We surveyed taxonomic position, isolation methods, phenotypic and molecular identification at the genus and species levels, antibiogram, treatment and epidemiology in the world from 1888 to 2017.
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Affiliation(s)
- Mehdi Fatahi-Bafghi
- Department of Microbiology, Faculty of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran.
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Roos EO, Buss P, de Klerk-Lorist LM, Hewlett J, Hausler GA, Rossouw L, McCall AJ, Cooper D, van Helden PD, Parsons SD, Miller MA. Test performance of three serological assays for the detection of Mycobacterium bovis infection in common warthogs (Phacochoerus africanus). Vet Immunol Immunopathol 2016; 182:79-84. [DOI: 10.1016/j.vetimm.2016.10.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 10/15/2016] [Accepted: 10/18/2016] [Indexed: 10/20/2022]
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9
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Lucheta AR, Otero XL, Macías F, Lambais MR. Bacterial and archaeal communities in the acid pit lake sediments of a chalcopyrite mine. Extremophiles 2013; 17:941-51. [DOI: 10.1007/s00792-013-0576-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 07/30/2013] [Indexed: 10/26/2022]
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10
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Molecular epidemiology of mycobacteriosis in wildlife and pet animals. Vet Clin North Am Exot Anim Pract 2011; 15:1-23, v. [PMID: 22244110 DOI: 10.1016/j.cvex.2011.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Abstract
The ecology of mycobacteria is shifting in accordance with environmental change and new patterns of interaction between wildlife, humans, and nondomestic animals. Infection of vertebrate hosts throughout the world is greater now than ever and includes a growing prevalence in free ranging and captive wild animals. Molecular epidemiologic studies using standardized methods with high discriminatory power are useful for tracking individual cases and outbreaks, identifying reservoirs, and describing patterns of transmission and are used with increasing frequency to characterize disease wildlife. This review describes current features of mycobacteriosis in wildlife species based on traditional descriptive studies and recent molecular applications.
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Robledo JA, Murillo AM, Rouzaud F. Physiological role and potential clinical interest of mycobacterial pigments. IUBMB Life 2011; 63:71-8. [PMID: 21360635 DOI: 10.1002/iub.424] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The production of pigments by bacterial colonies has sparked interest among bacteriologists since the 19th century, whether for taxonomy or, in the case of carotenoids for their association with antibiotics resistance. Mycobacteria have gained a very special place in the bacterial world due to their clinical importance. Alone, Mycobacterium tuberculosis is responsible for about two million deaths annually worldwide making tuberculosis one of the most influential diseases in the history of mankind. Almost half of the Nontuberculous Mycobacteria species identified are associated with opportunistic infections in animals and humans. Mycobacterial pigmentary characteristics started to be documented about 80 years ago; but to date, their main use has been only for limited taxonomic and identification purposes. While mycobacterial pigments, especially carotenoids have been clearly associated with cellular photoprotection and survival, the regulation of their production and their physiological role have been largely unstudied. Recent advances in deciphering mycobacterial genomes and characterization of carotenoid synthesis genes, combined with an urgent need for innovative approaches to understand Mycobacterium tuberculosis pathogenic properties open new avenues for exciting research opportunities that might lead to new therapeutic strategies against a devastating secular disease.
