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Biet F, Conde C, Cochard T, Mcintoch FA, Behr MA, Bannantine JP. Complete genome sequence of an ovine ancestral strain of Mycobacterium avium subspecies paratuberculosis 6756. Microbiol Resour Announc 2024; 13:e0120723. [PMID: 38441975 PMCID: PMC11008209 DOI: 10.1128/mra.01207-23] [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: 12/08/2023] [Accepted: 02/24/2024] [Indexed: 03/07/2024] Open
Abstract
The complete genome sequence of the most ancestral type SI strain of Mycobacterium avium subspecies paratuberculosis 6756, isolated from a sheep, was determined. The genome was sequenced using PacBio technology, yielding a genome size of 4,830,294 nucleotides with no identified plasmids.
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Affiliation(s)
- Franck Biet
- INRAE, Université de Tours ISP, Nouzilly, France
| | - Cyril Conde
- INRAE, Université de Tours ISP, Nouzilly, France
| | | | | | - Marcel A. Behr
- McGill University Health Centre, Montreal, Quebec, Canada
| | - John P. Bannantine
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, Iowa, USA
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Hodgeman R, Mann R, Djitro N, Savin K, Rochfort S, Rodoni B. The pan-genome of Mycobacterium avium subsp. paratuberculosis (Map) confirms ancestral lineage and reveals gene rearrangements within Map Type S. BMC Genomics 2023; 24:656. [PMID: 37907856 PMCID: PMC10619280 DOI: 10.1186/s12864-023-09752-0] [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: 07/04/2023] [Accepted: 10/18/2023] [Indexed: 11/02/2023] Open
Abstract
BACKGROUND To date genomic studies on Map have concentrated on Type C strains with only a few Type S strains included for comparison. In this study the entire pan-genome of 261 Map genomes (205 Type C, 52 Type S and 4 Type B) and 7 Mycobacterium avium complex (Mac) genomes were analysed to identify genomic similarities and differences between the strains and provide more insight into the evolutionary relationship within this Mycobacterial species. RESULTS Our analysis of the core genome of all the Map isolates identified two distinct lineages, Type S and Type C Map that is consistent with previous phylogenetic studies of Map. Pan-genome analysis revealed that Map has a larger accessory genome than Mycobacterium avium subsp. avium (Maa) and Type C Map has a larger accessory genome than Type S Map. In addition, we found large rearrangements within Type S strains of Map and little to none in Type C and Type B strains. There were 50 core genes identified that were unique to Type S Map and there were no unique core genes identified between Type B and Type C Map strains. In Type C Map we identified an additional CE10 CAZyme class which was identified as an alpha/beta hydrolase and an additional polyketide and non-ribosomal peptide synthetase cluster. Consistent with previous analysis no plasmids and only incomplete prophages were identified in the genomes of Map. There were 45 hypothetical CRISPR elements identified with no associated cas genes. CONCLUSION This is the most comprehensive comparison of the genomic content of Map isolates to date and included the closing of eight Map genomes. The analysis revealed that there is greater variation in gene synteny within Type S strains when compared to Type C indicating that the Type C Map strain emerged after Type S. Further analysis of Type C and Type B genomes revealed that they are structurally similar with little to no genetic variation and that Type B Map may be a distinct clade within Type C Map and not a different strain type of Map. The evolutionary lineage of Maa and Map was confirmed as emerging after M. hominissuis.
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Affiliation(s)
- Rachel Hodgeman
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia.
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia.
| | - Rachel Mann
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Noel Djitro
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Keith Savin
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Simone Rochfort
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, VIC, Australia
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, VIC, Australia
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Byrne A, Bissonnette N, Ollier S, Tahlan K. Investigating in vivo Mycobacterium avium subsp. paratuberculosis microevolution and mixed strain infections. Microbiol Spectr 2023; 11:e0171623. [PMID: 37584606 PMCID: PMC10581078 DOI: 10.1128/spectrum.01716-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/10/2023] [Indexed: 08/17/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's Disease (JD) in ruminants, which is responsible for significant economic loss to the global dairy industry. Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with genetically distinct strains of a pathogen, whereas within-host changes in an infecting strain leading to genetically distinguishable progeny is called microevolution. The two processes can influence host-pathogen dynamics, disease progression and outcomes, but not much is known about their prevalence and impact on JD. Therefore, we obtained up to 10 MAP isolates each from 14 high-shedding animals and subjected them to whole-genome sequencing. Twelve of the 14 animals examined showed evidence for the presence of MSIs and microevolution, while the genotypes of MAP isolates from the remaining two animals could be attributed solely to microevolution. All MAP isolates that were otherwise isogenic had differences in short sequence repeats (SSRs), of which SSR1 and SSR2 were the most diverse and homoplastic. Variations in SSR1 and SSR2, which are located in ORF1 and ORF2, respectively, affect the genetic reading frame, leading to protein products with altered sequences and computed structures. The ORF1 gene product is predicted to be a MAP surface protein with possible roles in host immune modulation, but nothing could be inferred regarding the function of ORF2. Both genes are conserved in Mycobacterium avium complex members, but SSR1-based modulation of ORF1 reading frames seems to only occur in MAP, which could have potential implications on the infectivity of this pathogen. IMPORTANCE Johne's disease (JD) is a major problem in dairy animals, and concerns have been raised regarding the association of Mycobacterium avium subsp. paratuberculosis (MAP) with Crohn's disease in humans. MAP is an extremely slow-growing bacterium with low genome evolutionary rates. Certain short sequence repeats (SSR1 and SSR2) in the MAP chromosome are highly variable and evolve at a faster rate than the rest of the chromosome. In the current study, multiple MAP isolates with genetic variations such as single-nucleotide polymorphisms, and more noticeably, diverse SSRs, could simultaneously infect animals. Variations in SSR1 and SSR2 affect the products of the respective genes containing them. Since multiple MAP isolates can infect the same animal and the possibility that the pathogen undergoes further changes within the host due to unstable SSRs, this could provide a compensative mechanism for an otherwise slow-evolving pathogen to increase phenotypic diversity for overcoming host responses.
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Affiliation(s)
- Alexander Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Séverine Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, Newfoundland and Labrador, Canada
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Genetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0339222. [PMID: 36445077 PMCID: PMC9769990 DOI: 10.1128/spectrum.03392-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Paratuberculosis is a chronic infection of the intestine, mainly the ileum, caused by Mycobacterium avium subsp. paratuberculosis in cattle and other ruminants. This enzootic disease is present worldwide and has a negative impact on the dairy cattle industry. For this subspecies, the current genotyping tools do not provide the needed resolution to investigate the genetic diversity of closely related strains. These limitations can be overcome by the application of whole-genome sequencing (WGS), particularly for clonal populations such as M. avium subsp. paratuberculosis. The purpose of the present study was to undertake a WGS analysis with a panel of 200 animal field M. avium subsp. paratuberculosis strains selected based on a previous large-scale longitudinal study of Prim'Holstein and Normande dairy breeds naturally infected with M. avium subsp. paratuberculosis in the West of France. The pangenome analysis revealed that M. avium subsp. paratuberculosis has a closed pangenome. The phylogeny, based on alignment of 2,786 nonhomoplasic single nucleotide polymorphisms (SNPs), showed that the strain population is structured into three clades independently of the cattle breed or geographic distribution. The increased resolution of phylogeny obtained by WGS confirmed the homoplasic nature of the markers variable-number tandem repeat (VNTR) and short sequence repeat (SSR) used for M. avium subsp. paratuberculosis genotyping. These phylogenetic data also revealed independent introductions of the different genotypes in two main waves since at least 2003. WGS applied to this sampling demonstrated the presence of mixed infections in herds and at the individual animal level. Collectively, the phylogeny results inferred with French isolates compared to M. avium subsp. paratuberculosis isolates from around the world suggest introductions of M. avium subsp. paratuberculosis genotypes through the animal trade. Relationships between genetic traits and epidemiological data can now be investigated to better understand transmission dynamics of the disease. IMPORTANCE Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants, which is present worldwide and has significant negative impacts on the dairy cattle industry and animal welfare. Prevention and control of M. avium subsp. paratuberculosis infection are hampered by knowledge gaps in strain virulence, genotype distribution, and transmission dynamics. This work has revealed new insights into M. avium subsp. paratuberculosis strains currently circulating in western France and how they are related to strains circulating globally. We applied whole-genome sequencing (WGS) to obtain comprehensive information on genome evolution and discrimination of closely related strains. This approach revealed the history of M. avium subsp. paratuberculosis infection in France, refined the pangenomic characteristics of M. avium subsp. paratuberculosis, and demonstrated the existence of mixed infection in animals. Finally, this study identified predominant genotypes, which allow a better understanding of disease transmission dynamics. This information will facilitate tracking of this pathogen on farms and across agricultural regions, thus informing transmission pathways and disease control points.
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Schmidt V, Köhler H, Heenemann K, Möbius P. Mycobacteriosis in Various Pet and Wild Birds from Germany: Pathological Findings, Coinfections, and Characterization of Causative Mycobacteria. Microbiol Spectr 2022; 10:e0045222. [PMID: 35852339 PMCID: PMC9430480 DOI: 10.1128/spectrum.00452-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/27/2022] [Indexed: 12/02/2022] Open
Abstract
A total of 50 birds diagnosed with mycobacteriosis were examined for pathomorphological lesions, coinfections, and causative agents. Mycobacterial species were identified and isolates differentiated using multilocus sequence typing (MLST) and mycobacterial interspersed repetitive-unit variable-number of tandem-repeat (MIRU-VNTR) analysis. Possible associations between mycobacterial species, pathomorphological findings, coinfections, bird orders, and husbandry conditions were evaluated statistically. Mycobacteria were isolated from 34 birds (13 of 22 Psittaciformes, 12 of 18 Passeriformes, five of six Columbiformes, and four other orders) belonging to 26 species in total. Mycobacterium genavense (Mg) was cultured from 15 birds, Mycobacterium avium subsp. avium (Maa) from 20 birds, and Mycobacterium avium subsp. hominissuis (Mah) from three birds; hence, four birds had mixed infections. About equal numbers of psittacines and passerines were infected with Ma and Mg. The genetic diversity differed; Mg isolates belonged to one MLST type, Maa to six, and Mah to three combined genotypes. Several coinfections were detected; viruses and/or endoparasites affected 44%, fungi 38%, and bacteria 29% of the birds. Pathological findings and mycobacteriosis-affected organs were independent of coinfections. Overall, gross pathological findings were more often seen in mycobacteriosis caused by Ma (95%) compared with Mg (66%). Organ distribution of mycobacteriosis was independent of the mycobacterial species. Pathomorphological changes were seen in the small intestine of 71% and the lung of 65% of the birds, suggesting oral or pulmonal ingestion of mycobacteria. There were no associations between mycobacterial species and bird orders or bird husbandry conditions. Not only Mg, but also Maa and Mah, were clearly identified as primary cause of mycobacteriosis in pet birds. IMPORTANCE In this study, the causative agents and confounding factors of mycobacteriosis in a set of pet and some wild birds from Germany were examined. Not only Mycobacterium genavense, but also M. avium subsp. avium and M. avium subsp. hominissuis, contributed to mycobacteriosis in these birds. Various coinfections did not affect the manifestation of mycobacteriosis. Due to different gross necropsy findings, however, a different pathogenicity of the two species was assumed. New strains of M. avium subsp. hominissuis originating from birds were identified and characterized, which is important for epidemiological studies and for understanding the zoonotic role of this pathogen, as the subsp. hominissuis represents an increasing public health concern. The study provides some evidence of correlation between M. avium subsp. avium genotypes and virulence which will have to be confirmed by broader studies.
