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Scherrer S, Schmitt S, Rademacher F, Kuhnert P, Ghielmetti G, Peterhans S, Stephan R. Development of a new multiplex quantitative PCR for the detection of Glaesserella parasuis, Mycoplasma hyorhinis, and Mycoplasma hyosynoviae. Microbiologyopen 2023; 12:e1353. [PMID: 37379423 PMCID: PMC10186005 DOI: 10.1002/mbo3.1353] [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: 12/06/2022] [Revised: 03/26/2023] [Accepted: 04/13/2023] [Indexed: 06/30/2023] Open
Abstract
Glaesserella parasuis, Mycoplasma hyorhinis, and Mycoplasma hyosynoviae are important porcine pathogens responsible for polyserositis, polyarthritis, meningitis, pneumonia, and septicemia causing significant economic losses in the swine industry. A new multiplex quantitative polymerase chain reaction (qPCR) was designed on one hand for the detection of G. parasuis and the virulence marker vtaA to distinguish between highly virulent and non-virulent strains. On the other hand, fluorescent probes were established for the detection and identification of both M. hyorhinis and M. hyosynoviae targeting 16S ribosomal RNA genes. The development of the qPCR was based on reference strains of 15 known serovars of G. parasuis, as well as on the type strains M. hyorhinis ATCC 17981T and M. hyosynoviae NCTC 10167T . The new qPCR was further evaluated using 21 G. parasuis, 26 M. hyorhinis, and 3 M. hyosynoviae field isolates. Moreover, a pilot study including different clinical specimens of 42 diseased pigs was performed. The specificity of the assay was 100% without cross-reactivity or detection of other bacterial swine pathogens. The sensitivity of the new qPCR was demonstrated to be between 11-180 genome equivalents (GE) of DNA for M. hyosynoviae and M. hyorhinis, and 140-1200 GE for G. parasuis and vtaA. The cut-off threshold cycle was found to be at 35. The developed sensitive and specific qPCR assay has the potential to become a useful molecular tool, which could be implemented in veterinary diagnostic laboratories for the detection and identification of G. parasuis, its virulence marker vtaA, M. hyorhinis, and M. hyosynoviae.
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Affiliation(s)
- Simone Scherrer
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Sarah Schmitt
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Fenja Rademacher
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Peter Kuhnert
- Institute of Veterinary Bacteriology, Vetsuisse FacultyUniversity of BernBernSwitzerland
| | - Giovanni Ghielmetti
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Sophie Peterhans
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
| | - Roger Stephan
- Section of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
- Institute for Food Safety and Hygiene, Vetsuisse FacultyUniversity of ZurichZurichSwitzerland
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Virulence and Inoculation Route Influence the Consequences of Mycoplasma hyorhinis Infection in Bama Miniature Pigs. Microbiol Spectr 2022; 10:e0249321. [PMID: 35446115 PMCID: PMC9241778 DOI: 10.1128/spectrum.02493-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycoplasma hyorhinis is a widespread pathogen in pig farms worldwide. Although the majority of M. hyorhinis-colonized pigs have no apparent clinical disease, the pathogen can induce diseases such as polyserositis, arthritis, and eustachitis in some cases. To explore the mechanisms for the occurrence of these diseases, we challenged 4 groups of Bama miniature pigs with M. hyorhinis isolated from pigs without clinical symptoms (non-clinical origin [NCO] strain) or with typical clinical symptoms (clinical origin [CO] strain) and investigated the impacts of different strains and inoculation routes (intranasal [IN], intravenous [IV] + intraperitoneal [IP], and IV+IP+IN) on disease induction. Another group of pigs was set as a negative control. Pigs inoculated with the CO strain through a combined intravenous and intraperitoneal (IV+IP) route showed a significant decrease in average daily weight gain (ADWG), serious joint swelling, and lameness compared with the pigs in the negative-control group. Furthermore, this group developed moderate-to-severe pericarditis, pleuritis, peritonitis, and arthritis, as well as high levels of IgG and IgM antibodies. Pigs inoculated IV+IP with the NCO strain developed less marked clinical, pathological changes and a weaker specific antibody response compared with the pigs inoculated with the CO strain. The challenging results of the NCO strain via different routes (IV+IP, IV+IP+IN, and IN) indicated that the combined route (IV+IP) induced the most serious disease compared to the other inoculation routes. Intranasal inoculation induced a smaller decrease in ADWG without obvious polyserositis or arthritis. These data suggest that differences in both strain virulence and inoculation route affect the consequences of M. hyorhinis infection. IMPORTANCE Mycoplasma hyorhinis is a widespread pathogen in pig farms worldwide. The mechanisms or conditions that lead to the occurrence of disease in M. hyorhinis-infected pigs are still unknown. The objective of this study was to evaluate the impact of differences in the virulence of strain and the inoculation route on the consequences of M. hyorhinis infection.
