Complete Genome Sequences of Three Mycoplasma anserisalpingitis (Mycoplasma sp. 1220) Strains

Comparative genomic analysis of Mycoplasma anatis strains

Background

The Gram-negative intracellular bacterium Mycoplasma anatis is a pathogen of respiratory infectious diseases in ducks and has caused significant economic losses in the poultry industry.

Objective

This study, as the first report of the structure and function of the pan-genome of Mycoplasma anatis, may provide a valuable genetic basis for many aspects of future research on the pathogens of waterfowl.

Methods

We sequenced the whole genomes of 15 Mycoplasma anatis isolated from ducks in China. Draft genome sequencing was carried out and whole-genome sequencing was performed by the sequencers of the PacBio Sequel and an IonTorrent Personal Genome Machine (PGM). Then the common genic elements of protein-coding genes, tRNAs, and rRNAs of Mycoplasma anatis genomes were predicted by using the pipeline Prokka v1.13.7. To investigate homologous protein clusters across Mycoplasma anatis genomes, we adopted Roary v3.13.0 to cluster orthologous genes (OGs) based on the following criteria.

Results

We obtained one complete genome and 14 genome sketches. Microbial mobile genetic element analysis revealed the distribution of insertion sequences (IS30, IS3, and IS1634), prophage regions, and CRISPR arrays in the genome of Mycoplasma anatis. Comparative genomic analysis decoded the genetic components and functional classification of the pan-genome of Mycoplasma anatis that comprised 646 core genes, 231 dispensable genes and among them 110 was strain-specific. Virulence-related gene profiles of Mycoplasma anatis were systematically identified, and the products of these genes included bacterial ABC transporter systems, iron transport proteins, toxins, and secretion systems.

Conclusion

A complete virulence-related gene profile of Mycoplasma anatis has been identified, most of the genes are highly conserved in all strains. Sequencing results are relevant to the molecular mechanisms of drug resistance, adaptive evolution of pathogens, population structure, and vaccine development.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13258-021-01129-5.

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.

The core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis

BACKGROUND

Mycoplasma anserisalpingitidis is a waterfowl pathogen that mainly infects geese, can cause significant economic losses and is present worldwide. With the advance of whole genome sequencing technologies, new methods are available for the researchers; one emerging methodology is the core genome Multi-Locus Sequence Typing (cgMLST). The core genome contains a high percentage of the coding DNA sequence (CDS) set of the studied strains. The cgMLST schemas are powerful genotyping tools allowing for the investigation of potential epidemics, and precise and reliable classification of the strains. Although whole genome sequences of M. anserisalpingitidis strains are available, to date, no cgMLST schema has been published for this species.

RESULTS

In this study, Illumina short reads of 81 M. anserisalpingitidis strains were used, including samples from Hungary, Poland, Sweden, and China. Draft genomes were assembled with the SPAdes software and analysed with the online available chewBBACA program. User made modifications in the program enabled analysis of mycoplasmas and provided similar results as the conventional SeqSphere+ software. The threshold of the presence of CDS in the strains was set to 93% due to the quality of the draft genomes, resulting in the most accurate and robust schema. Three hundred thirty-one CDSs constituted our cgMLST schema (representing 42,77% of the whole CDS set of M. anserisalpingitidis ATCC BAA-2147), and a Neighbor joining tree was created using the allelic profiles. The correlation was observed between the strains' cgMLST profile and geographical origin; however, strains from the same integration but different locations also showed close relationship. Strains isolated from different tissue samples of the same animal revealed highly similar cgMLST profiles.

CONCLUSIONS

The Neighbor joining tree from the cgMLST schema closely resembled the real-life spatial and temporal relationships of the strains. The incongruences between background data and the cgMLST profile in the strains from the same integration can be because of the higher probability of contacts between the flocks. This schema can help with the epidemiological investigation and can be used as a basis for further studies.

Isolation of Mycoplasma anserisalpingitidis from swan goose (Anser cygnoides) in China

Background

Mycoplasma anserisalpingitidis causes significant economic losses in the domestic goose (Anser anser) industry in Europe. As 95% of the global goose production is in China where the primary species is the swan goose (Anser cygnoides), it is crucial to know whether the agent is present in this region of the world.

Results

Purulent cloaca and purulent or necrotic phallus inflammation were observed in affected animals which represented 1–2% of a swan goose breeding flock (75,000 animals) near Guanghzou, China, in September 2019. From twelve sampled animals the cloaca swabs of five birds (three male, two female) were demonstrated to be M. anserisalpingitidis positive by PCR and the agent was successfully isolated from the samples of three female geese. Based on whole genome sequence analysis, the examined isolate showed high genetic similarity (84.67%) with the European isolates. The antibiotic susceptibility profiles of two swan goose isolates, determined by microbroth dilution method against 12 antibiotics and an antibiotic combination were also similar to the European domestic goose ones with tylvalosin and tiamulin being the most effective drugs.

Conclusions

To the best of our knowledge this is the first description of M. anserisalpingitidis infection in swan goose, thus the study highlights the importance of mycoplasmosis in the goose industry on a global scale.

Mycoplasma anserisalpingitidis sp. nov., isolated from European domestic geese (Anser anser domesticus) with reproductive pathology

In 1983, Mycoplasma sp. strain 1220 was isolated in Hungary from the phallus lymph of a gander with phallus inflammation. Between 1983 and 2017, Mycoplasma sp. 1220 was also identified and isolated from the respiratory tract, liver, ovary, testis, peritoneum and cloaca of diseased geese in several countries. Seventeen studied strains produced acid from glucose and fructose but did not hydrolyse arginine or urea, and all grew under aerobic, microaerophilic and anaerobic conditions at 35 to 37 ˚C in either SP4 or pleuropneumonia-like organism medium supplemented with glucose and serum. Colonies on agar showed a typical fried-egg appearance and transmission electron microscopy revealed a typical mycoplasma cellular morphology. Molecular characterization included analysis of the following genetic loci: 16S rRNA, 23S rRNA, 16S-23S rRNA ITS, rpoB, rpoC, rpoD, uvrA, parC, topA, dnaE, fusA and pyk. The genome was sequenced for type strain 1220^T. The 16S rRNA gene sequences of studied strains of Mycoplasma sp. 1220 shared 99.02-99.19 % nucleotide similarity with M. anatis strains but demonstrated ≤95.00-96.70 % nucleotide similarity to the 16S rRNA genes of other species of the genus Mycoplasma. Phylogenetic, average nucleotide and amino acid identity analyses revealed that the novel species was most closely related to Mycoplasma anatis. Based on the genetic data, we propose a novel species of the genus Mycoplasma, for which the name Mycoplasma anserisalpingitidis sp. nov. is proposed with the type strain 1220^T (=ATCC BAA-2147^T=NCTC 13513^T=DSM 23982^T). The G+C content is 26.70 mol%, genome size is 959110 bp.