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Grants
- Clinic for Birds and Reptiles, University of Leipzig, Germany
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Jena, Germany
- Institute for Virology, University of Leipzig, Germany
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Anmial Health), Jena, Germany
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Affiliation(s)
- Volker Schmidt
- Clinic for Birds and Reptiles, University of Leipzig, Leipzig, Germany
| | - Heike Köhler
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (Federal Research Institute for Animal Health), Jena, Germany
| | | | - Petra Möbius
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institute (Federal Research Institute for Animal Health), Jena, Germany
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Mizzi R, Plain KM, Whittington R, Timms VJ. Global Phylogeny of Mycobacterium avium and Identification of Mutation Hotspots During Niche Adaptation. Front Microbiol 2022; 13:892333. [PMID: 35602010 PMCID: PMC9121174 DOI: 10.3389/fmicb.2022.892333] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 04/06/2022] [Indexed: 12/27/2022] Open
Abstract
Mycobacterium avium is separated into four subspecies: M. avium subspecies avium (MAA), M. avium subspecies silvaticum (MAS), M. avium subspecies hominissuis (MAH), and M. avium subspecies paratuberculosis (MAP). Understanding the mechanisms of host and tissue adaptation leading to their clinical significance is vital to reduce the economic, welfare, and public health concerns associated with diseases they may cause in humans and animals. Despite substantial phenotypic diversity, the subspecies nomenclature is controversial due to high genetic similarity. Consequently, a set of 1,230 M. avium genomes was used to generate a phylogeny, investigate SNP hotspots, and identify subspecies-specific genes. Phylogeny reiterated the findings from previous work and established that Mycobacterium avium is a species made up of one highly diverse subspecies, known as MAH, and at least two clonal pathogens, named MAA and MAP. Pan-genomes identified coding sequences unique to each subspecies, and in conjunction with a mapping approach, mutation hotspot regions were revealed compared to the reference genomes for MAA, MAH, and MAP. These subspecies-specific genes may serve as valuable biomarkers, providing a deeper understanding of genetic differences between M. avium subspecies and the virulence mechanisms of mycobacteria. Furthermore, SNP analysis demonstrated common regions between subspecies that have undergone extensive mutations during niche adaptation. The findings provide insights into host and tissue specificity of this genetically conserved but phenotypically diverse species, with the potential to provide new diagnostic targets and epidemiological and therapeutic advances.
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Affiliation(s)
- Rachel Mizzi
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Karren M Plain
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia.,Microbiology and Parasitology Research, Elizabeth Macarthur Agricultural Institute, Menangle, NSW, Australia
| | - Richard Whittington
- Farm Animal Health, School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Verlaine J Timms
- Neilan Laboratory of Microbial and Molecular Diversity, College of Engineering, Science and Environment, The University of Newcastle, Newcastle, NSW, Australia
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High rate of reinfection and possible transmission of Mycobacterium avium complex in Northeast Thailand. One Health 2022; 14:100374. [PMID: 35198722 PMCID: PMC8855214 DOI: 10.1016/j.onehlt.2022.100374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 12/12/2021] [Accepted: 02/06/2022] [Indexed: 11/20/2022] Open
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Interaction Patterns between Wildlife and Cattle Reveal Opportunities for Mycobacteria Transmission in Farms from North-Eastern Atlantic Iberian Peninsula. Animals (Basel) 2021; 11:ani11082364. [PMID: 34438821 PMCID: PMC8388635 DOI: 10.3390/ani11082364] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/31/2021] [Accepted: 08/05/2021] [Indexed: 11/16/2022] Open
Abstract
Interactions taking place between sympatric wildlife and livestock may contribute to interspecies transmission of the Mycobacterium tuberculosis complex or non-tuberculous mycobacteria, leading to the spread of relevant mycobacterioses or to interferences with the diagnosis of tuberculosis. The aim of this study was to characterize the spatiotemporal patterns of interactions between wildlife and cattle in a low bovine tuberculosis prevalence Atlantic region. Camera traps were set during a one-year period in cattle farms with a history of tuberculosis and/or non-tuberculous mycobacterioses. The frequency and duration of wildlife visits, and the number of individuals per visit, were analysed through generalized linear mixed models. The seasons, type of place, type of point, and period of the day were the explanatory variables. A total of 1293 visits were recorded during 2741 days of camera observation. Only 23 visits showed direct contacts with cattle, suggesting that mycobacteria transmission at the wildlife-livestock interface would occur mainly through indirect interactions. Cattle pastures represented the most appropriate habitat for interspecies transmission of mycobacteria, and badgers' latrines appear to be a potential hotspot for mycobacteria circulation between badgers, wild boars, foxes, and cattle. According to both previous epidemiological information and the interaction patterns observed, wild boars, badgers, foxes, and small rodents are the species or group most often in contact with livestock, and thus may be the most involved in the epidemiology of mycobacterioses in the wildlife-livestock interface in this area.
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Conde C, Price-Carter M, Cochard T, Branger M, Stevenson K, Whittington R, Bannantine JP, Biet F. Whole-Genome Analysis of Mycobacterium avium subsp. paratuberculosis IS 900 Insertions Reveals Strain Type- Specific Modalities. Front Microbiol 2021; 12:660002. [PMID: 34040595 PMCID: PMC8141618 DOI: 10.3389/fmicb.2021.660002] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 04/07/2021] [Indexed: 01/14/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (Map) is the etiological agent of Johne’s disease in ruminants. The IS900 insertion sequence (IS) has been used widely as an epidemiological marker and target for PCR diagnosis. Updated DNA sequencing technologies have led to a rapid increase in available Map genomes, which makes it possible to analyze the distribution of IS900 in this slow-growing bacterium. The objective of this study is to characterize the distribution of the IS900 element and how it affects genomic evolution and gene function of Map. A secondary goal is to develop automated in silico restriction fragment length polymorphism (RFLP) analysis using IS900. Complete genomes from the major phylogenetic lineages known as C-type and S-type (including subtypes I and III), were chosen to represent the genetic diversity of Map. IS900 elements were located in these genomes using BLAST software and the relevant fragments extracted. An in silico RFLP analysis using the BstEII restriction site was performed to obtain exact sizes of the DNA fragments carrying a copy of IS900 and the resulting RFLP profiles were analyzed and compared by digital visualization of the separated restriction fragments. The program developed for this study allowed automated localization of IS900 sequences to identify their position within each genome along with the exact number of copies per genome. The number of IS900 copies ranged from 16 in the C-type isolate to 22 in the S-type subtype I isolate. A loci-by-loci sequence alignment of all IS900 copies within the three genomes revealed new sequence polymorphisms that define three sequevars distinguishing the subtypes. Nine IS900 insertion site locations were conserved across all genomes studied while smaller subsets were unique to a particular lineage. Preferential insertion motif sequences were identified for IS900 along with genes bordering all IS900 insertions. Rarely did IS900 insert within coding sequences as only three genes were disrupted in this way. This study makes it possible to automate IS900 distribution in Map genomes to enrich knowledge on the distribution dynamics of this IS for epidemiological purposes, for understanding Map evolution and for studying the biological implications of IS900 insertions.
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Affiliation(s)
- Cyril Conde
- INRAE, ISP, Université de Tours, Nouzilly, France
| | | | | | | | | | - Richard Whittington
- School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | | | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
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Matthews C, Cotter PD, O’ Mahony J. MAP, Johne's disease and the microbiome; current knowledge and future considerations. Anim Microbiome 2021; 3:34. [PMID: 33962690 PMCID: PMC8105914 DOI: 10.1186/s42523-021-00089-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/20/2021] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is the causative agent of Johne's disease in ruminants. As an infectious disease that causes reduced milk yields, effects fertility and, eventually, the loss of the animal, it is a huge financial burden for associated industries. Efforts to control MAP infection and Johne's disease are complicated due to difficulties of diagnosis in the early stages of infection and challenges relating to the specificity and sensitivity of current testing methods. The methods that are available contribute to widely used test and cull strategies, vaccination programmes also in place in some countries. Next generation sequencing technologies have opened up new avenues for the discovery of novel biomarkers for disease prediction within MAP genomes and within ruminant microbiomes. Controlling Johne's disease in herds can lead to improved animal health and welfare, in turn leading to increased productivity. With current climate change bills, such as the European Green Deal, targeting livestock production systems for more sustainable practices, managing animal health is now more important than ever before. This review provides an overview of the current knowledge on genomics and detection of MAP as it pertains to Johne's disease.
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Affiliation(s)
- Chloe Matthews
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
| | - Paul D. Cotter
- Teagasc, Food Research Centre, Food Biosciences Department, Fermoy, Co. Cork, Ireland
- APC Microbiome Institute, University College Cork, Co. Cork, Ireland
| | - Jim O’ Mahony
- Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
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Hodgeman R, Mann R, Savin K, Djitro N, Rochfort S, Rodoni B. Molecular characterisation of Mycobacterium avium subsp. paratuberculosis in Australia. BMC Microbiol 2021; 21:101. [PMID: 33789575 PMCID: PMC8012159 DOI: 10.1186/s12866-021-02140-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium avium subsp. paratuberculosis (Map) causes Johne's disease (JD), a chronic enteritis widespread in ruminants, resulting in substantial economic losses, especially to the dairy industry. Understanding the genetic diversity of Map in Australia will assist epidemiological studies for tracking disease transmission and identify subtype characteristics for use in development of improved diagnostic typing methods. Here we investigated the phylogenetic relationships of 351 Map isolates and compared different subtyping methods to assess their suitability for use in diagnostics and accuracy. RESULTS SNP-based phylogenetic analysis of 228 Australian isolates and 123 publicly available international isolates grouped Type S and Type C strains into two distinct lineages. Type C strains were highly monomorphic with only 20 SNP differences separating them. Type S strains, when aligned separately to the Telford strain, fell into two distinct clades: The first clade contained seven international isolates while the second clade contained one international isolate from Scotland and all 59 Australian isolates. The Australian Type B strain clustered with US bison strains. IS1311 PCR and Restriction Enzyme Analysis (REA) intermittently generated incorrect results when compared to Long Sequence Polymorphism (LSP) analysis, whole genome SNP-based phylogenetic analysis, IS1311 sequence alignment and average nucleotide identity (ANI). These alternative methods generated consistent Map typing results. A published SNP based assay for genotyping Map was found to be unsuitable for differentiating between Australian and international strain types of Map. CONCLUSION This is the first phylogenetic analysis of Australian Map isolates. The Type C lineage was highly monomorphic, and the Type S lineage clustered all Australian isolates into one clade with a single Scottish sheep strain. The Australian isolate classified as Type B by IS1311 PCR and REA is likely to be descended from bison and most closely related to US bison strains. Limitations of the current typing methods were identified in this study.
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Affiliation(s)
- Rachel Hodgeman
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia. .,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia.
| | - Rachel Mann
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Keith Savin
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Noel Djitro
- School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Simone Rochfort
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia.,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
| | - Brendan Rodoni
- Agriculture Victoria, AgriBio, La Trobe University, Bundoora, Victoria, Australia.,School of Applied Systems Biology, AgriBio, La Trobe University, Bundoora, Victoria, Australia
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Shin MK, Shin SJ. Genetic Involvement of Mycobacterium avium Complex in the Regulation and Manipulation of Innate Immune Functions of Host Cells. Int J Mol Sci 2021; 22:ijms22063011. [PMID: 33809463 PMCID: PMC8000623 DOI: 10.3390/ijms22063011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium avium complex (MAC), a collection of mycobacterial species representing nontuberculous mycobacteria, are characterized as ubiquitous and opportunistic pathogens. The incidence and prevalence of infectious diseases caused by MAC have been emerging globally due to complications in the treatment of MAC-pulmonary disease (PD) in humans and the lack of understating individual differences in genetic traits and pathogenesis of MAC species or subspecies. Despite genetically close one to another, mycobacteria species belonging to the MAC cause diseases to different host range along with a distinct spectrum of disease. In addition, unlike Mycobacterium tuberculosis, the underlying mechanisms for the pathogenesis of MAC infection from environmental sources of infection to their survival strategies within host cells have not been fully elucidated. In this review, we highlight unique genetic and genotypic differences in MAC species and the virulence factors conferring the ability to MAC for the tactics evading innate immune attacks of host cells based on the recent advances in genetic analysis by exemplifying M. avium subsp. hominissuis, a major representative pathogen causing MAC-PD in humans. Further understanding of the genetic link between host and MAC may contribute to enhance host anti-MAC immunity, but also provide novel therapeutic approaches targeting the pangenesis-associated genes of MAC.