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Bünger M, Posch M, Wiesauer J, Loncaric I, Cabal Rosel A, Ruppitsch W, Ladinig A, Spergser J. A core genome multilocus sequence typing scheme for Mycoplasma hyorhinis. Vet Microbiol 2021; 262:109249. [PMID: 34628273 DOI: 10.1016/j.vetmic.2021.109249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 09/30/2021] [Indexed: 10/20/2022]
Abstract
Mycoplasma (M.) hyorhinis is a commensal and pathobiont residing in the upper respiratory tract in swine and with the ability to spread systemically, mainly causing polyserositis and polyarthritis in nursery pigs. Since little is known on the epidemiology of M. hyorhinis infection, whole genome sequences of 73 strains isolated from pigs in Austria (n = 71) and Germany (n = 2), that have been isolated from clinically affected pigs during routine diagnostics, and publicly available genomes of eight M. hyorhinis strains were analyzed in the presented study. For this purpose, a core genome multi locus sequence typing (cgMLST) scheme encompassing 453 target genes was developed using the Ridom© SeqSphere + software. Results were compared to two previously described conventional MLST schemes and to a core genome single nucleotide polymorphism (cgSNP) analysis approach. Core genome MLST showed high diversity among the M. hyorhinis strains studied and while certain isolates from one farm or a single animal formed cgMLST clusters (≤ 8 allele differences), no isolates with identical allele profiles were identified. In addition, cgMLST had superior discriminatory power (Simpson's ID = 0.995) over conventional MLST (Simpson's ID = 0.952 and 0.985), while demonstrating a lack of congruence between conventional MLST and genome-wide relationship. Core genome SNP results were highly congruent with cgMLST results but lacked in resolution when comparing closely related isolates. Thus, cgMLST is the most suitable method for epidemiological investigations such as outbreak analysis, and to gain insights into M. hyorhinis population structure.
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Affiliation(s)
- Moritz Bünger
- University of Veterinary Medicine Vienna, Institute of Microbiology, Veterinärplatz 1, 1210, Vienna, Austria; University of Veterinary Medicine Vienna, University Clinic for Swine, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Magdalena Posch
- University of Veterinary Medicine Vienna, Institute of Microbiology, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Julia Wiesauer
- University of Veterinary Medicine Vienna, Institute of Microbiology, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Igor Loncaric
- University of Veterinary Medicine Vienna, Institute of Microbiology, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Adriana Cabal Rosel
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Währinger Straße 25A, 1096, Vienna, Austria.
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute of Medical Microbiology and Hygiene, Währinger Straße 25A, 1096, Vienna, Austria.
| | - Andrea Ladinig
- University of Veterinary Medicine Vienna, University Clinic for Swine, Veterinärplatz 1, 1210, Vienna, Austria.
| | - Joachim Spergser
- University of Veterinary Medicine Vienna, Institute of Microbiology, Veterinärplatz 1, 1210, Vienna, Austria.
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Wu Y, Jin L, Li Y, Zhang D, Zhao Y, Chu Y, Ma ZR, Ma XX, Shang Y. The nucleotide usages significantly impact synonymous codon usage in Mycoplasma hyorhinis. J Basic Microbiol 2021; 61:133-146. [PMID: 33426673 DOI: 10.1002/jobm.202000592] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 11/08/2022]
Abstract
Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics participate in forcing nucleotide usage bias at every codon position. Moreover, nucleotide usage bias directly contributes to synonymous codon usage biases with two different extremes. The overrepresented codons tended to have A/T in the third codon position, and the underrepresented codons strongly used G/C in the third position. Furthermore, correspondence analysis and neutrality plot reflect an obvious interplay between mutation pressure and natural selection mediating codon usage in M. hyorhinis genome. Due to significant bias in usages between A/T and G/C at the gene level, different selective forces have been proposed to contribute to codon usage preference in M. hyorhinis genome, including nucleotide composition constraint derived from mutation pressure, translational selection involved in natural selection, and strand-specific mutational bias represented by different nucleotide skew index. The systemic analyses of codon usage for M. hyorhinis can enable us to better understand the mechanisms of evolution in this species.
