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Bannantine JP, Duffy SC, Colombatti Olivieri MA, Behr MA, Biet F, Price NPJ. Genetic and chemical control of tuberculostearic acid production in Mycobacterium avium subspecies paratuberculosis. Microbiol Spectr 2024; 12:e0050824. [PMID: 38501867 PMCID: PMC11064506 DOI: 10.1128/spectrum.00508-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Tuberculostearic acid (TBSA) is a fatty acid unique to mycobacteria and some corynebacteria and has been studied due to its diagnostic value, biofuel properties, and role in membrane dynamics. In this study, we demonstrate that TBSA production can be abrogated either by addition of pivalic acid to mycobacterial growth cultures or by a bfaA gene knockout encoding a flavin adenine dinucleotide (FAD)-binding oxidoreductase. Mycobacterium avium subspecies paratuberculosis (Map) growth and TBSA production were inhibited in 0.5-mg/mL pivalic acid-supplemented cultures, but higher concentrations were needed to have a similar effect in other mycobacteria, including Mycobacterium smegmatis. While Map C-type strains, isolated from cattle and other ruminants, will produce TBSA in the absence of pivalic acid, the S-type Map strains, typically isolated from sheep, do not produce TBSA in any condition. A SAM-dependent methyltransferase encoded by bfaB and FAD-binding oxidoreductase are both required in the two-step biosynthesis of TBSA. However, S-type strains contain a single-nucleotide polymorphism in the bfaA gene, rendering the oxidoreductase enzyme vestigial. This results in the production of an intermediate, termed 10-methylene stearate, which is detected only in S-type strains. Fatty acid methyl ester analysis of a C-type Map bfaA knockout revealed the loss of TBSA production, but the intermediate was present, similar to the S-type strains. Collectively, these results demonstrate the subtle biochemical differences between two primary genetic lineages of Map and other mycobacteria as well as explain the resulting phenotype at the genetic level. These data also suggest that TBSA should not be used as a diagnostic marker for Map.IMPORTANCEBranched-chain fatty acids are a predominant cell wall component among species belonging to the Mycobacterium genus. One of these is TBSA, which is a long-chain middle-branched fatty acid used as a diagnostic marker for Mycobacterium tuberculosis. This fatty acid is also an excellent biolubricant. Control of its production is important for industrial purposes as well as understanding the biology of mycobacteria. In this study, we discovered that a carboxylic acid compound termed pivalic acid inhibits TBSA production in mycobacteria. Furthermore, Map strains from two separate genetic lineages (C-type and S-type) showed differential production of TBSA. Cattle-type strains of Mycobacterium avium subspecies paratuberculosis produce TBSA, while the sheep-type strains do not. This important phenotypic difference is attributed to a single-nucleotide deletion in sheep-type strains of Map. This work sheds further light on the mechanism used by mycobacteria to produce tuberculostearic acid.
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Affiliation(s)
- John P. Bannantine
- National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
| | - Shannon C. Duffy
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - María A. Colombatti Olivieri
- National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa, USA
- ARS Participation Program, Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Marcel A. Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Neil P. J. Price
- National Center for Agricultural Utilization Research, USDA Agricultural Research Service, Peoria, Illinois, USA
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Guo X, Zhang Z, Chen Q, Wang L, Xu X, Wei Z, Zhang Y, Chen K, Wang Z, Lu X, Liang Q. Whole Genome Sequencing Highlights the Pathogenic Profile in Nocardia Keratitis. Invest Ophthalmol Vis Sci 2024; 65:26. [PMID: 38502137 PMCID: PMC10959193 DOI: 10.1167/iovs.65.3.26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Purpose Nocardia keratitis is a serious and sight-threatening condition. This study aims to reveal the virulence and antimicrobial resistance gene profile of Nocardia strains using whole genome sequencing. Methods Whole-genome sequencing was performed on 23 cornea-derived Nocardia strains. Together with genomic data from the respiratory tract and the environment, 141 genomes were then utilized for phylogenetic and pan-genome analyses, followed by virulence and antibiotic resistance analysis. The correlations between virulence genes and pathogenicity were experimentally validated, including the characteristics of Nocardia colonies and clinical and histopathological evaluations of Nocardia keratitis mice models. Results Whole-genome sequencing of 141 Nocardia strains revealed a mean of 220 virulence genes contributed to bacterial pathogenesis. The mce gene family analysis led to the categorization of strains from the cornea into groups A, B, and C. The colonies of group C had the largest diameter, height, and fastest growth rate. The size of corneal ulcers and the clinical scores showed a significant increase in mouse models induced by group C. The relative expression levels of pro-inflammatory cytokines (CD4, IFN-γ, IL-6Rα, and TNF-α) in the lesion area exhibited an increasing trend from group A to group C. Antibiotic resistance genes (ARGs) spanned nine distinct drug classes, four resistance mechanisms, and seven primary antimicrobial resistance gene families. Conclusions Whole genome sequencing highlights the pathogenic role of mce gene family in Nocardia keratitis. Its distribution pattern may contribute to the distinct characteristics of the growth of Nocardia colonies and the clinical severity of the mice models.