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Affiliation(s)
- Min-Kyoung Shin
- Department of Microbiology and Convergence Medical Sciences, Institute of Health Sciences, College of Medicine, Gyeongsang National University, Jinju 52727, Korea;
| | - Sung Jae Shin
- Department of Microbiology and Institute for Immunology and Immunological Diseases, Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, Seoul 03722, Korea
- Correspondence: ; Tel.: +82-2-2228-1813
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13
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Wibberg D, Price-Carter M, Rückert C, Blom J, Möbius P. Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes. Microorganisms 2020; 9:microorganisms9010070. [PMID: 33383865 PMCID: PMC7823733 DOI: 10.3390/microorganisms9010070] [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: 12/01/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) is a worldwide-distributed obligate pathogen in ruminants causing Johne’s disease. Due to a lack of complete subtype III genome sequences, there is not yet conclusive information about genetic differences between strains of cattle (MAP-C, type II) and sheep (MAP-S) type, and especially between MAP-S subtypes I, and III. Here we present the complete, circular genome of MAP-S/type III strain JIII-386 (DE) closed by Nanopore-technology and its comparison with MAP-S/type I closed genome of strain Telford (AUS), MAP-S/type III draft genome of strain S397 (U.S.), twelve closed MAP-C strains, and eight closed M.-a.-complex-strains. Structural comparative alignments revealed clearly the mosaic nature of MAP, emphasized differences between the subtypes and the higher diversity of MAP-S genomes. The comparison of various genomic elements including transposases and genomic islands provide new insights in MAP genomics. MAP type specific phenotypic features may be attributed to genes of known large sequence polymorphisms (LSPSs) regions I–IV and deletions #1 and #2, confirmed here, but could also result from identified frameshifts or interruptions of various virulence-associated genes (e.g., mbtC in MAP-S). Comprehensive core and pan genome analysis uncovered unique genes (e.g., cytochromes) and genes probably acquired by horizontal gene transfer in different MAP-types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M.-a.-strains.
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Affiliation(s)
- Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Marian Price-Carter
- AgResearch, Hopkirk Research Institute, Grasslands Research Centre, Palmerston North 4442, New Zealand;
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, D-35390 Gießen, Germany;
| | - Petra Möbius
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, 07743 Jena, Germany
- Correspondence: ; Tel.: +49-(0)3641-8042280
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14
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Bannantine JP, Conde C, Bayles DO, Branger M, Biet F. Genetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences. Front Microbiol 2020; 11:1701. [PMID: 32849358 PMCID: PMC7426613 DOI: 10.3389/fmicb.2020.01701] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/29/2020] [Indexed: 11/13/2022] Open
Abstract
Mycobacterium avium comprises four subspecies that contain both human and veterinary pathogens. At the inception of this study, twenty-eight M. avium genomes had been annotated as RefSeq genomes, facilitating direct comparisons. These genomes represent strains from around the world and provided a unique opportunity to examine genome dynamics in this species. Each genome was confirmed to be classified correctly based on SNP genotyping, nucleotide identity and presence/absence of repetitive elements or other typing methods. The Mycobacterium avium subspecies paratuberculosis (Map) genome size and organization was remarkably consistent, averaging 4.8 Mb with a variance of only 29.6 kb among the 13 strains. Comparing recombination events along with the larger genome size and variance observed among Mycobacterium avium subspecies avium (Maa) and Mycobacterium avium subspecies hominissuis (Mah) strains (collectively termed non-Map) suggests horizontal gene transfer occurs in non-Map, but not in Map strains. Overall, M. avium subspecies could be divided into two major sub-divisions, with the Map type II (bovine strains) clustering tightly on one end of a phylogenetic spectrum and Mah strains clustering more loosely together on the other end. The most evolutionarily distinct Map strain was an ovine strain, designated Telford, which had >1,000 SNPs and showed large rearrangements compared to the bovine type II strains. The Telford strain clustered with Maa strains as an intermediate between Map type II and Mah. SNP analysis and genome organization analyses repeatedly demonstrated the conserved nature of Map versus the mosaic nature of non-Map M. avium strains. Finally, core and pangenomes were developed for Map and non-Map strains. A total of 80% Map genes belonged to the Map core genome, while only 40% of non-Map genes belonged to the non-Map core genome. These genomes provide a more complete and detailed comparison of these subspecies strains as well as a blueprint for how genetic diversity originated.
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Affiliation(s)
- John P Bannantine
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, IA, United States
| | - Cyril Conde
- INRAE, Université de Tours, ISP, Nouzilly, France
| | - Darrell O Bayles
- USDA-Agricultural Research Service, National Animal Disease Center, Ames, IA, United States
| | | | - Franck Biet
- INRAE, Université de Tours, ISP, Nouzilly, France
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15
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Cunha MV, Rosalino LM, Leão C, Bandeira V, Fonseca C, Botelho A, Reis AC. Ecological drivers of Mycobacterium avium subsp. paratuberculosis detection in mongoose (Herpestes ichneumon) using IS900 as proxy. Sci Rep 2020; 10:860. [PMID: 31964932 PMCID: PMC6972914 DOI: 10.1038/s41598-020-57679-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 01/02/2020] [Indexed: 01/10/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the etiological agent of Johne’s disease or paratuberculosis, a chronic infection affecting domestic ruminants worldwide. Despite sporadic reports of MAP occurrence in non-ruminants, information on the risk factors predisposing for infection is still scarce and evidence of transmission paths linking the livestock-wildlife-environment interfaces also remains lacking. In this study, we predicted that environmental, host-related, land use and human driven disturbance factors would modulate carnivore exposure to MAP. To test these hypotheses, we performed a retrospective survey, based on microbiological and molecular methods, in mainland Portugal including five sympatric species from the Herpestidae, Canidae, Viverridae, and Mustelidae families (n = 202) and examined 16 variables as putative predictors of MAP occurrence. Molecular evidence of MAP using IS900 as proxy was demonstrated in 7.43% (95%CI: 4.55–11.9) of surveyed carnivores, the highest proportions being registered for red fox (Vulpes vulpes) (10%; 95%CI: 4.0–23) and Egyptian mongoose (Herpestes ichneumon) (6.0%; 95%CI: 3.2–11). We demonstrate that important species of the Mediterranean carnivore guild, such as stone marten (Martes foina) and common genet (Genetta genetta), may also be exposed to MAP, being this the first time that occurrence in genet is reported. The high proportion of DNA-positive specimens, concurrent with the apparent lack of gastro-enteric lesions and molecular confirmation of IS900 in feces, argue for the presence of subclinical carriers that occasionally shed bacteria, potentially aiding as source of infection to susceptible species and possibly contributing for environmental contamination. Achievement of MAP isolation would prove beyond any doubt that MAP is present in this wildlife population. Ecological modelling results suggested that the probability of MAP infection using IS900 as proxy in mongoose is positively associated with higher altitude and temperature stability, as well as with lower annual rainfall. Density of livestock farms was found not to be a significant predictor, which may indicate that the livestock-wildlife interface is probably not important as an infection route for mongoose.
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Affiliation(s)
- Mónica V Cunha
- INIAV, IP- National Institute for Agrarian and Veterinary Research, Av. da República, Quinta do Marquês, 2780 -157, Oeiras, Portugal. .,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal. .,Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
| | - Luís Miguel Rosalino
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Célia Leão
- INIAV, IP- National Institute for Agrarian and Veterinary Research, Av. da República, Quinta do Marquês, 2780 -157, Oeiras, Portugal
| | - Victor Bandeira
- CESAM & Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Carlos Fonseca
- CESAM & Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Ana Botelho
- INIAV, IP- National Institute for Agrarian and Veterinary Research, Av. da República, Quinta do Marquês, 2780 -157, Oeiras, Portugal
| | - Ana C Reis
- INIAV, IP- National Institute for Agrarian and Veterinary Research, Av. da República, Quinta do Marquês, 2780 -157, Oeiras, Portugal.,Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.,Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
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16
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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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17
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McAloon CG, Roche S, Ritter C, Barkema HW, Whyte P, More SJ, O'Grady L, Green MJ, Doherty ML. A review of paratuberculosis in dairy herds - Part 1: Epidemiology. Vet J 2019; 246:59-65. [PMID: 30902190 DOI: 10.1016/j.tvjl.2019.01.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 11/24/2022]
Abstract
Bovine paratuberculosis is a chronic infectious disease of cattle caused by Mycobacterium avium subspecies paratuberculosis (MAP). This is the first in a two-part review of the epidemiology and control of paratuberculosis in dairy herds. Paratuberculosis was originally described in 1895 and is now considered endemic among farmed cattle worldwide. MAP has been isolated from a wide range of non-ruminant wildlife as well as humans and non-human primates. In dairy herds, MAP is assumed to be introduced predominantly through the purchase of infected stock with additional factors modulating the risk of persistence or fade-out once an infected animal is introduced. Faecal shedding may vary widely between individuals and recent modelling work has shed some light on the role of super-shedding animals in the transmission of MAP within herds. Recent experimental work has revisited many of the assumptions around age susceptibility, faecal shedding in calves and calf-to-calf transmission. Further efforts to elucidate the relative contributions of different transmission routes to the dissemination of infection in endemic herds will aid in the prioritisation of efforts for control on farm.
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Affiliation(s)
- Conor G McAloon
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland.
| | - Steven Roche
- Department of Population Medicine, University of Guelph, 50 Stone Rd., Guelph, ON, N1G 2W1, Canada
| | - Caroline Ritter
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive, Calgary, AB, T2N 1N4, Canada
| | - Herman W Barkema
- Department of Production Animal Health, Faculty of Veterinary Medicine, University of Calgary, 2500 University Drive, Calgary, AB, T2N 1N4, Canada
| | - Paul Whyte
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Simon J More
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Luke O'Grady
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
| | - Martin J Green
- School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Leicestershire, LE12 5RD, United Kingdom
| | - Michael L Doherty
- Section of Herd Health and Animal Husbandry, School of Veterinary Medicine, University College Dublin, Ireland
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18
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Turenne CY. Nontuberculous mycobacteria: Insights on taxonomy and evolution. INFECTION GENETICS AND EVOLUTION 2019; 72:159-168. [PMID: 30654178 DOI: 10.1016/j.meegid.2019.01.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/14/2022]
Abstract
Seventy years have passed since Ernest H. Runyon presented a phenotypic classification approach for nontuberculous mycobacteria (NTM), primarily as a starting point in trying to understand their clinical relevance. From numerical taxonomy (biochemical testing) to 16S rRNA gene sequencing to whole genome sequencing (WGS), our understanding of NTM has also evolved. Novel species are described at a rapid pace, while taxonomical relationships are re-defined in large part due to the accessibility of WGS. The evolutionary course of clonal complexes within species is better known for some NTM and less for others. In contrast with M. tuberculosis, much is left to learn about NTM as a whole.