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Affiliation(s)
- Jaime A Robledo
- Corporación para Investigaciones Biológicas, Unidad de Bacteriologia, Medellín, Colombia
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Sequence‐Based Identification and Characterization of Mycobacteria. Mol Microbiol 2011. [DOI: 10.1128/9781555816834.ch27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ravva SV, Sarreal CZ, Mandrell RE. Bacterial communities in aerosols and manure samples from two different dairies in central and Sonoma valleys of California. PLoS One 2011; 6:e17281. [PMID: 21364996 PMCID: PMC3041799 DOI: 10.1371/journal.pone.0017281] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Accepted: 01/28/2011] [Indexed: 11/19/2022] Open
Abstract
Aerosols have been suspected to transport food pathogens and contaminate fruits and vegetables grown in close proximity to concentrated animal feeding operations, but studies are lacking that substantiate such transport. To monitor the potential transport of bacteria originated from fresh or dry manure through aerosols on a dairy, we identified by 16S rRNA sequencing, bacteria in aerosols collected within 2 to 3 meters from dairy cows at two dairies. Gram-positive Firmicutes were predominant in aerosols from a dairy in Sonoma, California, and surrounded by vineyards, in contrast to sequences of Gram-negative Proteobacteria predominant in aerosols from a dairy in Modesto, California, also surrounded by other dairies. Although Firmicutes represented approximately 50% of the 10 most abundant sequences, aerosols from the Sonoma dairy also contained sequences of Bacteriodetes and Actinobacteria, identified previously with animal feces. While none of the top 10 sequences from fresh or dry manure from Modesto dairy were detected in aerosols, two of the sequences from the phylum Bacteriodetes and one from class Clostridia from fresh manure were detected in aerosols from Sonoma. Interestingly, none of the sequences from dry manure were in the top 10 sequences in aerosols from both dairies. The 10 most abundant sequences in aerosols from the Modesto dairy were all from Proteobacteria and nearly half of them were from genus Massilia, which have been isolated previously from immune-compromised people and aerosols. We conclude that the predominant bacteria in aerosols are diverse among locations and that they do not reflect the predominant species of bacteria present in cow feces and/or in close proximity to cows. These results suggest that the aerosol sequences did not originate from manure. Large volumes of aerosols would be required to determine if bacterial sequences from aerosols could be used to track bacteria in manure to crops grown in proximity.
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Affiliation(s)
- Subbarao V. Ravva
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, United States Department of Agriculture, Albany, California, United States of America
- * E-mail:
| | - Chester Z. Sarreal
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, United States Department of Agriculture, Albany, California, United States of America
| | - Robert E. Mandrell
- Produce Safety and Microbiology Research Unit, Western Regional Research Center, Agriculture Research Service, United States Department of Agriculture, Albany, California, United States of America
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14
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Thorel MF, Falkinham JO, Moreau RG. Environmental mycobacteria from alpine and subalpine habitats. FEMS Microbiol Ecol 2009; 49:343-7. [PMID: 19712284 DOI: 10.1016/j.femsec.2004.04.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Abstract Mycobacteria were isolated from a variety of materials such as soil, peat, humus, tufa, sphagnum, and wood, collected in alpine and subalpine habitats. Mycobacteria, including Mycobacterium kansasii, Mycobacterium malmoense, Mycobacterium szulgai, Mycobacterium gordonae, Mycobacterium terrae, Mycobacterium chelonae, and Mycobacterium fortuitum were recovered from 69 of 81 (85%) samples. All of the isolates were recovered on medium incubated at 20 and 30 degrees C. None were recovered if the medium was incubated at 37 degrees C. The isolation of mycobacteria confirms the presence of these opportunistic pathogens in alpine habitats.
