An update on novel taxa and revised taxonomic status of bacteria isolated from non-domestic animals described in 2022

Numbers of new and revised microbial taxa are continuously expanding, and the rapid accumulation of novel bacterial species is challenging to keep up with in the best of circumstances. With that in mind, following the template of reports on prokaryotic species isolated from humans, this is now the second publication summarizing new and revised taxa in non-domestic animal species in the Journal of Clinical Microbiology. The majority of new taxa were obtained as part of programs to identify bacteria from mucosal surfaces and the gastrointestinal tract from healthy wildlife. A few notable bacteria included new Erysipelothrix spp. from mammalian and aquatic sources and a novel Bartonella spp. isolated from a rodent, both of which could be considered members of emerging and re-emerging genera with pathogenic potential in humans and animals.

Mycoplasma phocimorsus sp. nov., isolated from Scandinavian patients with seal finger or septic arthritis after contact with seals

Seal finger (sealer's finger, spekk finger), an extremely painful hand infection contracted by individuals handling seals, has previously been associated with Mycoplasma phocacerebrale. From 2000 to 2014, six independent strains of a novel Mycoplasma species were isolated at Statens Serum Institut, Denmark, from Scandinavian patients with seal finger (M5725T, M6447, M6620, M6642 and M6879) or septic arthritis (M6921). Prior to the onset of infection, all patients had reported contact with unspeciated seals. All isolates grew within 2-5 days in Friis' modified broth and metabolized glucose and arginine but not urea. Strains M5725T, M6447, M6642 and M6921 also grew in Hayflick-type media. Colonies on agar media were large (0.5-1.0 mm) and had a typical 'fried egg' appearance, reduced tetrazolium, and were digitonin sensitive. Growth occurred at 32 °C but not at 42 °C. Strains were susceptible to doxycycline and moxifloxacin but resistant to azithromycin and erythromycin. The genomes of the six strains were sequenced and relatedness to all known Mycoplasma species was inferred. Phylogenetic analyses using 16S rRNA gene sequences and core genome single nucleotide polymorphisms showed that the isolated strains were highly similar and phylogenetically distinct from all other species within the genus Mycoplasma. The sizes of the genome sequences of the strains ranged from 744 321 to 772409 bp, with a G+C content of 25.0-25.2 mol%. Based on these analyses, we propose a novel species of the genus Mycoplasma with the name Mycoplasma phocimorsus sp. nov. with the first isolate M5725T (NCTC 14922T=DSM 116188T) as the proposed type strain and representative strains M6447, M6620, M6642, M6879 and M6921.

Comparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae

Mycoplasma feriruminatoris is a fast-growing Mycoplasma species isolated from wild Caprinae and first described in 2013. M. feriruminatoris isolates have been associated with arthritis, kerato conjunctivitis, pneumonia and septicemia, but were also recovered from apparently healthy animals. To better understand what defines this species, we performed a genomic survey on 14 strains collected from free-ranging or zoo-housed animals between 1987 and 2017, mostly in Europe. The average chromosome size of the M. feriruminatoris strains was 1,040±0,024 kbp, with 24 % G+C and 852±31 CDS. The core genome and pan-genome of the M. feriruminatoris species contained 628 and 1312 protein families, respectively. The M. feriruminatoris strains displayed a relatively closed pan-genome, with many features and putative virulence factors shared with species from the M. mycoides cluster, including the MIB-MIP Ig cleavage system, a repertoire of DUF285 surface proteins and a complete biosynthetic pathway for galactan. M. feriruminatoris genomes were found to be mostly syntenic, although repertoires of mobile genetic elements, including Mycoplasma Integrative and Conjugative Elements, insertion sequences, and a single plasmid varied. Phylogenetic- and gene content analyses confirmed that M. feriruminatoris was closer to the M. mycoides cluster than to the ruminant species M. yeatsii and M. putrefaciens. Ancestral genome reconstruction showed that the emergence of the M. feriruminatoris species was associated with the gain of 17 gene families, some of which encode defence enzymes and surface proteins, and the loss of 25 others, some of which are involved in sugar transport and metabolism. This comparative study suggests that the M. mycoides cluster could be extended to include M. feriruminatoris. We also find evidence that the specific organization and structure of the DnaA boxes around the oriC of M. feriruminatoris may contribute to drive the remarkable fast growth of this minimal bacterium.