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Affiliation(s)
- Christine Y Turenne
- Department of Medical Microbiology and Infectious Diseases, Max Rady College of Medicine, University of Manitoba, Winnipeg, MB, Canada; Shared Health - Diagnostic Services, Winnipeg, MB, Canada.
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19
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Schiavano GF, De Santi M, Sisti M, Amagliani G, Brandi G. Disinfection of Mycobacterium avium subspecies hominissuis in drinking tap water using ultraviolet germicidal irradiation. ENVIRONMENTAL TECHNOLOGY 2018; 39:3221-3227. [PMID: 28862077 DOI: 10.1080/09593330.2017.1375028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 08/30/2017] [Indexed: 06/07/2023]
Abstract
Nontuberculous mycobacteria are resistant to conventional water treatments, and are opportunistic human pathogen, particularly in hospitalized patients. The aim of this investigation was to assess the effectiveness of an ultraviolet UV-C lamp treatment against Mycobacterium avium subspecies hominissuis in drinking tap water. Ultraviolet treatments (0-192 mJ/cm2) were performed using UV lamp immerged onto cylindrical glass tubes containing artificially contaminated water. The results showed that susceptibility to UV varied considerably according to the strains and the diameter of the tube. With a dose of 32 mJ/cm2, a significant inactivation (p < .05) of 3 log (99.9%) or more was obtained in only 5 of the 14 strains. To obtain a complete inactivation of all strains an irradiation of 192 mJ/cm2 was needed, a dose that is much higher than the limits recommended by the international standards for UV disinfection of drinking water. In conclusion, it may be difficult to standardize a UV dose for the elimination of waterborne mycobacteria.
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Affiliation(s)
- Giuditta Fiorella Schiavano
- a Department of Biomolecular Science, Toxicological, Hygiene and Environmental Sciences Unit , University of Urbino Carlo Bo , Urbino , PU , Italy
| | - Mauro De Santi
- a Department of Biomolecular Science, Toxicological, Hygiene and Environmental Sciences Unit , University of Urbino Carlo Bo , Urbino , PU , Italy
| | - Maurizio Sisti
- a Department of Biomolecular Science, Toxicological, Hygiene and Environmental Sciences Unit , University of Urbino Carlo Bo , Urbino , PU , Italy
| | - Giulia Amagliani
- a Department of Biomolecular Science, Toxicological, Hygiene and Environmental Sciences Unit , University of Urbino Carlo Bo , Urbino , PU , Italy
| | - Giorgio Brandi
- a Department of Biomolecular Science, Toxicological, Hygiene and Environmental Sciences Unit , University of Urbino Carlo Bo , Urbino , PU , Italy
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20
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Hulinova Stromerova N, Faldyna M. Mycobacterium avium complex infection in pigs: A review. Comp Immunol Microbiol Infect Dis 2018; 57:62-68. [PMID: 30017080 DOI: 10.1016/j.cimid.2018.06.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 04/18/2018] [Accepted: 06/10/2018] [Indexed: 11/19/2022]
Abstract
Mycobacterial infections in pigs are caused particularly by the Mycobacterium avium complex (MAC) and these infections lead to great economic losses mainly within the countries with high pork meat production. The importance of the MAC infections in humans is rising because of its higher prevalence and also higher mortality rates particularly in advanced countries. In addition, treatment of the MAC infections in humans tends to be complicated because of its increasing resistance to antimicrobial agents. Several studies across Europe have documented the MAC occurrence in the slaughtered pigs - not only in their lymph nodes and tonsils, which are the most frequent, but also in the diaphragmas, other organs and not least in meat. This is why we need both more specific and more sensitive methods for the MAC infection detection. Different PCR assays were established as well as advanced intravital testing by the gamma interferon release test. On the other hand, tuberculin skin test is still one of the cheapest methods of mycobacterial infections detection.
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Affiliation(s)
- Nikola Hulinova Stromerova
- State Veterinary Institute Olomouc, Jakoubka ze Stříbra 1, 779 00 Olomouc, Czech Republic; Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic
| | - Martin Faldyna
- Veterinary Research Institute, Hudcova 70, 621 00 Brno, Czech Republic.
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21
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Yano H, Iwamoto T, Nishiuchi Y, Nakajima C, Starkova DA, Mokrousov I, Narvskaya O, Yoshida S, Arikawa K, Nakanishi N, Osaki K, Nakagawa I, Ato M, Suzuki Y, Maruyama F. Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis. Genome Biol Evol 2018; 9:2403-2417. [PMID: 28957464 PMCID: PMC5622343 DOI: 10.1093/gbe/evx183] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most common nontuberculous mycobacterial species responsible for chronic lung disease in humans. Despite increasing worldwide incidence, little is known about the genetic mechanisms behind the population evolution of MAH. To elucidate the local adaptation mechanisms of MAH, we assessed genetic population structure, the mutual homologous recombination, and gene content for 36 global MAH isolates, including 12 Japanese isolates sequenced in the present study. We identified five major MAH lineages and found that extensive mutual homologous recombination occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant in the Japanese isolates. We identified alleles unique to these two East Asian lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in one mammalian cell entry operon, which presumably originated from as yet undiscovered mycobacterial lineages. Several genes and alleles unique to East Asian strains were located in the fragments introduced via recombination between East Asian lineages, suggesting implication of recombination in local adaptation. These patterns of MAH genomes are consistent with the signature of distribution conjugative transfer, a mode of sexual reproduction reported for other mycobacterial species.
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Affiliation(s)
- Hirokazu Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | | | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Olga Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Ken Osaki
- TOMY Digital Biology Co. Ltd, Taito-Ku, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku-Ku, Tokyo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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22
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Scherrer S, Landolt P, Carroli N, Stephan R. Molecular Characterization of Mycobacterium avium subsp. hominissuis of Two Groups of Lymph Nodes, Being Intradermal Tuberculin or Interferon-Gamma Test Positive and Negative, Isolated from Swiss Cattle at Slaughter. Front Vet Sci 2018; 5:32. [PMID: 29556502 PMCID: PMC5844927 DOI: 10.3389/fvets.2018.00032] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/15/2018] [Indexed: 11/15/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is an important zoonotic pathogen with raising global health concerns. In humans, MAH is one of the most widespread non-tuberculous mycobacterial species responsible for lung disease. In animals, MAH is frequently isolated from pigs; however, it is also an opportunistic pathogen for other mammals including cattle. To elucidate the genetic diversity of MAH in cattle, a molecular characterization of isolates (n = 26) derived from lymph nodes was performed. Fourteen isolates originated from slaughtered cattle with visible altered lymph nodes at meat inspection, whereas 12 isolates were from lymph nodes without any gross pathological changes of healthy slaughtered cattle. Variable number of tandem repeat (VNTR) analysis was performed at 20 loci to examine genetic differences of isolates and to compare to previously reported VNTR data of human isolates from different countries. Genetic elements IS901, IS1245, IS1311, LSPA17, ITS1 sequevar, and hsp65 code were determined. Interestingly, two bovine MAH isolates harbored ISMav6 and hsp65 code 15, which so far has only been observed in human isolates. We supposed that VNTR data of Swiss samples would show clustering with European samples. Minimum spanning tree and unweighted pair group method using arithmetic averages analyses based on the VNTR data indicated a specific cluster of MAH isolates obtained from lymph nodes without any gross pathological changes of healthy slaughtered cattle. Comparing Swiss isolates with isolates from different other countries, no geographical clustering was observed; however, four Swiss isolates had an identical VNTR profile as human isolates from the Netherlands, the United States, and Japan. These findings indicate a possible public health issue.
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Affiliation(s)
- Simone Scherrer
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Patricia Landolt
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Natasha Carroli
- Vetsuisse Faculty, Institute of Veterinary Bacteriology, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich, Zurich, Switzerland
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23
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Zhu L, Peng Y, Ye J, Wang T, Bian Z, Qin Y, Zhang H, Ding J. Isolation, Identification, and Characterization of a New Highly Pathogenic Field Isolate of Mycobacterium avium spp. avium. Front Vet Sci 2018; 4:243. [PMID: 29379790 PMCID: PMC5775284 DOI: 10.3389/fvets.2017.00243] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/20/2017] [Indexed: 01/27/2023] Open
Abstract
Avian tuberculosis is a chronic, contagious zoonotic disease affecting birds, mammals, and humans. The disease is most often caused by Mycobacterium avium spp. avium (MAA). Strain resources are important for research on avian tuberculosis and vaccine development. However, there has been little reported about the newly identified MAA strain in recent years in China. In this study, a new strain was isolated from a fowl with symptoms of avian tuberculosis by bacterial culture. The isolated strain was identified to be MAA by culture, staining, and biochemical and genetic analysis, except for different colony morphology. The isolated strain was Ziehl-Zeelsen staining positive, resistant to p-nitrobenzoic acid, and negative for niacin production, Tween-80 hydrolysis, heat stable catalase and nitrate production. The strain had the DnaJ gene, IS1245, and IS901, as well. Serum agglutination indicated that the MAA strain was of serotype 1. The MAA strain showed strong virulence via mortality in rabbits and chickens. The prepared tuberculin of the MAA strain had similar potency compared to the MAA reference strain and standard tuberculin via a tuberculin skin test. Our studies suggested that this MAA strain tends to be a novel subtype, which might enrich the strain resource of avian tuberculosis.
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Affiliation(s)
- Liangquan Zhu
- China Institute of Veterinary Drug Control, Beijing, China
| | - Yong Peng
- China Institute of Veterinary Drug Control, Beijing, China
| | - Junxian Ye
- China Institute of Veterinary Drug Control, Beijing, China
| | - Tuanjie Wang
- China Institute of Veterinary Drug Control, Beijing, China
| | - Zengjie Bian
- China Institute of Veterinary Drug Control, Beijing, China
| | - Yuming Qin
- China Institute of Veterinary Drug Control, Beijing, China
| | - He Zhang
- China Institute of Veterinary Drug Control, Beijing, China
| | - Jiabo Ding
- China Institute of Veterinary Drug Control, Beijing, China
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24
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Bannantine JP, Etienne G, Laval F, Stabel JR, Lemassu A, Daffé M, Bayles DO, Ganneau C, Bonhomme F, Branger M, Cochard T, Bay S, Biet F. Cell wall peptidolipids of Mycobacterium avium: from genetic prediction to exact structure of a nonribosomal peptide. Mol Microbiol 2017; 105:525-539. [PMID: 28558126 DOI: 10.1111/mmi.13717] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/22/2017] [Indexed: 10/19/2022]
Abstract
Mycobacteria have a complex cell wall structure that includes many lipids; however, even within a single subspecies of Mycobacterium avium these lipids can differ. Total lipids from an M. avium subsp. paratuberculosis (Map) ovine strain (S-type) contained no identifiable glycopeptidolipids or lipopentapeptide (L5P), yet both lipids are present in other M. avium subspecies. We determined the genetic and phenotypic basis for this difference using sequence analysis as well as biochemical and physico-chemical approaches. This strategy showed that a nonribosomal peptide synthase, encoded by mps1, contains three amino acid specifying modules in ovine strains, compared to five modules in bovine strains (C-type). Sequence analysis predicted these modules would produce the tripeptide Phe-N-Methyl-Val-Ala with a lipid moiety, termed lipotripeptide (L3P). Comprehensive physico-chemical analysis of Map S397 extracts confirmed the structural formula of the native L3P as D-Phe-N-Methyl-L-Val-L-Ala-OMe attached in N-ter to a 20-carbon fatty acid chain. These data demonstrate that S-type strains, which are more adapted in sheep, produce a unique lipid. There is a dose-dependent effect observed for L3P on upregulation of CD25+ CD8 T cells from infected cows, while L5P effects were static. In contrast, L5P demonstrated a significantly stronger induction of CD25+ B cells from infected animals compared to L3P.