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15
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Gey van Pittius NC, Sampson SL, Lee H, Kim Y, van Helden PD, Warren RM. Evolution and expansion of the Mycobacterium tuberculosis PE and PPE multigene families and their association with the duplication of the ESAT-6 (esx) gene cluster regions. BMC Evol Biol 2006; 6:95. [PMID: 17105670 PMCID: PMC1660551 DOI: 10.1186/1471-2148-6-95] [Citation(s) in RCA: 311] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2006] [Accepted: 11/15/2006] [Indexed: 11/18/2022] Open
Abstract
Background The PE and PPE multigene families of Mycobacterium tuberculosis comprise about 10% of the coding potential of the genome. The function of the proteins encoded by these large gene families remains unknown, although they have been proposed to be involved in antigenic variation and disease pathogenesis. Interestingly, some members of the PE and PPE families are associated with the ESAT-6 (esx) gene cluster regions, which are regions of immunopathogenic importance, and encode a system dedicated to the secretion of members of the potent T-cell antigen ESAT-6 family. This study investigates the duplication characteristics of the PE and PPE gene families and their association with the ESAT-6 gene clusters, using a combination of phylogenetic analyses, DNA hybridization, and comparative genomics, in order to gain insight into their evolutionary history and distribution in the genus Mycobacterium. Results The results showed that the expansion of the PE and PPE gene families is linked to the duplications of the ESAT-6 gene clusters, and that members situated in and associated with the clusters represent the most ancestral copies of the two gene families. Furthermore, the emergence of the repeat protein PGRS and MPTR subfamilies is a recent evolutionary event, occurring at defined branching points in the evolution of the genus Mycobacterium. These gene subfamilies are thus present in multiple copies only in the members of the M. tuberculosis complex and close relatives. The study provides a complete analysis of all the PE and PPE genes found in the sequenced genomes of members of the genus Mycobacterium such as M. smegmatis, M. avium paratuberculosis, M. leprae, M. ulcerans, and M. tuberculosis. Conclusion This work provides insight into the evolutionary history for the PE and PPE gene families of the mycobacteria, linking the expansion of these families to the duplications of the ESAT-6 (esx) gene cluster regions, and showing that they are composed of subgroups with distinct evolutionary (and possibly functional) differences.
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Affiliation(s)
- Nicolaas C Gey van Pittius
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, US/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Samantha L Sampson
- Department of Molecular Microbiology and Infection, Centre for Molecular Microbiology and Infection, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Kangwon-do, Korea
| | - Yeun Kim
- Department of Biomedical Laboratory Science, College of Health Science, Yonsei University, Kangwon-do, Korea
| | - Paul D van Helden
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, US/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M Warren
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, US/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
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16
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Park H, Kim C, Park KH, Chang CL. Development and evaluation of triplex PCR for direct detection of mycobacteria in respiratory specimens. J Appl Microbiol 2006; 100:161-7. [PMID: 16405696 DOI: 10.1111/j.1365-2672.2005.02719.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To develop a method for the simultaneous detection of Mycobacterium tuberculosis, Mycobacterium avium-intracellularecomplex (MAC), and other mycobacteria in clinical specimens using triplex PCR. METHODS AND RESULTS The target of amplification was the internal transcribed spacer region between the l6S and 23S rDNA genes. Twenty-two mycobacterial type strains, 118 M. tuberculosis, 87 other mycobacteria, 75 nonmycobacterial pathogens, 115 respiratory specimens from confirmed cases of tuberculous or other mycobacterial diseases, and sputa from 50 patients with nonmycobacterial respiratory diseases were tested. In M. tuberculosis, 322 bp pan-mycobacterial and 133 bp species-specific bands were observed. In MAC, the respective bands were 322 and 84 bp. The other mycobacteria showed single pan-mycobacterial bands of approx. 300-350 bp. Nonspecific amplicons were not found in any of the nonmycobacterial pathogens. In the tuberculosis specimens, 96.4% of smear-positive specimens and 70.2% of smear-negative specimens showed positive reactions. Specimens from two patients with MAC infection were MAC positive. Only 1 of 50 specimens from nonmycobacterial diseases was positive (2.0%). CONCLUSION, SIGNIFICANCE AND IMPACT OF THE STUDY Triplex PCR enables accurate and rapid diagnosis of tuberculosis and probably is useful for the detection of MAC and other mycobacteria in respiratory specimens.