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Affiliation(s)
- Xiaoyan Guo
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zijun Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qiankun Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Leying Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xizhan Xu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhenyu Wei
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Yang Zhang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Kexin Chen
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Zhiqun Wang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Xinxin Lu
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
| | - Qingfeng Liang
- Beijing Institute of Ophthalmology, Beijing Tongren Eye Center, Beijing Tongren Hospital, Capital Medical University, Beijing, China
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Turco S, Russo S, Pietrucci D, Filippi A, Milanesi M, Luzzago C, Garbarino C, Palladini G, Chillemi G, Ricchi M. High clonality of Mycobacterium avium subsp. paratuberculosis field isolates from red deer revealed by two different methodological approaches of comparative genomic analysis. Front Vet Sci 2024; 11:1301667. [PMID: 38379925 PMCID: PMC10876796 DOI: 10.3389/fvets.2024.1301667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 01/10/2024] [Indexed: 02/22/2024] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the aetiological agent of paratuberculosis (Johne's disease) in both domestic and wild ruminants. In the present study, using a whole-genome sequence (WGS) approach, we investigated the genetic diversity of 15 Mycobacterium avium field strains isolated in the last 10 years from red deer inhabiting the Stelvio National Park and affected by paratuberculosis. Combining de novo assembly and a reference-based method, followed by a pangenome analysis, we highlight a very close relationship among 13 MAP field isolates, suggesting that a single infecting event occurred in this population. Moreover, two isolates have been classified as Mycobacterium avium subsp. hominissuis, distinct from the other MAPs under comparison but close to each other. This is the first time that this subspecies has been found in Italy in samples without evident epidemiological correlations, having been isolated in two different locations of the Stelvio National Park and in different years. Our study highlights the importance of a multidisciplinary approach incorporating molecular epidemiology and ecology into traditional infectious disease knowledge in order to investigate the nature of infectious disease in wildlife populations.
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Affiliation(s)
- Silvia Turco
- Dipartimento di Scienze Agrarie e Forestali (DAFNE), Università degli Studi della Tuscia, Viterbo, Italy
| | - Simone Russo
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Daniele Pietrucci
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Viterbo, Italy
| | - Anita Filippi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Marco Milanesi
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Viterbo, Italy
| | - Camilla Luzzago
- Department of Veterinary Medicine and Animal Sciences, Coordinated Research Centre "EpiSoMI", University of Milan, Lodi, Italy
| | - Chiara Garbarino
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Giorgia Palladini
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Giovanni Chillemi
- Dipartimento per l'Innovazione nei Sistemi Biologici, Agroalimentari e Forestali (DIBAF), Università degli Studi della Tuscia, Viterbo, Italy
- Institute of Translational Pharmacology, National Research Council, CNR, Rome, Italy
| | - Matteo Ricchi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
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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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Tigani-Asil ETAE, Abdelwahab GED, Abdu EHAM, Terab AMA, Khalil NAH, Marri ZJMA, Yuosf MF, Shah AAM, Khalafalla AI, Ishag HZA. Pathological, microscopic, and molecular diagnosis of paratuberculosis/John's disease in naturally infected dromedary camel ( Camelus dromedarius). Vet World 2023; 16:1277-1283. [PMID: 37577185 PMCID: PMC10421554 DOI: 10.14202/vetworld.2023.1277-1283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 05/15/2023] [Indexed: 08/15/2023] Open
Abstract
Background and Aim Paratuberculosis (PTB) or John's disease is a chronic disease of ruminants impeding the reproduction and productivity of the livestock sector worldwide. Since there is a lack of pathological studies explaining the nature and development of the disease in camels, this study aimed to highlight the anatomopathological changes of PTB in camels, which may help in verifying and validating some diagnostic tests used to detect the etiology of the disease in camel tissues. Materials and Methods In August 2017, at Alselaa border's Veterinary Clinic of Al Dhafra Region, Western Abu Dhabi, UAE, one imported culled she-camel of 2 years old was subjected to clinical, microscopic, and anatomopathological investigations along with real-time quantitative polymerase chain reaction (q-PCR) to confirm the infection and correlate between clinical signs and pathological lesions of the PTB in dromedary camels. Results Clinically, typical clinical signs compliant with the pathognomonic gross and histologic lesions of PTB were seen in naturally infected dromedary camel. As presumptive diagnosis microscopically, acid-fast coccobacillus bacterium clumps were demonstrated in direct fecal smears as well as in scraped mucosal and crushed mesenteric lymph node films, and in histopathological sections prepared from a necropsied animal and stained by Ziehl-Neelsen stain. Free and intracellular acid-fast clump phagosomes were further confirmed as Mycobacterium avium subsp. paratuberculosis by q-PCR. Conclusion Clinical signs and pathological lesions of paratuberculosis in a dromedary camel were found to be similar to those of the other susceptible hosts.