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Affiliation(s)
- Yaqin Wu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China.,Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Li Jin
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Yicong Li
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Derong Zhang
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Yongqing Zhao
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Yuefeng Chu
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
| | - Zhong-Ren Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Xiao-Xia Ma
- Biomedical Research Center, Northwest Minzu University, Lanzhou, P.R. China
| | - Youjun Shang
- State Key Laboratory of Veterinary Etiological Biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, P.R. China
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Genotyping Mycoplasma hyorhinis by multi-locus sequence typing and multiple-locus variable-number tandem-repeat analysis. Vet Microbiol 2020; 249:108836. [PMID: 32956967 DOI: 10.1016/j.vetmic.2020.108836] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/10/2020] [Indexed: 11/20/2022]
Abstract
Mycoplasma hyorhinis is a swine pathogen bacterium, which causes significant economic losses. The infection spreads through direct contact between the animals. Powerful genotyping methods like PCR based multi-locus sequence typing (MLST) and multiple-locus variable-number tandem-repeat analysis (MLVA) are necessary to monitor the infections and to conduct epidemiological investigations; hence supporting the control of the disease. The aims of the present study were to examine M. hyorhinis isolates originating mainly from Hungary with MLST and MLVA developed in the study, and to compare the results of the two typing methods. To characterize 39 M. hyorhinis isolates and the type strain (NCTC 10,130), six house-keeping genes were selected for MLST and six tandem-repeat regions were chosen for MLVA. We were able to differentiate 31 sequence types and 37 genotypes within the 40 analyzed isolates by the MLST and the MLVA, respectively. With the combination of the two newly developed assays all examined isolates were distinguished with the exception of the ones originating from the same animal. The developed MLST assay provided a robust and high resolution phylogenetic tree, while the MLVA system is suitable for the differentiation of closely related isolates from the same farm, hence the assay is appropriate for epidemiologic studies.
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Clavijo MJ, Sreevatsan S, Johnson TJ, Rovira A. Molecular epidemiology of Mycoplasma hyorhinis porcine field isolates in the United States. PLoS One 2019; 14:e0223653. [PMID: 31634349 PMCID: PMC6802821 DOI: 10.1371/journal.pone.0223653] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 09/25/2019] [Indexed: 01/29/2023] Open
Abstract
Mycoplasma hyorhinis is one of the causative agents of polyserositis and arthritis in post-weaning pigs. Here we describe the development of a multi-locus sequence typing (MLST) protocol for the characterization of M. hyorhinis field isolates. A total of 104 field isolates from different geographical locations, swine production systems, and clinical backgrounds, were analyzed. Twenty-seven genes, including housekeeping and those encoding surface proteins, were evaluated to index diversity. Genes encoding surface proteins were included to increase the discriminatory power of the MLST. Four target gene fragments were selected to be included in the final MLST-s (surface) protocol: pdhB, p95, mtlD and ung. Within each locus the nucleotide variation ranged from 1.4% to 20%. The 104 field isolates were classified into 39 distinct sequence types (STs). Multiple STs were found within the same production system and within the same pig. The majority of STs grouped strains from the same production system; however, cases existed where multiple systems shared a ST, indicating potential relationships between pig flows. The majority of the nucleotide changes observed in these genes generated synonymous changes, while non-synonymous changes were exclusively in the mtlD gene fragment, suggesting that this protein is undergoing selection. Molecular typing of M. hyorhinis will primarily aid swine practitioners with pig flow management and identifying sources of infection during outbreaks.
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Affiliation(s)
- Maria J. Clavijo
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota, United States of America
| | - Srinand Sreevatsan
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota, United States of America
| | - Timothy J. Johnson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St Paul, Minnesota, United States of America
| | - Albert Rovira
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St Paul, Minnesota, United States of America
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Genomic polymorphism of Mycoplasma flocculare revealed by a newly developed multilocus sequence typing scheme. Vet Microbiol 2019; 237:108422. [PMID: 31585641 DOI: 10.1016/j.vetmic.2019.108422] [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: 07/26/2019] [Revised: 09/13/2019] [Accepted: 09/15/2019] [Indexed: 11/22/2022]
Abstract
Mycoplasma flocculare is genetically closely related to M. hyopneumoniae, the etiologic agent of porcine enzootic pneumonia, and is frequently isolated with this second species. In this article, we report on the development of the first multilocus sequence typing (MLST) scheme for M. flocculare, based on three genes (adk, rpoB and tpiA). In total, 5022 bp of sequence were analyzed. MLST was used to characterize seven M. flocculare isolates and the reference strain. Eight distinct sequence types were defined, showing the great intraspecies variability of M. flocculare, and the high discriminatory power of the new typing method. The relative contribution of recombinations to the genomic evolution of M. flocculare was revealed by calculating the index of association (IA: 0.0185). This MLST scheme is now available for the acquisition of new knowledge on M. flocculare epidemiology via an online database comprising the DNA sequences of each allele, available at http://pubmlst.org/mflocculare/.
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