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Affiliation(s)
- John P Bannantine
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, IA, 50010, USA
| | - Gilles Etienne
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.,Université de Toulouse, UPS, IPBS, Toulouse, 31000, France
| | - Françoise Laval
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.,Université de Toulouse, UPS, IPBS, Toulouse, 31000, France
| | - Judith R Stabel
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, IA, 50010, USA
| | - Anne Lemassu
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.,Université de Toulouse, UPS, IPBS, Toulouse, 31000, France
| | - Mamadou Daffé
- Institut de Pharmacologie et de Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France.,Université de Toulouse, UPS, IPBS, Toulouse, 31000, France
| | - Darrell O Bayles
- National Animal Disease Center, USDA-Agricultural Research Service, Ames, IA, 50010, USA
| | - Christelle Ganneau
- Institut Pasteur, Unité Chimie des Biomolécules, 75724 Paris Cedex 15, France.,CNRS UMR 3523, 75724 Paris Cedex 15, France
| | - Frédéric Bonhomme
- Institut Pasteur, Unité Chimie des Biomolécules, 75724 Paris Cedex 15, France.,CNRS UMR 3523, 75724 Paris Cedex 15, France
| | - Maxime Branger
- Infectiologie et Santé Publique, INRA, Université de Tours, UMR1282, Nouzilly, F-37380, France
| | - Thierry Cochard
- Infectiologie et Santé Publique, INRA, Université de Tours, UMR1282, Nouzilly, F-37380, France
| | - Sylvie Bay
- Institut Pasteur, Unité Chimie des Biomolécules, 75724 Paris Cedex 15, France.,CNRS UMR 3523, 75724 Paris Cedex 15, France
| | - Franck Biet
- Infectiologie et Santé Publique, INRA, Université de Tours, UMR1282, Nouzilly, F-37380, France
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25
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Sevilla IA, Molina E, Tello M, Elguezabal N, Juste RA, Garrido JM. Detection of Mycobacteria by Culture and DNA-Based Methods in Animal-Derived Food Products Purchased at Spanish Supermarkets. Front Microbiol 2017. [PMID: 28649235 PMCID: PMC5465283 DOI: 10.3389/fmicb.2017.01030] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Mycobacteria include obligate and opportunistic pathogens that cause significant human and animal disease. The burden of tuberculosis has been largely reduced in developed territories but remains a huge problem worldwide. The significance of nontuberculous mycobacteria is growing considerably, especially in developed regions with higher life expectancy and more therapy-related immunosuppressed individuals. Due to their robustness mycobacteria can contaminate animal products by direct transmission from infected individuals or by environmental contamination during processing. The situation at market level is poorly known. Most studies analyzing commercially available foods are limited to a small or local scale and mainly focused on a particular mycobacterial species. There is a need to investigate if animal products that have passed the established controls to be for sale at main supermarkets could represent a route of contact with any mycobacteria. Thus, our goal was to study the prevalence of mycobacteria in these foods to assess if this could represent a source of human exposure. Five stores from the main supermarket chains in Spain were selected. 138 dairy and 119 meat products were purchased. All were processed using culture and multiplex real-time PCR methods. Additional molecular methods were used to specifically identify any positive result. Mycobacterium avium subsp. hominissuis (2), M. avium subsp. avium (1), and M. fortuitum (1) were isolated from powdered infant formula and ground beef, chicken sausage, and mortadella cold cut, respectively. Mycobacterial DNA (M. avium, M. tuberculosis complex and other nontuberculous mycobacteria) was detected in 15% of dairy products and 2% of meat products. These results show that the prevalence of viable mycobacteria in foods of animal origin obtained at the supermarket was not substantial although a considerable proportion of them contained mycobacterial DNA. Contact with mycobacteria through this route could be ensured over time. Further investigation is necessary to determine the real impact of foodborne mycobacterial exposure on human health and identify critical points in the food production system to enable setting up more stringent control measures.
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Affiliation(s)
- Iker A Sevilla
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Bizkaia Science and Technology Park 812LDerio, Spain
| | - Elena Molina
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Bizkaia Science and Technology Park 812LDerio, Spain
| | - Maitane Tello
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Bizkaia Science and Technology Park 812LDerio, Spain
| | - Natalia Elguezabal
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Bizkaia Science and Technology Park 812LDerio, Spain
| | - Ramón A Juste
- SERIDA-Servicio Regional de Investigación y Desarrollo Agrario, Carretera de OviedoVillaviciosa, Spain
| | - Joseba M Garrido
- Animal Health Department, NEIKER-Instituto Vasco de Investigación y Desarrollo Agrario, Bizkaia Science and Technology Park 812LDerio, Spain
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26
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Nishiuchi Y, Iwamoto T, Maruyama F. Infection Sources of a Common Non-tuberculous Mycobacterial Pathogen, Mycobacterium avium Complex. Front Med (Lausanne) 2017; 4:27. [PMID: 28326308 PMCID: PMC5339636 DOI: 10.3389/fmed.2017.00027] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Numerous studies have revealed a continuous increase in the worldwide incidence and prevalence of non-tuberculous mycobacteria (NTM) diseases, especially pulmonary Mycobacterium avium complex (MAC) diseases. Although it is not clear why NTM diseases have been increasing, one possibility is an increase of mycobacterial infection sources in the environment. Thus, in this review, we focused on the infection sources of pathogenic NTM, especially MAC. The environmental niches for MAC include water, soil, and dust. The formation of aerosols containing NTM arising from shower water, soil, and pool water implies that these niches can be infection sources. Furthermore, genotyping has shown that clinical isolates are identical to environmental ones from household tap water, bathrooms, potting soil, and garden soil. Therefore, to prevent and treat MAC diseases, it is essential to identify the infection sources for these organisms, because patients with these diseases often suffer from reinfections and recurrent infections with them. In the environmental sources, MAC and other NTM organisms can form biofilms, survive within amoebae, and exist in a free-living state. Mycobacterial communities are also likely to occur in these infection sources in households. Water distribution systems are a transmission route from natural water reservoirs to household tap water. Other infection sources include areas with frequent human contact, such as soil and bathrooms, indicating that individuals may carry NTM organisms that concomitantly attach to their household belongings. To explore the mechanisms associated with the global spread of infection and MAC transmission routes, an epidemiological population-wide genotyping survey would be very useful. A good example of the power of genotyping comes from M. avium subsp. hominissuis, where close genetic relatedness was found between isolates of it from European patients and pigs in Japan and Europe, implying global transmission of this bacterium. It is anticipated that whole genome sequencing technologies will improve NTM surveys so that the mechanisms for the global spread of MAC disease will become clearer in the near future. Better understanding of the niches exploited by MAC and its ecology is essential for preventing MAC infections and developing new methods for its effective treatment and elimination.
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Affiliation(s)
- Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School , Toyonaka , Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health , Kobe , Japan
| | - Fumito Maruyama
- Section of Microbiology, Graduate School of Medicine and Faculty of Medicine, Kyoto University , Kyoto , Japan
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27
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Bruffaerts N, Vluggen C, Roupie V, Duytschaever L, Van den Poel C, Denoël J, Wattiez R, Letesson JJ, Fretin D, Rigouts L, Chapeira O, Mathys V, Saegerman C, Huygen K. Virulence and immunogenicity of genetically defined human and porcine isolates of M. avium subsp. hominissuis in an experimental mouse infection. PLoS One 2017; 12:e0171895. [PMID: 28182785 PMCID: PMC5300754 DOI: 10.1371/journal.pone.0171895] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/27/2017] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (Mah) represents a health concern for humans and to a lesser extent for pigs, but its zoonotic potential remains elusive. Using multispacer sequence typing (MST) we previously identified 49 different genotypes of Mah among Belgian clinical and porcine isolates, with 5 MSTs shared by both hosts. Using experimental intranasal infection of BALB/c mice, we compared the virulence and immunogenicity of porcine and clinical human isolates with shared genotype or with a genotype only found in humans or pigs. Bacterial replication was monitored for 20 weeks in lungs, spleen and liver and mycobacteria specific spleen cell IFN-γ, IL-10 and IL-17 production as well as serum antibody responses were analyzed. Isolates varied in virulence, with human and porcine isolates sharing MST22 genotype showing a thousand fold higher bacterial replication in lungs and more dissemination to spleen and liver than the human and porcine MST91 isolates. Virulent MST22 type was also associated with progressive suppression of IFN-γ and IL-17 responses, and increased IL-10 production. Whole genome sequencing of the two virulent isolates with MST22 genotype and two avirulent isolates of genotype MST91 and comparison with two well-studied M. avium subsp. hominissuis reference strains i.e. Mah 104 and Mah TH135, identified in the two MST22 isolates nine specific virulence factors of the mammalian cell entry family, that were identical with Mah 104 strain. Despite the obvious limitations of the mouse model, a striking link of virulence and identity at the genome level of porcine and human isolates with the same multisequence type, for which no correlation of place of residence (humans) or farm of origin (pigs) was observed, seems to point to the existence in the environment of certain genotypes of Mah which may be more infectious both for humans and pigs than other genotypes.
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Affiliation(s)
- Nicolas Bruffaerts
- Service Immunology, Operational Direction Communicable and infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
- * E-mail: (NB); (KH)
| | - Christelle Vluggen
- Service Bacterial diseases, Operational Direction Communicable and infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Virginie Roupie
- Unit Bacterial Zoonoses of livestock, Operational Direction Bacterial Diseases, Veterinary and Agrochemical Research Centre, Brussels, Belgium
| | - Lucille Duytschaever
- Unit Bacterial Zoonoses of livestock, Operational Direction Bacterial Diseases, Veterinary and Agrochemical Research Centre, Brussels, Belgium
- Research Unit in Epidemiology and Risk Analysis applied to Veterinary Sciences, Fundamental and Applied Research for Animal and Health, Université of Liège, Liège, Belgium
| | - Christophe Van den Poel
- Service Immunology, Operational Direction Communicable and infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Joseph Denoël
- Research Unit in Epidemiology and Risk Analysis applied to Veterinary Sciences, Fundamental and Applied Research for Animal and Health, Université of Liège, Liège, Belgium
| | - Ruddy Wattiez
- Service Protéomique et Microbiologie, Université de Mons, Mons, Belgium
| | - Jean-Jacques Letesson
- Unité de Recherche en Biologie des Microorganismes, Université de Namur, Namur, Belgium
| | - David Fretin
- Unit Bacterial Zoonoses of livestock, Operational Direction Bacterial Diseases, Veterinary and Agrochemical Research Centre, Brussels, Belgium
| | - Leen Rigouts
- Department Biomedical Sciences, University of Antwerp, Antwerp, Belgium
- Unit Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Vanessa Mathys
- Service Bacterial diseases, Operational Direction Communicable and infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Claude Saegerman
- Research Unit in Epidemiology and Risk Analysis applied to Veterinary Sciences, Fundamental and Applied Research for Animal and Health, Université of Liège, Liège, Belgium
| | - Kris Huygen
- Service Immunology, Operational Direction Communicable and infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
- * E-mail: (NB); (KH)
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28
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Uchiya KI, Tomida S, Nakagawa T, Asahi S, Nikai T, Ogawa K. Comparative genome analyses of Mycobacterium avium reveal genomic features of its subspecies and strains that cause progression of pulmonary disease. Sci Rep 2017; 7:39750. [PMID: 28045086 PMCID: PMC5206733 DOI: 10.1038/srep39750] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 11/28/2016] [Indexed: 11/25/2022] Open
Abstract
Pulmonary disease caused by nontuberculous mycobacteria (NTM) is increasing worldwide. Mycobacterium avium is the most clinically significant NTM species in humans and animals, and comprises four subspecies: M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS), M. avium subsp. paratuberculosis (MAP), and M. avium subsp. hominissuis (MAH). To improve our understanding of the genetic landscape and diversity of M. avium and its role in disease, we performed a comparative genome analysis of 79 M. avium strains. Our analysis demonstrated that MAH is an open pan-genome species. Phylogenetic analysis based on single nucleotide variants showed that MAH had the highest degree of sequence variability among the subspecies, and MAH strains isolated in Japan and those isolated abroad possessed distinct phylogenetic features. Furthermore, MAP strains, MAS and MAA strains isolated from birds, and many MAH strains that cause the progression of pulmonary disease were grouped in each specific cluster. Comparative genome analysis revealed the presence of genetic elements specific to each lineage, which are thought to be acquired via horizontal gene transfer during the evolutionary process, and identified potential genetic determinants accounting for the pathogenic and host range characteristics of M. avium.