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Affiliation(s)
- El Tigani Ahmed El Tigani-Asil
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - Ghada El Derdiri Abdelwahab
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - El Hadi Ahmed Mohamed Abdu
- Extension Services and Animal Health Division, Animal Wealth Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - Abdelnasir Mohammed Adam Terab
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - Nasareldien Altaib Hussein Khalil
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - Zhaya Jaber Mohammed Al Marri
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - Mohd Farouk Yuosf
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - Asma Abdi Mohamed Shah
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - Abdelmalik Ibrahim Khalafalla
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
| | - Hassan Zackaria Ali Ishag
- Biosecurity Affairs Division, Development and Innovation Sector, Abu Dhabi Agriculture and Food Safety Authority, Abu Dhabi, United Arab Emirates
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Byrne A, Ollier S, Tahlan K, Biet F, Bissonnette N. Genomic epidemiology of Mycobacterium avium subsp. paratuberculosis isolates from Canadian dairy herds provides evidence for multiple infection events. Front Genet 2023; 14:1043598. [PMID: 36816022 PMCID: PMC9934062 DOI: 10.3389/fgene.2023.1043598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 01/18/2023] [Indexed: 02/05/2023] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the pathogen responsible for paratuberculosis or Johne's Disease (JD) in ruminants, which is responsible for substantial economic losses worldwide. MAP transmission primarily occurs through the fecal-oral route, and the introduction of an MAP infected animal into a herd is an important transmission route. In the current study, we characterized MAP isolates from 67 cows identified in 20 herds from the provinces of Quebec and Ontario, Canada. Whole genome sequencing (WGS) was performed and an average genome coverage (relative to K-10) of ∼14.9 fold was achieved. The total number of SNPs present in each isolate varied from 51 to 132 and differed significantly between herds. Isolates with the highest genetic variability were generally present in herds from Quebec. The isolates were broadly separated into two main clades and this distinction was not influenced by the province from which they originated. Analysis of 8 MIRU-VNTR loci and 11 SSR loci was performed on the 67 isolates from the 20 dairy herds and publicly available references, notably major genetic lineages and six isolates from the province of Newfoundland and Labrador. All 67 field isolates were phylogenetically classified as Type II (C-type) and according to MIRU-VNTR, the predominant type was INMV 2 (76.1%) among four distinct patterns. Multilocus SSR typing identified 49 distinct INMV SSR patterns. The discriminatory index of the multilocus SSR typing was 0.9846, which was much higher than MIRU-VNTR typing (0.3740). Although multilocus SSR analysis provides good discriminatory power, the resolution was not informative enough to determine inter-herd transmission. In select cases, SNP-based analysis was the only approach able to document disease transmission between herds, further validated by animal movement data. The presence of SNPs in several virulence genes, notably for PE, PPE, mce and mmpL, is expected to explain differential antigenic or pathogenetic host responses. SNP-based studies will provide insight into how MAP genetic variation may impact host-pathogen interactions. Our study highlights the informative power of WGS which is now recommended for epidemiological studies and to document mixed genotypes infections.
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Affiliation(s)
- Alexander Byrne
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Séverine Ollier
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL, Canada
| | - Franck Biet
- INRAE, ISP, Université de Tours, Nouzilly, France
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada,*Correspondence: Nathalie Bissonnette,
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Kim E, Yang SM, Kim IS, Lee SY, Kim HY. Identification of Leuconostoc species based on novel marker genes identified using real-time PCR via computational pangenome analysis. Front Microbiol 2022; 13:1014872. [PMID: 36212836 PMCID: PMC9537375 DOI: 10.3389/fmicb.2022.1014872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
Leuconostoc species are important microorganisms in food fermentation but also cause food spoilage. Although these species are commercially important, their taxonomy is still based on inaccurate identification methods. Here, we used computational pangenome analysis to develop a real-time PCR-based method for identifying and differentiating the 12 major Leuconostoc species found in food. Analysis of pan and core-genome phylogenies showed clustering of strains into 12 distinct groups according to the species. Pangenome analysis of 130 Leuconostoc genomes from these 12 species enabled the identification of each species-specific gene. In silico testing of the species-specific genes against 143 publicly available Leuconostoc and 100 other lactic acid bacterial genomes showed that all the assays had 100% inclusivity/exclusivity. We also verified the specificity for each primer pair targeting each specific gene using 23 target and 124 non-target strains and found high specificity (100%). The sensitivity of the real-time PCR method was 102 colony forming units (CFUs)/ml in pure culture and spiked food samples. All standard curves showed good linear correlations, with an R2 value of ≥0.996, suggesting that screened targets have good specificity and strong anti-interference ability from food sample matrices and non-target strains. The real-time PCR method can be potentially used to determine the taxonomic status and identify the Leuconostoc species in foods.
