Development of Mycoplasma synoviae (MS) core genome multilocus sequence typing (cgMLST) scheme
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Published on: December 7, 2021
Mostafa Ghanem1, Mohamed El-Gazzar2
1Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA; Faculty of Veterinary Medicine, Alexandria University, Rasheed El-Mahmoudeya, Markaz Rasheed, El Beheira Governorate, P.O. Box 22758, Egypt.
Abstract:
Mycoplasma synoviae (MS) is a poultry pathogen with reported increased prevalence and virulence in recent years. MS strain identification is essential for prevention, control efforts and epidemiological outbreak investigations. Multiple multilocus based sequence typing schemes have been developed for MS, yet the resolution of these schemes could be limited for outbreak investigation. The cost of whole genome sequencing became close to that of sequencing the seven MLST targets; however, there is no standardized method for typing MS strains based on whole genome sequences. In this paper, we propose a core genome multilocus sequence typing (cgMLST) scheme as a standardized and reproducible method for typing MS based whole genome sequences. A diverse set of 25 MS whole genome sequences were used to identify 302 core genome genes as cgMLST targets (35.5% of MS genome) and 44 whole genome sequences of MS isolates from six countries in four continents were used for typing applying this scheme. cgMLST based phylogenetic trees displayed a high degree of agreement with core genome SNP based analysis and available epidemiological information. cgMLST allowed evaluation of two conventional MLST schemes of MS. The high discriminatory power of cgMLST allowed differentiation between samples of the same conventional MLST type. cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation between MS isolates. Like conventional MLST, it provides stable and expandable nomenclature, allowing for comparing and sharing the typing results between different laboratories worldwide.
Insights
A new core genome multilocus sequence typing (cgMLST) scheme offers a standardized method for identifying Mycoplasma synoviae (MS) strains. This highly discriminatory approach improves poultry disease outbreak investigations and global strain comparison.
Area of Science:
- Veterinary Microbiology
- Genomics
- Epidemiology
Background:
- Mycoplasma synoviae (MS) is an increasingly prevalent and virulent poultry pathogen.
- Accurate MS strain identification is crucial for disease control and outbreak investigations.
- Existing multilocus sequence typing (MLST) schemes lack sufficient resolution for detailed epidemiological studies.
Purpose of the Study:
- To develop and validate a standardized core genome multilocus sequence typing (cgMLST) scheme for Mycoplasma synoviae.
- To establish a reproducible whole genome sequencing-based typing method for MS.
- To assess the discriminatory power of cgMLST compared to conventional MLST schemes.
Main Methods:
- Identification of 302 core genome genes from 25 diverse MS whole genome sequences.
- Application of the developed cgMLST scheme to type 44 MS isolates from six countries.
- Phylogenetic analysis of cgMLST data and comparison with core genome SNP analysis and epidemiological information.
Main Results:
- The cgMLST scheme targets 302 core genes, representing 35.5% of the MS genome.
- cgMLST phylogenetic trees showed high concordance with SNP-based analysis and epidemiological data.
- cgMLST demonstrated superior discriminatory power, differentiating isolates within the same conventional MLST type.
Conclusions:
- cgMLST provides a standardized, accurate, and highly discriminatory method for typing Mycoplasma synoviae isolates.
- The scheme enables reproducible strain differentiation and facilitates global data sharing through a stable nomenclature.
- cgMLST significantly enhances the capability for poultry disease outbreak investigations and epidemiological surveillance.
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