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Affiliation(s)
- Kei-Ichi Uchiya
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan
| | - Shuta Tomida
- Department of Biobank, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8558, Japan
| | - Taku Nakagawa
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, Nagoya 465-8620, Japan.,Department of Respiratory Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya 465-8620, Japan
| | - Shoki Asahi
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan
| | - Toshiaki Nikai
- Department of Microbiology, Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan
| | - Kenji Ogawa
- Department of Clinical Research, National Hospital Organization, Higashinagoya National Hospital, Nagoya 465-8620, Japan.,Department of Respiratory Medicine, National Hospital Organization, Higashinagoya National Hospital, Nagoya 465-8620, Japan
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29
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Khare S, Drake KL, Lawhon SD, Nunes JES, Figueiredo JF, Rossetti CA, Gull T, Everts RE, Lewin HA, Adams LG. Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections. PLoS One 2016; 11:e0161946. [PMID: 27653506 PMCID: PMC5031438 DOI: 10.1371/journal.pone.0161946] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/15/2016] [Indexed: 02/06/2023] Open
Abstract
It has long been a quest in ruminants to understand how two very similar mycobacterial species, Mycobacterium avium ssp. paratuberculosis (MAP) and Mycobacterium avium ssp. avium (MAA) lead to either a chronic persistent infection or a rapid-transient infection, respectively. Here, we hypothesized that when the host immune response is activated by MAP or MAA, the outcome of the infection depends on the early activation of signaling molecules and host temporal gene expression. To test our hypothesis, ligated jejuno-ileal loops including Peyer’s patches in neonatal calves were inoculated with PBS, MAP, or MAA. A temporal analysis of the host transcriptome profile was conducted at several times post-infection (0.5, 1, 2, 4, 8 and 12 hours). When comparing the transcriptional responses of calves infected with the MAA versus MAP, discordant patterns of mucosal expression were clearly evident, and the numbers of unique transcripts altered were moderately less for MAA-infected tissue than were mucosal tissues infected with the MAP. To interpret these complex data, changes in the gene expression were further analyzed by dynamic Bayesian analysis. Bayesian network modeling identified mechanistic genes, gene-to-gene relationships, pathways and Gene Ontologies (GO) biological processes that are involved in specific cell activation during infection. MAP and MAA had significant different pathway perturbation at 0.5 and 12 hours post inoculation. Inverse processes were observed between MAP and MAA response for epithelial cell proliferation, negative regulation of chemotaxis, cell-cell adhesion mediated by integrin and regulation of cytokine-mediated signaling. MAP inoculated tissue had significantly lower expression of phagocytosis receptors such as mannose receptor and complement receptors. This study reveals that perturbation of genes and cellular pathways during MAP infection resulted in host evasion by mucosal membrane barrier weakening to access entry in the ileum, inhibition of Ca signaling associated with decreased phagosome-lysosome fusion as well as phagocytosis inhibition, bias toward Th2 cell immune response accompanied by cell recruitment, cell proliferation and cell differentiation; leading to persistent infection. Contrarily, MAA infection was related to cellular responses associated with activation of molecular pathways that release chemicals and cytokines involved with containment of infection and a strong bias toward Th1 immune response, resulting in a transient infection.
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Affiliation(s)
- Sangeeta Khare
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
- Division of Microbiology, National Center for Toxicological Research, US Food and Drug Administration, Jefferson, Arkansas, 72079, United States of America
- * E-mail: (SK); (LGA)
| | | | - Sara D. Lawhon
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Jairo E. S. Nunes
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Josely F. Figueiredo
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Carlos A. Rossetti
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Tamara Gull
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
| | - Robin E. Everts
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America
| | - Harris. A. Lewin
- Department of Animal Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America
| | - Leslie Garry Adams
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, Texas, 77843, United States of America
- * E-mail: (SK); (LGA)
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30
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Vluggen C, Soetaert K, Duytschaever L, Denoël J, Fauville-Dufaux M, Smeets F, Bruffaerts N, Huygen K, Fretin D, Rigouts L, Saegerman C, Mathys V. Genotyping and strain distribution of Mycobacterium avium subspecies hominissuis isolated from humans and pigs in Belgium, 2011-2013. ACTA ACUST UNITED AC 2016; 21:30111. [PMID: 26835872 DOI: 10.2807/1560-7917.es.2016.21.3.30111] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 07/05/2015] [Indexed: 11/20/2022]
Abstract
Mycobacterium avium represents a health concern for both humans and pigs. The characterisation of its subspecies is an important step improving the understanding of the epidemiology and the control of this pathogen. Ninety-two human M. avium strains were selected for a retrospective study. Subspecies determination by rpoB sequencing and IS1245/IS901 analysis showed that 98.9% of Belgian human M. avium strains belong to the subspecies hominissuis (MAH). Some of these MAH strains present particular IS1245/IS901 profiles (absence of IS1245 and false IS901 detection provoked by the presence of ISMav6). In addition, 54 MAH strains isolated from submandibular lymph nodes of Belgian pigs with lymphadenitis were included in this study. Genotyping of human and porcine isolates was performed using multispacer sequence typing (MST). In total, 49 different MST types were identified among pig (n = 11) and human (n = 43) MA isolates, with only five shared by both hosts. Among these MST types, 34 were newly identified. Our findings demonstrate the extensive genetic diversity among MAH isolates. Some genotypes were more prevalent in human or pigs but no correlation was observed between MST type and place of residence or the farm of origin for human and porcine isolates respectively, suggesting an environmental source of infection.
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Affiliation(s)
- Christelle Vluggen
- Bacterial Diseases Service, Operational Direction Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
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31
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Kalvisa A, Tsirogiannis C, Silamikelis I, Skenders G, Broka L, Zirnitis A, Jansone I, Ranka R. MIRU-VNTR genotype diversity and indications of homoplasy in M. avium strains isolated from humans and slaughter pigs in Latvia. INFECTION GENETICS AND EVOLUTION 2016; 43:15-21. [PMID: 27178993 DOI: 10.1016/j.meegid.2016.05.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 05/06/2016] [Accepted: 05/08/2016] [Indexed: 10/21/2022]
Abstract
Diseases which are caused by non-tuberculous mycobacteria (NTM) are an increasing problem in the developed countries. In Latvia, one of the most clinically important members of NTM is Mycobacterium avium (M. avium), an opportunistic pathogen which has been isolated from several lung disease patients and tissue samples of slaughter pigs. This study was designed to characterize the genetic diversity of the M. avium isolates in Latvia and to compare the distribution of genotypic patterns among humans and pigs. Eleven (Hall and Salipante, 2010) clinical M. avium samples, isolated from patients of Center of Tuberculosis and Lung Diseases (years 2003-2010), and 32 isolates from pig necrotic mesenterial lymph nodes in different regions (years 2003-2007) were analyzed. The majority (42 of 43) of samples were identified as M. avium subsp. hominissuis; one porcine isolate belonged to M. avium subsp. avium. MIRU-VNTR genotyping revealed 13 distinct genotypes, among which nine genotype patterns, including M. avium subsp. avium isolate, were newly identified. IS1245 RFLP fingerprinting of 25 M. avium subsp. hominissuis samples yielded 17 different IS1245 RFLP patterns, allowing an efficient discrimination of isolates. Clusters of identical RFLP profiles were observed within host species, geographical locations and time frame of several years. Additional in silico analysis on simulated MIRU-VNTR genotype population datasets showed that the MIRU-VNTR pattern similarity could partly arise due to probabilistic increase of acquiring homoplasy among subpopulations, thus the similar MIRU-VNTR profiles of M. avium strains even in close geographical proximity should be interpreted with caution.
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Affiliation(s)
- Adrija Kalvisa
- Latvian Biomedical Research and Study Centre (LV BMC), Riga, Latvia; Riga Stradins University (RSU), Riga, Latvia
| | | | | | - Girts Skenders
- Riga East University Hospital, Tuberculosis and Lung Diseases Center, Latvia
| | - Lonija Broka
- Riga East University Hospital, Tuberculosis and Lung Diseases Center, Latvia
| | - Agris Zirnitis
- Department of Veterinary Medicine, Latvia University of Agriculture, Jelgava, Latvia
| | - Inta Jansone
- Latvian Biomedical Research and Study Centre (LV BMC), Riga, Latvia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre (LV BMC), Riga, Latvia; Riga Stradins University (RSU), Riga, Latvia.
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32
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Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out. Trends Microbiol 2016; 24:637-648. [PMID: 27068531 DOI: 10.1016/j.tim.2016.03.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/13/2016] [Accepted: 03/15/2016] [Indexed: 01/29/2023]
Abstract
Antimicrobial resistance (AMR) threats are typically represented by bacteria capable of extensive horizontal gene transfer (HGT). One clear exception is Mycobacterium tuberculosis (Mtb). It is an obligate human pathogen with limited genetic diversity and a low mutation rate which lacks any evidence for HGT. Such features should, in principle, reduce its ability to rapidly evolve AMR. We identify key features in its biology and epidemiology that allow it to overcome its low adaptive potential. We focus in particular on its innate resistance to drugs, its unusual life cycle, including an often extensive latent phase, and its ability to shelter from exposure to antimicrobial drugs within cavities it induces in the lungs.
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33
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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: 10] [Impact Index Per Article: 1.3] [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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Li L, Katani R, Schilling M, Kapur V. Molecular Epidemiology ofMycobacterium aviumsubsp.paratuberculosison Dairy Farms. Annu Rev Anim Biosci 2016; 4:155-76. [DOI: 10.1146/annurev-animal-021815-111304] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Lingling Li
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; , , ,
| | - Robab Katani
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; , , ,
| | - Megan Schilling
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; , , ,
| | - Vivek Kapur
- Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania 16802; , , ,
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Iron Acquisition in Mycobacterium avium subsp. paratuberculosis. J Bacteriol 2015; 198:857-66. [PMID: 26712939 PMCID: PMC4810606 DOI: 10.1128/jb.00922-15] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 12/18/2015] [Indexed: 01/26/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis is a host-adapted pathogen that evolved from the environmental bacterium M. avium subsp. hominissuis through gene loss and gene acquisition. Growth of M. avium subsp. paratuberculosis in the laboratory is enhanced by supplementation of the media with the iron-binding siderophore mycobactin J. Here we examined the production of mycobactins by related organisms and searched for an alternative iron uptake system in M. avium subsp. paratuberculosis. Through thin-layer chromatography and radiolabeled iron-uptake studies, we showed that M. avium subsp. paratuberculosis is impaired for both mycobactin synthesis and iron acquisition. Consistent with these observations, we identified several mutations, including deletions, in M. avium subsp. paratuberculosis genes coding for mycobactin synthesis. Using a transposon-mediated mutagenesis screen conditional on growth without myobactin, we identified a potential mycobactin-independent iron uptake system on a M. avium subsp. paratuberculosis-specific genomic island, LSPP15. We obtained a transposon (Tn) mutant with a disruption in the LSPP15 gene MAP3776c for targeted study. The mutant manifests increased iron uptake as well as intracellular iron content, with genes downstream of the transposon insertion (MAP3775c to MAP3772c [MAP3775-2c]) upregulated as the result of a polar effect. As an independent confirmation, we observed the same iron uptake phenotypes by overexpressing MAP3775-2c in wild-type M. avium subsp. paratuberculosis. These data indicate that the horizontally acquired LSPP15 genes contribute to iron acquisition by M. avium subsp. paratuberculosis, potentially allowing the subsequent loss of siderophore production by this pathogen. IMPORTANCE Many microbes are able to scavenge iron from their surroundings by producing iron-chelating siderophores. One exception is Mycobacterium avium subsp. paratuberculosis, a fastidious, slow-growing animal pathogen whose growth needs to be supported by exogenous mycobacterial siderophore (mycobactin) in the laboratory. Data presented here demonstrate that, compared to other closely related M. avium subspecies, mycobactin production and iron uptake are different in M. avium subsp. paratuberculosis, and these phenotypes may be caused by numerous deletions in its mycobactin biosynthesis pathway. Using a genomic approach, supplemented by targeted genetic and biochemical studies, we identified that LSPP15, a horizontally acquired genomic island, may encode an alternative iron uptake system. These findings shed light on the potential physiological consequence of horizontal gene transfer in M. avium subsp. paratuberculosis evolution.