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Park HT, Lee SM, Ko S, Kim S, Park HE, Shin MK, Kim D, Yoo HS. Delineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis. Vet Res 2022; 53:71. [PMID: 36100945 PMCID: PMC9469519 DOI: 10.1186/s13567-022-01089-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 08/13/2022] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne’s disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts. In the present study, host–pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. These observations suggest that the utilization of metabolites such as arginine by intracellular MAP might affect host NO production. Our dual RNA-seq data can provide novel insights by capturing the global transcriptome with higher resolution, especially in MAP, thus enabling a more systematic understanding of host–pathogen interactions.
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Affiliation(s)
- Hong-Tae Park
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Korea
| | - Sang-Mok Lee
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Seyoung Ko
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea
| | - Suji Kim
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Korea
| | - Hyun-Eui Park
- Department of Microbiology, College of Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Min-Kyoung Shin
- Department of Microbiology, College of Medicine, Research Institute of Life Science, Gyeongsang National University, Jinju, 52828, Korea
| | - Donghyuk Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Korea.
| | - Han Sang Yoo
- Department of Infectious Diseases, College of Veterinary Medicine, Seoul National University, Seoul, 08826, Korea.
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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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Ssekitoleko J, Ojok L, Abd El Wahed A, Erume J, Amanzada A, Eltayeb E, Eltom KH, Okuni JB. Mycobacterium avium subsp. paratuberculosis Virulence: A Review. Microorganisms 2021; 9:2623. [PMID: 34946224 PMCID: PMC8707695 DOI: 10.3390/microorganisms9122623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/08/2021] [Accepted: 12/16/2021] [Indexed: 11/17/2022] Open
Abstract
To propose a solution for control of Mycobacterium avium subsp. paratuberculosis (MAP) infections in animals as well as in humans, and develop effective prevention, diagnostic and treatment strategies, it is essential to understand the molecular mechanisms of MAP pathogenesis. In the present review, we discuss the mechanisms utilised by MAP to overcome the host defense system to achieve the virulence status. Putative MAP virulence genes are mentioned and their probable roles in view of other mycobacteria are discussed. This review provides information on MAP strain diversity, putative MAP virulence factors and highlights the knowledge gaps regarding MAP virulence mechanisms that may be important in control and prevention of paratuberculosis.
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Affiliation(s)
- Judah Ssekitoleko
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P. O. Box 7062, Uganda; (J.S.); (L.O.); (J.E.)
- Department of Livestock Health Research, Rwebitaba Zonal Agricultural Research and Development Institute, National Agricultural Research Organisation, Entebbe P. O. Box 295, Uganda
| | - Lonzy Ojok
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P. O. Box 7062, Uganda; (J.S.); (L.O.); (J.E.)
- Department of Pathology, Faculty of Medicine, Gulu University, Gulu P. O. Box 166, Uganda
| | - Ahmed Abd El Wahed
- Institute of Animal Hygiene and Veterinary Public Health, Leipzig University, D-04103 Leipzig, Germany
| | - Joseph Erume
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P. O. Box 7062, Uganda; (J.S.); (L.O.); (J.E.)
| | - Ahmad Amanzada
- Department of Gastroenterology and Gastrointestinal Oncology, University Medical Centre Goettingen, D-37075 Goettingen, Germany;
| | - ElSagad Eltayeb
- Ibn Sina Specialised Hospital, Mohammed Najeeb St., Khartoum 11560, Sudan;
- Faculty of Medicine, Al Neelain University, 52nd St., Khartoum 11112, Sudan
| | - Kamal H. Eltom
- Unit of Animal Health and Safety of Animal Products, Institute for Studies and Promotion of Animal Exports, University of Khartoum, Shambat, Khartoum North 13314, Sudan;
| | - Julius Boniface Okuni
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala P. O. Box 7062, Uganda; (J.S.); (L.O.); (J.E.)
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11
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Draft Genome Sequences of Two Bison-Type and Two Sheep-Type Strains of Mycobacterium avium subsp. paratuberculosis. Microbiol Resour Announc 2021; 10:e0052621. [PMID: 34264114 PMCID: PMC8280876 DOI: 10.1128/mra.00526-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genome sequences of two type B and two type S strains of Mycobacterium avium subsp. paratuberculosis are presented. These strains were isolated in the United States from sheep, bison, and cattle suffering from Johne’s disease. These genomes will increase our understanding of the minor differences that exist among strains of this genetically stable subspecies.
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