Scrofimicrobium appendicitidis sp. nov., isolated from a patient with ruptured appendicitis.

Abstract

A clinical isolate, R131, was isolated from the peritoneal swab of a patient who suffered from ruptured appendicitis with abscess and gangrene in Hong Kong in 2018. Cells are facultatively anaerobic, non-motile, Gram-positive coccobacilli. Colonies were small, grey, semi-translucent, low convex and alpha-haemolytic. The bacterium grew on blood agar but not on Brain Heart Infusion (BHI) and Mueller-Hinton agars. It was negative for catalase, oxidase, indole and aesculin hydrolysis. The initial identification attempts via matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S rRNA gene sequencing yielded inconclusive results. The 16S rRNA gene analysis showed that R131 shared >99% nucleotide identity with certain uncultured Actinomycetales bacteria. In this retrospective investigation, a complete genome of R131 was constructed, disclosing a DNA G+C content of 64%. Phylogenetic analysis showed that the bacterium was mostly related to Scrofimicrobium canadense WB03_NA08, which was first described in 2020. However, its 16S rRNA gene shared only 94.15% nucleotide identity with that of S. canadense WB03_NA08. Notably, the orthoANI between R131 and S. canadense WB03_NA08 was 67.81%. A pan-genome analysis encompassing R131 and 4 Scrofimicrobium genomes showed 986 core gene clusters shared with the Scrofimicrobium species, along with 601 cloud genes. The average nucleotide identity comparisons within the pan-genome analysis ranged from 59.78 to 62.51% between R131 and the other Scrofimicrobium species. Correspondingly, the dDDH values ranged from 19.20 to 22.30%, while the POCP values spanned from 57.48 to 60.94%. Therefore, a novel species, Scrofimicrobium appendicitidis sp. nov., is proposed. The type strain is R131^T (=JCM 36615^T=LMG 33627^T).