The core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis

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.

Core-genome multilocus sequence typing and core-SNP analysis of Clostridium neonatale strains isolated in different spatio-temporal settings

IMPORTANCE

Clostridium neonatale has been isolated from the fecal samples of asymptomatic neonates and cases of necrotizing enterocolitis (NEC). Taking advantage of a large collection of independent strains isolated from different spatio-temporal settings, we developed and established a cgMLST scheme for the molecular typing of C. neonatale. Both the cgMLST and cgSNP methods demonstrate comparable discrimination power. Results indicate geographic- and temporal- independent clustering of C. neonatale NEC-associated strains. No specific cgMLST clade of C. neonatale was genetically associated with NEC.

Development of molecular assays for the analysis of genetic relationships of Mycoplasma iowae

Mycoplasma iowae is a worldwide spread and economically important avian pathogen that mostly infects turkeys. Currently, multi-locus sequence typing (MLST) serves as the gold standard method for strain identification in M. iowae. However, additional robust genotyping methods are required to effectively monitor M. iowae infections and conduct epidemiological investigations. The first aim of this study was to develop genotyping assays with high resolution, that specifically target M. iowae, namely a multiple-locus variable number of tandem-repeats analysis (MLVA) and a core genome multi-locus sequence typing (cgMLST) schema. The second aim was the determination of relationships among a diverse selection of M. iowae strains and clinical isolates with a previous and the newly developed assays. The MLVA was designed based on the analyses of tandem-repeat (TR) regions in the six serotype reference strains (I, J, K, N, Q and R). The cgMLST schema was developed based on the coding sequences (CDSs) common in 95% of the examined 99 isolates. The samples were submitted for a previously published MLST assay for comparison with the developed methods. Out of 94 TR regions identified, 17 alleles were selected for further evaluation by PCR. Finally, seven alleles were chosen to establish the MLVA assay. Additionally, whole genome sequence analyses identified a total of 676 CDSs shared by 95% of the isolates, all of which were included into the developed cgMLST schema. The MLVA discriminated 19 distinct genotypes (GT), while with the cgMLST assay 79 sequence types (ST) could be determined with Simpson's diversity indices of 0.810 (MLVA) and 0.989 (cgMLST). The applied assays consistently identified the same main clusters among the diverse selection of isolates, thereby demonstrating their suitability for various genetic analyses and their ability to yield congruent results.

Characterization of atypical Mycoplasma anserisalpingitidis strains

Mycoplasma anserisalpingitidis is a waterfowl colonizing mycoplasma, mainly found in geese. In this study, we compared the whole genomes of five atypical M. anserisalpingitidis strains originating from China, Vietnam and Hungary, with the rest of the collection. Common methods used in the description of species are genomic analyses like the analysis of 16 S - intergenic transcribed spacer (ITS) - 23 S rRNA, of housekeeping genes, of the average nucleotide identity (ANI) and average amino acid identity (AAI) and phenotypic analyses like testing the growth inhibition and the growth parameters of the strains. The atypical strains showed notable genomic differences in all of the genetic analyses: on average ANI and AAI 95% (M. anserisalpingitidis ANI Minimum: 92.45, Maximum: 95.10; AAI Minimum: 93.34, Maximum: 96.37). The atypical strains formed a separate branch among the M. anserisalpingitidis strains in all phylogenetic studies. The small genome size and possibly higher mutation rate of the M. anserisalpingitidis species likely contributed to the observed genetic difference. Based on genetic analyses, the studied strains clearly represent a new genotype of M. anserisalpingitidis. The atypical strains showed slower growth in the medium containing fructose and three of the atypical strains showed diminished growth in the inhibition test. However, no definitive geno-phenotype associations were found regarding the fructose metabolism pathway in the atypical strains. The atypical strains are potentially at an early stage of speciation.