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Möbius P, Hölzer M, Felder M, Nordsiek G, Groth M, Köhler H, Reichwald K, Platzer M, Marz M. Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany. Genome Biol Evol 2015; 7:2585-2601. [PMID: 26384038 PMCID: PMC4607514 DOI: 10.1093/gbe/evv154] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP)—the etiologic agent of Johne’s disease—affects cattle, sheep, and other ruminants worldwide. To decipher phenotypic differences among sheep and cattle strains (belonging to MAP-S [Type-I/III], respectively, MAP-C [Type-II]), comparative genome analysis needs data from diverse isolates originating from different geographic regions of the world. This study presents the so far best assembled genome of a MAP-S-strain: Sheep isolate JIII-386 from Germany. One newly sequenced cattle isolate (JII-1961, Germany), four published MAP strains of MAP-C and MAP-S from the United States and Australia, and M. a. subsp. hominissuis (MAH) strain 104 were used for assembly improvement and comparisons. All genomes were annotated by BacProt and results compared with NCBI (National Center for Biotechnology Information) annotation. Corresponding protein-coding sequences (CDSs) were detected, but also CDSs that were exclusively determined by either NCBI or BacProt. A new Shine–Dalgarno sequence motif (5′-AGCTGG-3′) was extracted. Novel CDSs including PE-PGRS family protein genes and about 80 noncoding RNAs exhibiting high sequence conservation are presented. Previously found genetic differences between MAP-types are partially revised. Four of ten assumed MAP-S-specific large sequence polymorphism regions (LSPSs) are still present in MAP-C strains; new LSPSs were identified. Independently of the regional origin of the strains, the number of individual CDSs and single nucleotide variants confirms the strong similarity of MAP-C strains and shows higher diversity among MAP-S strains. This study gives ambiguous results regarding the hypothesis that MAP-S is the evolutionary intermediate between MAH and MAP-C, but it clearly shows a higher similarity of MAP to MAH than to Mycobacterium intracellulare.
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Affiliation(s)
- Petra Möbius
- NRL for Paratuberculosis, Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Straße 96a, 07743 Jena, Germany
| | - Martin Hölzer
- RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
| | - Marius Felder
- Leibniz Institute for Age Research - Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Gabriele Nordsiek
- Department of Genome Analysis, Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany
| | - Marco Groth
- Leibniz Institute for Age Research - Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Heike Köhler
- NRL for Paratuberculosis, Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Straße 96a, 07743 Jena, Germany
| | - Kathrin Reichwald
- Leibniz Institute for Age Research - Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Matthias Platzer
- Leibniz Institute for Age Research - Fritz-Lipmann-Institute (FLI), Beutenbergstraße 11, 07745 Jena, Germany
| | - Manja Marz
- RNA Bioinformatics and High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Leutragraben 1, 07743 Jena, Germany
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Molecular identification of Mycobacterium avium subsp. silvaticum by duplex high-resolution melt analysis and subspecies-specific real-time PCR. J Clin Microbiol 2015; 53:1582-7. [PMID: 25740770 DOI: 10.1128/jcm.03556-14] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Accepted: 02/20/2015] [Indexed: 11/20/2022] Open
Abstract
Accurate identification of mycobacterial species and subspecies is essential to evaluate their significance and to perform epidemiological studies. The subspecies of Mycobacterium avium have different attributes but coincide in their zoonotic potential. Our knowledge about M. avium subsp. silvaticum is limited, since its identification is uncertain. Mycobacterium avium subsp. avium and M. avium subsp. silvaticum can be discriminated from each other based only on phenotypic characteristics, as they have almost identical genome sequences. Here we describe the development of a diagnostic method which enables the molecular identification of M. avium subsp. silvaticum and discrimination from M. avium subsp. avium based on genomic differences in a duplex high-resolution melt and M. avium subsp. silvaticum-specific mismatch real-time PCR. The developed assay was tested on reference strains and 199 field isolates, which were analyzed by phenotypic methods previously. This assay not only identified all 63 M. avium subsp. silvaticum and 138 M. avium subsp. avium strains correctly but also enabled the detection of mixed M. avium subsp. avium-M. avium subsp. silvaticum cultures. This is the first time that such a large panel of strains has been analyzed, and we also report the first isolation of M. avium subsp. silvaticum from red fox, red deer, wild boar, cattle, and badger. This assay is reliable, rapid, simple, inexpensive, and robust. It eliminates the long-existing problem of ambiguous phenotypic identification and opens up the possibility for detailed and comprehensive strain studies.
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Rana A, Rub A, Akhter Y. Proteome-wide B and T cell epitope repertoires in outer membrane proteins of Mycobacterium avium subsp. paratuberculosis have vaccine and diagnostic relevance: a holistic approach. J Mol Recognit 2015; 28:506-20. [PMID: 25727233 DOI: 10.1002/jmr.2458] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 12/05/2014] [Accepted: 12/16/2014] [Indexed: 11/11/2022]
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is an etiological agent of chronic inflammation of the intestine among ruminants and humans. Currently, there are no effective vaccines and sensitive diagnostic tests available for its control and detection. For this, it is of paramount importance to identify the MAP antigens, which may be immunologically recognized by the host immune system. To address this challenge, we performed identification of the immunogenic epitopes in the MAP outer membrane proteins (OMPs). We have previously identified 57 MAP proteins as OMPs [Rana A, Rub A, Akhter Y. 2014. Molecular BioSystems, 10:2329-2337] and have evaluated them for the epitope selection and analysis employing a computational approach. Thirty-five MAP OMPs are reported with nine-mer peptides showing high binding affinity to major histocompatibility complex (MHC) class I molecules and 28 MAP OMPs with 15-mer peptides of high binding affinity for MHC class II molecules. The presence of MHC binding epitopes indicates the potential cell-mediated immune response inducing capacity of these MAP OMPs in infected host. To further investigate the humoral response inducing properties of OMPs of MAP, we report potential B cell epitopes based on the sequences of peptide antigens and their molecular structures. We also report 10 proteins having epitopes for both B and T cells representing potential candidates which may invoke both humoral and cellular immune responses in the host. These findings will greatly accelerate and expedite the formulation of effective and cost-efficient vaccines and diagnostic tests against MAP infection.
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Affiliation(s)
- Aarti Rana
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, 176206, India
| | - Abdur Rub
- Infection and Immunity Laboratory, Department of Biotechnology, Jamia Millia Islamia (A Central University), New Delhi,, 110025, India
| | - Yusuf Akhter
- School of Life Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, 176206, India
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Rónai Z, Csivincsik Á, Gyuranecz M, Kreizinger Z, Dán Á, Jánosi S. Molecular analysis and MIRU-VNTR typing of Mycobacterium avium
subsp. paratuberculosis
strains from various sources. J Appl Microbiol 2014; 118:275-83. [DOI: 10.1111/jam.12702] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2014] [Revised: 11/05/2014] [Accepted: 11/13/2014] [Indexed: 10/24/2022]
Affiliation(s)
- Z. Rónai
- Veterinary Diagnostic Directorate; National Food Chain Safety Office (NFCSO); Budapest Hungary
| | - Á. Csivincsik
- Food-chain Safety and Animal Health Directorate; Government Office of Somogy County; Kaposvár Hungary
| | - M. Gyuranecz
- Institute for Veterinary Medical Research; Centre for Agricultural Research, Hungarian Academy of Sciences; Budapest Hungary
| | - Z. Kreizinger
- Institute for Veterinary Medical Research; Centre for Agricultural Research, Hungarian Academy of Sciences; Budapest Hungary
| | - Á. Dán
- Veterinary Diagnostic Directorate; National Food Chain Safety Office (NFCSO); Budapest Hungary
| | - S. Jánosi
- Veterinary Diagnostic Directorate; National Food Chain Safety Office (NFCSO); Budapest Hungary
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Rue-Albrecht K, Magee DA, Killick KE, Nalpas NC, Gordon SV, MacHugh DE. Comparative functional genomics and the bovine macrophage response to strains of the mycobacterium genus. Front Immunol 2014; 5:536. [PMID: 25414700 PMCID: PMC4220711 DOI: 10.3389/fimmu.2014.00536] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/10/2014] [Indexed: 02/06/2023] Open
Abstract
Mycobacterial infections are major causes of morbidity and mortality in cattle and are also potential zoonotic agents with implications for human health. Despite the implementation of comprehensive animal surveillance programs, many mycobacterial diseases have remained recalcitrant to eradication in several industrialized countries. Two major mycobacterial pathogens of cattle are Mycobacterium bovis and Mycobacterium avium subspecies paratuberculosis (MAP), the causative agents of bovine tuberculosis (BTB) and Johne's disease (JD), respectively. BTB is a chronic, granulomatous disease of the respiratory tract that is spread via aerosol transmission, while JD is a chronic granulomatous disease of the intestines that is transmitted via the fecal-oral route. Although these diseases exhibit differential tissue tropism and distinct complex etiologies, both M. bovis and MAP infect, reside, and replicate in host macrophages - the key host innate immune cell that encounters mycobacterial pathogens after initial exposure and mediates the subsequent immune response. The persistence of M. bovis and MAP in macrophages relies on a diverse series of immunomodulatory mechanisms, including the inhibition of phagosome maturation and apoptosis, generation of cytokine-induced necrosis enabling dissemination of infection through the host, local pathology, and ultimately shedding of the pathogen. Here, we review the bovine macrophage response to infection with M. bovis and MAP. In particular, we describe how recent advances in functional genomics are shedding light on the host macrophage-pathogen interactions that underlie different mycobacterial diseases. To illustrate this, we present new analyses of previously published bovine macrophage transcriptomics data following in vitro infection with virulent M. bovis, the attenuated vaccine strain M. bovis BCG, and MAP, and discuss our findings with respect to the differing etiologies of BTB and JD.