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Affiliation(s)
- H Park
- Department of Biochemistry, College of Medicine, Pusan National University, Busan, Korea
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17
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Rhodes MW, Kator H, McNabb A, Deshayes C, Reyrat JM, Brown-Elliott BA, Wallace R, Trott KA, Parker JM, Lifland B, Osterhout G, Kaattari I, Reece K, Vogelbein W, Ottinger CA. Mycobacterium pseudoshottsii sp. nov., a slowly growing chromogenic species isolated from Chesapeake Bay striped bass (Morone saxatilis). Int J Syst Evol Microbiol 2005; 55:1139-1147. [PMID: 15879246 DOI: 10.1099/ijs.0.63343-0] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A group of slowly growing photochromogenic mycobacteria was isolated from Chesapeake Bay striped bass (Morone saxatilis) during an epizootic of mycobacteriosis. Growth characteristics, acid-fastness and 16S rRNA gene sequencing results were consistent with those of the genus Mycobacterium. Biochemical reactions, growth characteristics and mycolic acid profiles (HPLC) resembled those of Mycobacterium shottsii, a non-pigmented mycobacterium also isolated during the same epizootic. Sequencing of the 16S rRNA genes, the gene encoding the exported repeated protein (erp) and the gene encoding the 65 kDa heat-shock protein (hsp65) and restriction enzyme analysis of the hsp65 gene demonstrated that this group of isolates is unique. Insertion sequences associated with Mycobacterium ulcerans, IS2404 and IS2606, were detected by PCR. These isolates could be differentiated from other slowly growing pigmented mycobacteria by their inability to grow at 37 °C, production of niacin and urease, absence of nitrate reductase, negative Tween 80 hydrolysis and resistance to isoniazid (1 μg ml−1), p-nitrobenzoic acid, thiacetazone and thiophene-2-carboxylic hydrazide. On the basis of this polyphasic study, it is proposed that these isolates represent a novel species, Mycobacterium pseudoshottsii sp. nov. The type strain, L15T, has been deposited in the American Type Culture Collection as ATCC BAA-883T and the National Collection of Type Cultures (UK) as NCTC 13318T.
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MESH Headings
- Animals
- Anti-Bacterial Agents/pharmacology
- Bacterial Proteins/genetics
- Bacterial Typing Techniques
- Bass/microbiology
- Chaperonin 60
- Chaperonins/genetics
- DNA Transposable Elements
- DNA, Bacterial/chemistry
- DNA, Bacterial/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/isolation & purification
- Genes, rRNA
- Molecular Sequence Data
- Mycobacterium/classification
- Mycobacterium/isolation & purification
- Mycobacterium/physiology
- Mycolic Acids/analysis
- Mycolic Acids/isolation & purification
- Phylogeny
- Polymorphism, Restriction Fragment Length
- RNA, Bacterial/genetics
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Virginia
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Affiliation(s)
- Martha W Rhodes
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, USA
| | - Howard Kator
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, USA
| | - Alan McNabb
- Laboratory Services, British Columbia Centre for Disease Control, Vancouver BC, Canada V5Z 4R4
| | - Caroline Deshayes
- Avenir Group, Inserm U570, Avenir Group, Faculté de Médecine Necker-Enfants Malades, 75730 Paris Cedex 15, France
| | - Jean-Marc Reyrat
- Avenir Group, Inserm U570, Avenir Group, Faculté de Médecine Necker-Enfants Malades, 75730 Paris Cedex 15, France
| | | | - Richard Wallace
- Mycobacteria/Nocardia Laboratory, University of Texas Health Center, Tyler, TX 75708, USA
| | - Kristin A Trott
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - John M Parker
- Office of Laboratory Animal Care, University of California, Berkeley, CA 94720, USA
| | - Barry Lifland
- Department of Comparative Medicine, Stanford University, Stanford, CA 94305, USA
| | | | - Ilsa Kaattari
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, USA
| | - Kimberly Reece
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, USA
| | - Wolfgang Vogelbein
- Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, USA
| | - Christopher A Ottinger
- US Geological Survey, Leetown Science Center, National Fish Health Research Laboratory, Kearneysville, WV 25430, USA
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18
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Tortoli E, Rindi L, Garcia MJ, Chiaradonna P, Dei R, Garzelli C, Kroppenstedt RM, Lari N, Mattei R, Mariottini A, Mazzarelli G, Murcia MI, Nanetti A, Piccoli P, Scarparo C. Proposal to elevate the genetic variant MAC-A, included in the Mycobacterium avium complex, to species rank as Mycobacterium chimaera sp. nov. Int J Syst Evol Microbiol 2004; 54:1277-1285. [PMID: 15280303 DOI: 10.1099/ijs.0.02777-0] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The possibility that the strains included within the Mycobacterium avium complex (MAC), but not belonging either to M. avium or to Mycobacterium intracellulare, may be members of undescribed taxa, has already been questioned by several taxonomists. A very homogeneous cluster of 12 strains characterized by identical nucleotide sequences both in the 16S rDNA and in the 16S–23S internal transcribed spacer was investigated. Similar strains, previously reported in the literature, had been assigned either to the species M. intracellulare on the basis of the 16S rDNA similarity or to the group of MAC intermediates. However, several phenotypical and epidemiological characteristics seem to distinguish these strains from all other MAC organisms. The unique mycolic acid pattern obtained by HPLC is striking as it is characterized by two clusters of peaks, instead of the three presented by all other MAC organisms. All of the strains have been isolated from humans and all but one came from the respiratory tract of elderly people. The clinical significance of these strains, ascertained for seven patients, seems to suggest an unusually high virulence. The characteristics of all the strains reported in the literature, genotypically identical to the ones described here, seem to confirm our data, without reports of isolations from animals or the environment or, among humans, from AIDS patients. Therefore, an elevation of the MAC variant was proposed and characterized here, with the name Mycobacterium chimaera sp. nov.; this increases the number of species included in the M. avium complex. The type strain is FI-01069T (=CIP 107892T=DSM 44623T).
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Affiliation(s)
- Enrico Tortoli
- Regional Reference Center for Mycobacteria, Microbiology and Virology Laboratory, Careggi Hospital, 50134 Florence, Italy
| | - Laura Rindi
- Department of Experimental Pathology, Medical Biotechnologies, Infectivology and Epidemiology, University of Pisa, 56127 Pisa, Italy
| | - Maria J Garcia
- Department of Preventive Medicine, Autonoma University of Madrid, 28029 Madrid, Spain
| | - Patrizia Chiaradonna
- Microbiology and Virology Laboratory, S. Camillo-Forlanini Hospitals, 00149 Rome, Italy
| | - Rosanna Dei
- Department of Public Health, University of Florence, 50134 Florence, Italy
| | - Carlo Garzelli
- Department of Experimental Pathology, Medical Biotechnologies, Infectivology and Epidemiology, University of Pisa, 56127 Pisa, Italy
| | | | - Nicoletta Lari
- Department of Experimental Pathology, Medical Biotechnologies, Infectivology and Epidemiology, University of Pisa, 56127 Pisa, Italy
| | - Romano Mattei
- Clinical Laboratory, Campo di Marte Hospital, 55100 Lucca, Italy
| | - Alessandro Mariottini
- Genetics and Cytogenetics Unit, Careggi Hospital, 50134 Florence, Italy
- Regional Reference Center for Mycobacteria, Microbiology and Virology Laboratory, Careggi Hospital, 50134 Florence, Italy
| | - Gianna Mazzarelli
- Microbiological and Virological Serum-immunology Laboratory, Careggi Hospital, 50134 Florence, Italy
- Regional Reference Center for Mycobacteria, Microbiology and Virology Laboratory, Careggi Hospital, 50134 Florence, Italy
| | - Martha I Murcia
- Department of Preventive Medicine, Autonoma University of Madrid, 28029 Madrid, Spain
| | - Anna Nanetti
- Department of Specialized and Experimental Clinical Medicine, Microbiology Division, University of Bologna, 40138 Bologna, Italy