Development and evaluation of temperature-sensitive Mycoplasma anserisalpingitidis clones as vaccine candidates

Mycoplasma anserisalpingitidis is economically the most important pathogenic Mycoplasma species of waterfowl in Europe and Asia. The lack of commercially available vaccines against M. anserisalpingitidis had prompted this study with the aim to produce temperature-sensitive (ts⁺) clones as candidates for an attenuated live vaccine. The production of ts⁺ clones was performed by N-methyl-N'-nitro-N-nitrosoguanidine (NTG)-evoked mutagenesis of Hungarian M. anserisalpingitidis field isolates. The clones were administered via eye drop and intracloacally to 33-day-old geese. Colonisation ability was examined by PCR and isolation from the trachea and cloaca, while the serological response of the birds was tested by ELISA. Pathological and histopathological examinations were performed at the eighth week after inoculation. Whole-genome sequence (WGS) analysis of the selected clone and its parent strain was also performed. NTG-treatment provided three ts⁺ mutants (MA177/1/11, MA177/1/12, MA271). MA271 was detected at the highest rate from cloacal (86.25%) and tracheal (30%) samples, while MA177/1/12 and MA271 elicited remarkable serological responses with 90% of the animals showing seroconversion. Re-isolates of MA271 remained ts⁺ throughout the experiment. Based on these properties, clone MA271 was found to be the most promising vaccine candidate. WGS analysis revealed 59 mutations in the genome of MA271 when compared to its parent strain, affecting both polypeptides involved in different cellular processes and proteins previously linked to bacterial fitness and virulence. Although further studies are needed to prove that MA271 is in all aspects a suitable vaccine strain, it is expected that this ts⁺ clone will contribute to the control of M. anserisalpingitidis infection.

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.

Mycoplasma species in the male reproductive organs and the fresh and frozen semen of the Hungarian native goose

The objective of this study was to clarify whether the most common species of Mycoplasma can be detected in the reproductive organs and the cloaca, as well as in the semen of asymptomatic native Hungarian male geese. As it is necessary for the semen of that breed to be preserved pathogen-free in an in vitro gene-conservation programme, the presence of and sources of infection, as well as prevention of the survival of pathogens following semen cryopreservation, are key issues. Ten asymptomatic, 2-year-old ganders were tested. For the detection of mycoplasmas, samples were taken from both fresh and frozen/thawed semen, cloaca, phallus lymph, testes and vas deferens; that is five samples from each of the 10 ganders. The semen was statically frozen using dimethyl-formamide as a cryoprotectant and stored in liquid nitrogen at -196°C. Species-specific PCR systems targeting M. anserisalpingitidis, M. anseris and M. cloacale were used for screening and identification. Results of this study have shown, for the first time, that (1) among the three Mycoplasma species examined, all were detectable in the indigenous Hungarian ganders, with no clinical signs; (2) the pathogens could be detected in the cloaca, in both fresh and cryopreserved semen samples, but remained undetected within the inner reproductive organs; and (3) as pathogens were able to survive the freezing/storing/thawing procedures, the possibility of vertical transmission of the pathogens during artificial inseminations does exist, which causes problems in the in vitro gene-conservation programmes for this breed.

Occurrence of Mycoplasma spp. in wild birds: phylogenetic analysis and potential factors affecting distribution

Different Mycoplasma species have been reported in avian hosts. However, the majority of studies focus on one particular species of Mycoplasma or one host. In our research, we screened a total of 1141 wild birds representing 55 species, 26 families, and 15 orders for the presence of mycoplasmas by conventional PCR based on the 16S rRNA gene. Selected PCR products were sequenced to perform the phylogenetic analysis. All mycoplasma-positive samples were tested for M. gallisepticum and M. synoviae, which are considered the major pathogens of commercial poultry. We also verified the influence of ecological characteristics of the tested bird species including feeding habits, habitat types, and movement patterns. The presence of Mycoplasma spp. was confirmed in 498 birds of 29 species, but none of the tested birds were positive for M. gallisepticum or M. synoviae. We found possible associations between the presence of Mycoplasma spp. and all investigated ecological factors. The phylogenetic analysis showed a high variability of Mycoplasma spp.; however, some clustering of sequences was observed regarding particular bird species. We found that wild migratory waterfowl, particularly the white-fronted goose (Anser albifrons) and mallard (Anas platyrhynchos) could be reservoirs and vectors of mycoplasmas pathogenic to commercial waterfowl.