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Affiliation(s)
- Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - David A. Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Kate E. Killick
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- Systems Biology Ireland, UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Nicolas C. Nalpas
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Stephen V. Gordon
- UCD School of Veterinary Medicine, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - David E. MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
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Genetic characterization of German Mycobacterium avium strains isolated from different hosts and specimens by multilocus sequence typing. Int J Med Microbiol 2014; 304:941-8. [DOI: 10.1016/j.ijmm.2014.06.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Revised: 02/17/2014] [Accepted: 06/01/2014] [Indexed: 01/29/2023] Open
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Biet F, Boschiroli ML. Non-tuberculous mycobacterial infections of veterinary relevance. Res Vet Sci 2014; 97 Suppl:S69-77. [PMID: 25256964 DOI: 10.1016/j.rvsc.2014.08.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Revised: 08/13/2014] [Accepted: 08/23/2014] [Indexed: 11/17/2022]
Abstract
Mycobacteria play an important role in human and animal health fields. We here examine the place of non tuberculous mycobacteria (NTM) infections in the veterinary context. Relevant aspects of a reference laboratory experience and a literature review are presented in this article. Importance is given both to productivity and to economic losses due to misdiagnosis with bovine tuberculosis and paratuberculosis. The impact NTM may have is relative to geographical location, ecology, husbandry, extent of surveillance programs and bovine tuberculosis and paratuberculosis prevalence. The role of the most relevant NTM in animal disease is summarized with a special focus on Mycobacterium avium subsp. paratuberculosis, given its role as causative agent of paratuberculosis, a disease with huge economic consequences for ruminant livestock.
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Affiliation(s)
- Franck Biet
- Institut National de la Recherche Agronomique, Infectiologie et Santé Publique, INRA Centre Val de Loire, Université de Tours, Unité Mixte de Recherches 1282, 37380 Nouzilly, France
| | - Maria Laura Boschiroli
- University Paris-Est, Anses, Laboratory for Animal Health, Bovine tuberculosis National Reference Laboratory, Bacterial Zoonoses Unit, 23, avenue du Général de Gaulle, 94706 Maisons-Alfort, France.
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Atreya R, Bülte M, Gerlach GF, Goethe R, Hornef MW, Köhler H, Meens J, Möbius P, Roeb E, Weiss S. Facts, myths and hypotheses on the zoonotic nature of Mycobacterium avium subspecies paratuberculosis. Int J Med Microbiol 2014; 304:858-67. [PMID: 25128370 DOI: 10.1016/j.ijmm.2014.07.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of paratuberculosis (Johne's disease [JD]), a chronic granulomatous enteritis in ruminants. JD is one of the most widespread bacterial diseases of domestic animals with significant economic impact. The histopathological picture of JD resembles that of Crohn's disease (CD), a human chronic inflammatory bowel disease of still unresolved aetiology. An aetiological relevance of MAP for CD has been proposed. This and the ambiguity of other published epidemiological findings raise the question whether MAP represents a zoonotic agent. In this review, we will discuss evidence that MAP has zoonotic capacity.
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Affiliation(s)
- Raja Atreya
- Medical Clinic 1, University of Erlangen-Nuermberg, Ulmenweg 18, D-91054 Erlangen, Germany
| | - Michael Bülte
- Institute of Veterinary Food Science, Faculty of Veterinary Medicine, Justus Liebig University, Frankfurter Straße 92, 35392 Gießen, Germany
| | | | - Ralph Goethe
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany.
| | - Mathias W Hornef
- Department of Microbiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Heike Köhler
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Str. 96a, 07743 Jena, Germany
| | - Jochen Meens
- Institute for Microbiology, Department of Infectious Diseases, University of Veterinary Medicine Hannover, Bischofsholer Damm 15, 30173 Hannover, Germany
| | - Petra Möbius
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut (Federal Research Institute for Animal Health), Naumburger Str. 96a, 07743 Jena, Germany
| | - Elke Roeb
- Justus-Liebig-University Giessen, Department of Gastroenterology, Klinikstr.33, 35392 Giessen, Germany
| | - Siegfried Weiss
- Helmholtz Centre for Infection Research, Molecular Immunology, Inhoffenstraße 7, 38124 Braunschweig, Germany
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Drancourt M. Looking in amoebae as a source of mycobacteria. Microb Pathog 2014; 77:119-24. [PMID: 25017516 DOI: 10.1016/j.micpath.2014.07.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/01/2014] [Accepted: 07/03/2014] [Indexed: 11/16/2022]
Abstract
Mycobacteria exhibit various relationships with amoebae, ranging from the killing of one partner by the other one, to amoebae hosting mycobacteria in trophozoites and cysts. This observation indicates that poorly described biological factors affect the relationships, including mycobacterial cell-wall glycolipids and the size of the mycobacteria. Experimental observations indicate that a majority of environmental, opportunistic mycobacteria but also obligate pathogens including Mycobacterium tuberculosis, Mycobacterium leprae and Mycobacterium ulcerans are inter-amoebal organisms. Amoebae may give opportunities for genetic exchanges between mycobacteria, sympatric intra-amoebal organisms and the amoebae themselves. Amoebae clearly protect opportunistic mycobacterial pathogens during their environmental life but their role for obligate mycobacterial infection remains to be established. Accordingly, water was the source for emerging, community-acquired and health care-associated infection with amoeba-resisting mycobacteria of the Mycobacterium avium, Mycobacterium abscessus and Mycobacterium fortuitum groups, among others. Amoebae are organisms where mycobacteria can be found and, accordingly, amoeba co-culture can be used for the isolation of mycobacteria from environmental and clinical specimens. Looking in amoebae may help recovering new species of mycobacteria.
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Affiliation(s)
- M Drancourt
- Aix Marseille Université, URMITE, UM 63 UMR_S1095 UMR 7278, Méditerranée Infection, 13385, Marseille, France.
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Wang J, Pritchard JR, Kreitmann L, Montpetit A, Behr MA. Disruption of Mycobacterium avium subsp. paratuberculosis-specific genes impairs in vivo fitness. BMC Genomics 2014; 15:415. [PMID: 24885784 PMCID: PMC4058006 DOI: 10.1186/1471-2164-15-415] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 05/27/2014] [Indexed: 01/08/2023] Open
Abstract
Background Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to contribute to its pathogenesis, as these genetic elements are absent from its putative ancestor, M. avium subsp. hominissuis (MAH), an environmental organism with lesser pathogenicity. In this study, high-throughput sequencing of MAP transposon libraries were analyzed to qualitatively and quantitatively determine the contribution of individual genes to bacterial survival during infection. Results Out of 52384 TA dinucleotides present in the MAP K-10 genome, 12607 had a MycoMarT7 transposon in the input pool, interrupting 2443 of the 4350 genes in the MAP genome (56%). Of 96 genes situated in MAP-specific genomic islands, 82 were disrupted in the input pool, indicating that MAP-specific genomic regions are dispensable for in vitro growth (odds ratio = 0.21). Following 5 independent in vivo infections with this pool of mutants, the correlation between output pools was high for 4 of 5 (R = 0.49 to 0.61) enabling us to define genes whose disruption reproducibly reduced bacterial fitness in vivo. At three different thresholds for reduced fitness in vivo, MAP-specific genes were over-represented in the list of predicted essential genes. We also identified additional genes that were severely depleted after infection, and several of them have orthologues that are essential genes in M. tuberculosis. Conclusions This work indicates that the genetic elements required for the in vivo survival of MAP represent a combination of conserved mycobacterial virulence genes and MAP-specific genes acquired via horizontal gene transfer. In addition, the in vitro and in vivo essential genes identified in this study may be further characterized to offer a better understanding of MAP pathogenesis, and potentially contribute to the discovery of novel therapeutic and vaccine targets. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-415) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC H3A 2B4, Canada.
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48
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Subspecies identification and significance of 257 clinical strains of Mycobacterium avium. J Clin Microbiol 2014; 52:1201-6. [PMID: 24501026 DOI: 10.1128/jcm.03399-13] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium avium is abundant in the environment. It has four subspecies of three types: the human or porcine type, M. avium subsp. hominissuis; the bird type, including M. avium subsp. avium serotype 1 and serotype 2, 3 (also M. avium subsp. silvaticum); and the ruminant type, M. avium subsp. paratuberculosis. We determined the subspecies of 257 M. avium strains isolated from patients at the M.D. Anderson Cancer Center from 2001 to 2010 and assessed their clinical significance. An assay of multiplex PCR was used for the typing. Results showed M. avium subsp. hominissuis to be most common (n = 238, 92.6%), followed by M. avium subsp. avium serotype 1 (n = 12, 4.7%) and serotype 2, 3 (n = 7, 2.7%). No strains of M. avium subsp. paratuberculosis were found. Of the 238 patients with M. avium subsp. hominissuis, 65 (27.3%) showed evidence of definite or probable infections, mostly in the respiratory tract, whereas the rest had weak evidence of infection. The bird-type subspecies, despite being infrequently isolated, caused relatively more definite and probable infections (10 of 19 strains, 52.6%). Overall, women of 50 years of age or older were more prone to M. avium infection than younger women or men of all ages were. We therefore conclude that M. avium subsp. hominissuis is the dominant M. avium subspecies clinically, that the two bird-type subspecies do cause human infections, and that M. avium infects mainly postmenopausal women. The lack of human clinical isolation of the ruminant type subspecies may need further investigation.
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Current methods in the molecular typing of Mycobacterium tuberculosis and other mycobacteria. BIOMED RESEARCH INTERNATIONAL 2014; 2014:645802. [PMID: 24527454 PMCID: PMC3914561 DOI: 10.1155/2014/645802] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 11/18/2013] [Indexed: 11/18/2022]
Abstract
In the epidemiology of tuberculosis (TB) and nontuberculous mycobacterial (NTM) diseases, as in all infectious diseases, the key issue is to define the source of infection and to disclose its routes of transmission and dissemination in the environment. For this to be accomplished, the ability of discerning and tracking individual Mycobacterium strains is of critical importance. Molecular typing methods have greatly improved our understanding of the biology of mycobacteria and provide powerful tools to combat the diseases caused by these pathogens. The utility of various typing methods depends on the Mycobacterium species under investigation as well as on the research question. For tuberculosis, different methods have different roles in phylogenetic analyses and person-to-person transmission studies. In NTM diseases, most investigations involve the search for environmental sources or phylogenetic relationships. Here, too, the type of setting determines which methodology is most suitable. Within this review, we summarize currently available molecular methods for strain typing of M. tuberculosis and some NTM species, most commonly associated with human disease. For the various methods, technical practicalities as well as discriminatory power and accomplishments are reviewed.
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Rindi L, Garzelli C. Genetic diversity and phylogeny of Mycobacterium avium. INFECTION GENETICS AND EVOLUTION 2013; 21:375-83. [PMID: 24345519 DOI: 10.1016/j.meegid.2013.12.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Revised: 12/02/2013] [Accepted: 12/02/2013] [Indexed: 02/02/2023]
Abstract
Mycobacterium avium, one of the species of the M. avium complex (MAC), includes 4 subspecies, i.e., M. avium subsp. hominissuis (MAH), M. avium subsp. avium (MAA), M. avium subsp. silvaticum (MAS) and M. avium subsp. paratuberculosis (MAP), in turn classified into the S (sheep) and C (cattle) types. These subspecies, although closely related, represent distinct organisms, each endowed with specific pathogenetic and host range characteristics, ranging from environmental opportunistic bacteria that cause infections in swine and immunocompromised patients to pathogens of birds and ruminants. The present review summarizes the basic epidemiological and pathological features of the M. avium subspecies, describes the major genomic events responsible of M. avium subspecies diversity (insertion sequences, sequence variations in specific chromosome loci or genes, deletions, duplications and insertions of large genomic regions) and then reconstructs the phylogenetic relationships among the M. avium subspecies.
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Affiliation(s)
- Laura Rindi
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, I-56127 Pisa, Italy.
| | - Carlo Garzelli
- Dipartimento di Ricerca Traslazionale e delle Nuove Tecnologie in Medicina e Chirurgia, Università di Pisa, I-56127 Pisa, Italy
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