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Scherrer S, Stephan R. Novel multiplex TaqMan assay for differentiation of the four major pathogenic Brachyspira species in swine. Microbiologyopen 2021; 10:e1169. [PMID: 33650802 PMCID: PMC7887428 DOI: 10.1002/mbo3.1169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 01/24/2023] Open
Abstract
A novel TaqMan 5-plex real-time PCR using a combination of locked nucleic acid-modified (LNA)- and minor groove binding (MGB)-conjugated DNA probes was developed for identification and differentiation between the four main pathogenic Brachyspira species in swine. B. hyodysenteriae, B. pilosicoli, and B. suanatina are identified using three hydrolysis probes targeting cpn60, while B. hampsonii is recognized by another nox specific probe. The assay also includes an exogenous internal control simultaneously verifying the PCR competency of the DNA samples. Validation of the novel assay was performed using DNA samples from 18 Brachyspira reference strains and 477 clinical samples obtained from porcine rectal swabs by comparing them with different PCR-based methods targeting nox, 16S rDNA, and 23S rDNA. The specificity of the assay was 100% without cross-reactivity or detection of different pathogens. Depending on the Brachyspira species, the limit of detection was between 10 and 20 genome equivalents with a cut-off threshold cycle (Ct) value of 37. The developed highly sensitive and specific 5-plex real-time PCR assay is easy to implement in routine veterinary diagnostic laboratories and enables rapid differentiation between the main four pathogenic Brachyspira species recognized in pigs using a single-tube approach.
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Affiliation(s)
- Simone Scherrer
- Department of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Roger Stephan
- Department of Veterinary Bacteriology, Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
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Pandey A, Humbert MV, Jackson A, Passey JL, Hampson DJ, Cleary DW, La Ragione RM, Christodoulides M. Evidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli. Microb Genom 2020; 6:mgen000470. [PMID: 33174833 PMCID: PMC8116685 DOI: 10.1099/mgen.0.000470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022] Open
Abstract
The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus Brachyspira. Our study revealed that an additional isolate that was unable to be species typed against any other Brachyspira lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the B. pilosicoli as random mutation (r/m=1.02). Comparative genomics has informed Brachyspira diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.
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Affiliation(s)
- Anish Pandey
- Molecular Microbiology, School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK
- Southampton NIHR Biomedical Research Centre, University Hospital Southampton NHS Trust, SO166YD, UK
| | - Maria Victoria Humbert
- Molecular Microbiology, School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Alexandra Jackson
- Molecular Microbiology, School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Jade L. Passey
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL, UK
| | - David J. Hampson
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - David W. Cleary
- Molecular Microbiology, School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK
- Southampton NIHR Biomedical Research Centre, University Hospital Southampton NHS Trust, SO166YD, UK
| | - Roberto M. La Ragione
- Department of Pathology and Infectious Diseases, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7AL, UK
| | - Myron Christodoulides
- Molecular Microbiology, School of Clinical and Experimental Sciences, University of Southampton Faculty of Medicine, Southampton General Hospital, Southampton SO16 6YD, UK
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Abstract
In 1967, Harland and Lee made a startling discovery: in some humans, the colonic epithelium is covered with a "forest" of spirochetes (W. A. Harlan, and F. D. Lee, Br Med J 3:718-719, 1967, https://doi.org/10.1136/bmj.3.5567.718). In this issue of Journal of Bacteriology, Thorell et al. present a systematic analysis of the prevalence and diversity of the spirochetes Brachyspira aalborgi and Brachyspira pilosicoli in the human colon. These and prior studies provide avenues toward resolving important questions: what bacterial and host parameters contribute to this extensive colonization, and what impact does it have on human health?
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The Spirochete Brachyspira pilosicoli, Enteric Pathogen of Animals and Humans. Clin Microbiol Rev 2017; 31:31/1/e00087-17. [PMID: 29187397 DOI: 10.1128/cmr.00087-17] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Brachyspira pilosicoli is a slow-growing anaerobic spirochete that colonizes the large intestine. Colonization occurs commonly in pigs and adult chickens, causing colitis/typhlitis, diarrhea, poor growth rates, and reduced production. Colonization of humans also is common in some populations (individuals living in village and peri-urban settings in developing countries, recent immigrants from developing countries, homosexual males, and HIV-positive patients), but the spirochete rarely is investigated as a potential human enteric pathogen. In part this is due to its slow growth and specialized growth requirements, meaning that it is not detectable in human fecal samples using routine diagnostic methods. Nevertheless, it has been identified histologically attached to the colon and rectum in patients with conditions such as chronic diarrhea, rectal bleeding, and/or nonspecific abdominal discomfort, and one survey of Australian Aboriginal children showed that colonization was significantly associated with failure to thrive. B. pilosicoli has been detected in the bloodstream of elderly patients or individuals with chronic conditions such as alcoholism and malignancies. This review describes the spirochete and associated diseases. It aims to encourage clinicians and clinical microbiologists to consider B. pilosicoli in their differential diagnoses and to develop and use appropriate diagnostic protocols to identify the spirochete in clinical specimens.
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