Co-Infection of Escherichia coli, Enterococcus faecalis and Chlamydia psittaci Contributes to Salpingitis of Laying Layers and Breeder Ducks

Salpingitis is manifested as hemorrhagic follicular inflammation exudations and peritonitis, leading to reduced egg production and high culling of breeder flocks. From 2018 to 2021, increasing salpingitis during egg peak is threatening the poultry industry post-artificial insemination, both in breeder layers and breeder ducks across China. In our study, Escherichia coli (E. coli), Enterococcus faecalis(E. faecalis) and Chlamydia psittaci (C. psittaci) were isolated and identified from the diseased oviducts using biochemical tests and PCR. To identify and isolate pathogenicity, we inoculated the isolates into laying hens via an intravaginal route. Later, laying hens developed typical salpingitis after receiving the combination of the aforementioned three isolates (1 × 10⁵ IFU/mL of C. psittaci and 1 × 10⁶ CFU/mL of E. faecalis and E. coli, respectively), while less oviduct inflammation was observed in the layers inoculated with the above isolate alone. Furthermore, 56 breeder ducks were divided into seven groups, eight ducks per group. The birds received the combination of three isolates, synergic infection of E. coli and E. faecalis, and C. psittaci alone via vaginal tract, while the remaining ducks were inoculated with physiological saline as the control group. Egg production was monitored daily and lesions of oviducts and follicles were determined post-infection on day 6. Interestingly, typical salpingitis, degenerated follicles and yolk peritonitis were obviously found in the synergic infection of three isolates and the birds inoculated with C. psittaci alone developed hemorrhagic follicles and white exudates in oviducts, while birds with E. faecalis or E. coli alone did not develop typical salpingitis. Finally, higher E. coli loads were determined in the oviducts as compared to E. faecalis and C. psittaci infection. Taken together, the combination of E. coli and E. faecalis, and C. psittaci could induce typical salpingitis and yolk peritonitis both in laying hens and breeder ducks. Secondary infection of E. coli and E. faecalis via artificial insemination is urgently needed for investigation against salpingitis.

Novel prophage-like sequences in Mycoplasma anserisalpingitidis

Mycoplasma anserisalpingitidis is a bacterial waterfowl pathogen. In these days of growing antibiotic resistance, it is necessary to search for alternative methods of defense against Mycoplasma impacts in flocks. In order to identify prophage-like sequences, three established bioinformatics tools (PHASTER, PhiSpy, Prophage Hunter) were used in this study for the in silico screening of 82 M. anserisalpingitidis whole genomes. The VIBRANT software was used as a novel approach to further investigate the possibility of prophages in the sequences. The commonly used softwares found prophage-like sequences in the strains, but the results were inconclusive. The VIBRANT search resulted in multiple hits, and many of them were over 10,000 base pairs (bp). These putative prophages are comparable in size to the few described mycoplasma phages. The translated coding DNA sequences of the putative prophages were checked with protein BLAST. The functions of the proteins found by the BLASTP search are common among bacteriophages. The BLASTN search of the sequences found that many of these were more similar to the M. anatis NCTC 10156 strain, rather than the available M. anserisalpingitidis strains. The initial screening pointed at the presence of novel bacteriophages in the M. anserisalpingitidis and M. anatis strains. The VIBRANT search results were very similar to each other and none of these sequences were part of the core genome of M. anserisalpingitidis, with a few exceptions. The VIBRANT analysis explored presumably intact, novel prophages.

Multilocus sequence typing of the goose pathogen Mycoplasma anserisalpingitidis

Mycoplasma anserisalpingitidis infection is associated with the inflammation of the genital tract and cloaca, embryo lethality, and decreased egg production in geese, leading to serious economic losses. M. anserisalpingitidis has been detected mainly in Central and Eastern Europe, especially in Hungary, but the pathogen was identified recently in China, predicting it's worldwide occurrence. In this study, a novel multilocus sequence typing (MLST) scheme was developed to analyse phylogenetic relationships between M. anserisalpingitidis field isolates and clinical specimens originating from different geographical locations. Five loci (atpG, fusA, pgiB, plsY, and uvrA) were selected for the final MLST study. The examined 89 M. anserisalpingitidis samples yielded 76 unique sequence types with a 0.994 Simpson's index of diversity. The samples were originated from Hungary, Poland, Ukraine, China, and Vietnam. Phylogenetic analysis revealed the existence of three distinct clades (A-C) and six subclades within clade C. Generally, samples originating from the same geographical locations or livestock integration clustered together. Isolates in clade A showed the closest relationships to the M. anatis outgroup due to sequence similarity of the plsY locus. The highest genetic distance was observed in 5C among the subclades of clade C, containing the Asian and some Hungarian field isolates. The developed MLST assay revealed high diversity of the investigated M. anserisalpingitidis samples. The method proved to be a valuable and cost-effective tool for sequence typing of this waterfowl Mycoplasma species, enabling the better understanding of its phylogeny and providing a robust assay for future molecular epidemiological investigations.