| | - Paola Piccoli
- Regional Reference Center for Mycobacteria, S. Bortolo Hospital, 36100 Vicenza, Italy
| | - Claudio Scarparo
- Regional Reference Center for Mycobacteria, S. Bortolo Hospital, 36100 Vicenza, Italy
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Selvarangan R, Wu WK, Nguyen TT, Carlson LDC, Wallis CK, Stiglich SK, Chen YC, Jost KC, Prentice JL, Wallace RJ, Barrett SLR, Cookson BT, Coyle MB. Characterization of a novel group of mycobacteria and proposal of Mycobacterium sherrisii sp. nov. J Clin Microbiol 2004; 42:52-9. [PMID: 14715731 PMCID: PMC321678 DOI: 10.1128/jcm.42.1.52-59.2004] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe here the characterization of five isolates of Mycobacterium simiae-like organisms representing a novel group based on whole-cell fatty acid analysis and genotypic evaluation. Two of the five isolates in this study, W55 and W58, were previously considered to belong to M. simiae serotype 2. Analysis of cellular fatty acids by gas-liquid chromatography indicated a close clustering of this group, which was well differentiated from the other M. simiae-like species. Molecular characterization was performed by nucleic acid sequencing of the small subunit rRNA gene and the gene encoding the 65-kDa heat shock protein and genomic DNA hybridization. Sequence analysis of the entire 16S rRNA gene showed a unique sequence most closely related to those of M. triplex and M. simiae. The hsp65 partial gene sequence was identical for the five isolates, with 97% identity to the M. simiae type strain. However, qualitative whole genomic DNA hybridization analysis confirmed that this group is genetically distinct from M. simiae and M. triplex. Antimicrobial susceptibilities for this group resemble those of M. simiae and M. lentiflavum. We conclude that this group represents a unique Mycobacterium species for which we propose the name Mycobacterium sherrisii sp. nov.
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Affiliation(s)
- Rangaraj Selvarangan
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA.
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20
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Häfner B, Haag H, Geiss HK, Nolte O. Different molecular methods for the identification of rarely isolated non-tuberculous mycobacteria and description of new hsp65 restriction fragment length polymorphism patterns. Mol Cell Probes 2004; 18:59-65. [PMID: 15036371 DOI: 10.1016/j.mcp.2003.09.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2003] [Accepted: 09/09/2003] [Indexed: 12/01/2022]
Abstract
Analysis of heat shock protein 65 (hsp65) gene restriction fragment length polymorphism (RFLP) is done frequently to identify non-tuberculous mycobacteria (NTM) on a genetic basis. Here we report the results of analysing the hsp65 patterns of some rarely isolated NTM for which patterns have not been published before (Mycobacterium bohemicum, Mycobacterium hassiacum, Mycobacterium heckeshornense, Mycobacterium monacense, and Mycobacterium triplex). Furthermore new hsp65-variants for Mycobacterium interjectum (type II), Mycobacterium mucogenicum (type V), Mycobacterium gordonae (type VIII) and Mycobacterium paraffinicum (perhaps synonymous to Mycobacterium scrofulaceum) are described. All species were characterised by hsp65-RFLP, sequencing a 441-bp fragment of the hsp65 gene and sequencing the hypervariable region of the 16S rDNA. Additional data for less frequently isolated mycobacteria are provided and the hitherto described data for the Mycobacterium gordonae complex are summarised. Although the hsp65-RFLP analysis turned out to be a useful method a number of restraints (lack of standardisation, slight variability in fragment length) limits its broader use. Reliable identification of NTM needs, however, more than one molecular method. Identification results obtained by applying different methods yielded conflicting results. Confusion may be caused by older data base entries which are not updated and not longer reflect the actual systematic and taxonomy of the genus Mycobacterium.
