Application of Four Genotyping Methods to Mycoplasma bovis Isolates Derived from Western Canadian Feedlot Cattle

Multilocus sequence typing schemes for the emerging swine pathogen Mycoplasma hyosynoviae

Mycoplasma (M.) hyosynoviae is a commensal of the upper respiratory tract in swine, which has the potential to spread systemically, usually resulting in arthritis in fattening pigs and gilts. To date, very little is known about the epidemiology of M. hyosynoviae, mainly due to a lack of suitable typing methods. Therefore, this study aimed to develop both a conventional multi locus sequence typing (MLST) and a core genome (cg) MLST scheme. The development of the cgMLST was based on whole genome sequences of 64 strains isolated from pigs and wild boars during routine diagnostics as well as nine publicly available genomes. A cgMLST scheme containing 390 target genes was established using the Ridom© SeqSphere+ software. Using this scheme as a foundation, seven housekeeping genes were selected for conventional MLST based on their capability to reflect genome wide relatedness and subsequently, all 73 strains were typed by applying both methods. Core genome MLST results revealed a high diversity of the studied strain population and less than 100 allele differences between epidemiologically unrelated strains were only detected for four isolates from the US. On the other hand, seven clonal clusters (≤ 12 allele differences) comprising 20 isolates were identified. Comparison of the two typing methods resulted in highly congruent phylogenetic trees and an Adjusted Rand Coefficient of 0.893, while cgMLST showed marginally higher resolution when comparing closely related isolates, indicated by a slightly higher Simpson's ID (0.992) than conventional MLST (Simpson's ID = 0.990). Overall, both methods seem well suited for epidemiological analyses for scientific as well as diagnostic purposes. While MLST is faster and cheaper, cgMLST can be used to further differentiate closely related isolates.

Prevalence of Mycoplasma bovis in Algeria and Characterisation of the Isolated Clones

Bovine respiratory disease (BRD) is common in calves in Algeria, but to date, Mycoplasma bovis has never been monitored as a potential etiological agent. Here, to assess the presence (direct detection) and circulation (indirect detection) of M. bovis, broncho-alveolar lavage fluids (BALF) and serum samples were collected from 60 veal calf farms in Algeria. A commercial ELISA kit (ID Screen^® ELISA) was used to screen for the presence of specific antibodies against M. bovis in 351 blood sera collected from both diseased and healthy calves, and 69% (241 sera) tested positive. BALFs from the 176 diseased calves were used to screen for M. bovis by real-time-PCR (rt-PCR), and 102 (58%) tested positive. A non-exhaustive set of 53 clones were isolated from 44 calves and further subtyped using polC gene sequencing. No predominant subtype was found, and two clones exhibited a new subtype. Fourteen clones were further characterized by multilocus sequence typing, and results showed a high degree of genetic diversity, with some clones having new alleles and subtypes. The minimum inhibitory concentrations (MICs) of 5 antimicrobials regularly used to treat BRD was determined on 45 clones. Susceptibility profiles showed very broad diversity, confirming the variety of clones actively circulating. We detected clones with high MICs, including increased MICs of enrofloxacin (n = 5). This is the first study to report the presence of M. bovis in Algeria in calves with BRD. This research also finds broad genetic and phenotypic diversity in the actively circulating isolates.

Comparative genomic analysis of Canadian Mycoplasma bovis strains isolated from Bison and Cattle

Mycoplasma bovis (M. bovis) in cattle causes pneumonia, arthritis, otitis media, and mastitis. In addition, multiple outbreaks have been recorded in North American bison. The genomic data on Canadian M. bovis in bison and cattle to date is limited. Whole-genome sequencing (WGS) was used to assess the degree of genome conservation across four Canadian M. bovis strains recovered from bison and cattle. Whole-genome sequences of four M. bovis isolates (Mb1, Mb160, Mb300, Mb304) and the PG45 reference genome were utilized to identify the M. bovis genomic similarity, whole-genome single nucleotide polymorphism (WGS-SNP), virulence determinants, and genomic islands. The pan-genome analysis showed that M. bovis encodes a minimum of 971 genes, while the core genome contained 637 genes. Comparative genomics revealed limited diversity in gene content between bison and cattle isolates. Whole-genome SNP analysis showed that the four M. bovis isolates differed from each other and to PG45. A total of 40 putative virulence genes associated with adhesion, colonization, and destruction of tissues were found in the bison and cattle isolates using the virulence factors database (VFDB). These putative virulence factors were equally distributed among isolates. Genomic Islands (GIs) ranging from 4 to 9 and associated with transposases, restriction-modification, ribosomal hypothetical proteins, variable surface lipoproteins, and unknowns were also identified. Overall, the genomic characterization of these isolates may provide new insights into the mechanisms of pathogenicity in M. bovis.

Epidemiological Investigations and Multi-locus Sequence Typing of Mycoplasma synoviae Isolates from Chicken Farms in China

Mycoplasma synoviae (M. synoviae) is an important pathogen in poultry industry and has led to major economic losses. Understanding the epidemiology is crucial to improve control and eradication program of M. synoviae. In this study, 487 samples suspected with M. synoviae infection were collected from August 2020 to June 2021 in China. Among 487 samples, 324 samples were MS positive, the positive rate was 66.53%, and 104 strains were isolated from 324 positive samples. The multilocus sequence typing (MLST) method based on seven housekeeping genes was used to conduct genotyping 104 M. synoviae strains isolated, and the 104 isolates belonged to 8 sequence types (STs) after MLST genotyping, and ST-34 had the highest proportion. After BURST analysis, all 104 isolates were divided into group 12 with other 56 strains isolated from China. Phylogenetic tree constructed by neighbor-joining method showed that nearly all of Chinese isolates (160 isolates) clustered together and separated from other reference isolates (217 isolates) in the PubMLST database. In conclusion, this study suggested that the M. synoviae strains in China were highly similar and independent of abroad strains.

A core genome multilocus sequence typing scheme for Mycoplasma hyorhinis

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.