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 R131T (=JCM 36615T=LMG 33627T).