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Affiliation(s)
- Bernhard Häfner
- Department of Hygiene and Medical Microbiology, Hygiene-Institute, University of Heidelberg, Im Neuenheimer Feld 324, D-69120 Heidelberg, Germany
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21
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Huard RC, Lazzarini LCDO, Butler WR, van Soolingen D, Ho JL. PCR-based method to differentiate the subspecies of the Mycobacterium tuberculosis complex on the basis of genomic deletions. J Clin Microbiol 2003; 41:1637-50. [PMID: 12682155 PMCID: PMC153936 DOI: 10.1128/jcm.41.4.1637-1650.2003] [Citation(s) in RCA: 193] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The classical Mycobacterium tuberculosis complex (MtbC) subspecies include Mycobacterium tuberculosis, Mycobacterium africanum (subtypes I and II), Mycobacterium bovis (along with the attenuated M. bovis bacillus Calmette-Guérin [BCG]), and Mycobacterium microti; increasingly recognized MtbC groupings include Mycobacterium bovis subsp. caprae and "Mycobacterium tuberculosis subsp. canettii." Previous investigations have documented each MtbC subspecies as a source of animal and/or human tuberculosis. However, study of these organisms is hindered by the lack of a single protocol that quickly and easily differentiates all of the MtbC groupings. Towards this end we have developed a rapid, simple, and reliable PCR-based MtbC typing method that makes use of MtbC chromosomal region-of-difference deletion loci. Here, seven primer pairs (which amplify within the loci 16S rRNA, Rv0577, IS1561', Rv1510, Rv1970, Rv3877/8, and Rv3120) were run in separate but simultaneous reactions. Each primer pair either specifically amplified a DNA fragment of a unique size or failed, depending upon the source mycobacterial DNA. The pattern of amplification products from all of the reactions, visualized by agarose gel electrophoresis, allowed immediate identification either as MtbC composed of M. tuberculosis (or M. africanum subtype II), M. africanum subtype I, M. bovis, M. bovis BCG, M. caprae, M. microti, or "M. canettii" or as a Mycobacterium other than MtbC (MOTT). This MtbC PCR typing panel provides an advanced approach to determine the subspecies of MtbC isolates and to differentiate them from clinically important MOTT species. It has proven beneficial in the management of Mycobacterium collections and may be applied for practical clinical and epidemiological use.
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Affiliation(s)
- Richard C Huard
- Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, New York, New York 10021, USA
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22
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Tortoli E. Impact of genotypic studies on mycobacterial taxonomy: the new mycobacteria of the 1990s. Clin Microbiol Rev 2003; 16:319-54. [PMID: 12692101 PMCID: PMC153139 DOI: 10.1128/cmr.16.2.319-354.2003] [Citation(s) in RCA: 343] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The advancement of genetic techniques has greatly boosted taxonomic studies in recent years. Within the genus Mycobacterium, 42 new species have been detected since 1990, most of which were grown from clinical samples. Along with species for which relatively large numbers of strains have been reported, some of the new species of mycobacteria have been detected rarely or even only once. From the phenotypic point of view, among the new taxa, chromogens exceed nonchromogens while the numbers of slowly and rapidly growing species are equivalent. Whereas conventional identification tests were usually inconclusive, an important role was played by lipid analyses and in particular by high-performance liquid chromatography. Genotypic investigations based on sequencing of 16S rRNA gene have certainly made the most important contribution. The investigation of genetic relatedness led to the redistribution of the species previously included in the classically known categories of slow and rapid growers into new groupings. Within slow growers, the intermediate branch related to Mycobacterium simiae and the cluster of organisms related to Mycobacterium terrae have been differentiated; among rapid growers, the group of thermotolerant mycobacteria has emerged. The majority of species are resistant to isoniazid and, to a lesser extent, to rifampin. Many of the new species of mycobacteria are potentially pathogenic, and there are numerous reports of their involvement in diseases. Apart from disseminated and localized diseases in immunocompromised patients, the most frequent infections in immunocompetent people involve the lungs, skin, and, in children, cervical lymph nodes. The awareness of such new mycobacteria, far from being a merely speculative exercise, is therefore important for clinicians and microbiologists.
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Affiliation(s)
- Enrico Tortoli
- Regional Reference Center for Mycobacteria, Microbiological and Virological Laboratory, Careggi Hospital, 50134 Florence, Italy.
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