Complete genome sequence and characterization of Clostridium perfringens type D carrying optrA-plasmid and Tn6218-like transposon.

Abstract

Clostridium perfringens toxinotype D strains are known to cause the most common form of clostridial enterotoxaemia in sheep, goats and occasionally cattle.1,2 As a member of the ABC-F family, the optrA gene codes for an ATP-binding cassette protein that confers resistance to both phenicols and oxazolidinones by protecting the ribosomes of the bacteria.3 In recent years, the oxazolidinone/phenicol-resistant gene optrA has been reported to mediate high-level resistance to florfenicol and linezolid in isolates from animals, humans and the environment, posing a potential threat to public health.4–6 Tn6218 variants have been reported as widespread in Clostridioides difficile isolates and occasionally Enterococcus faecium isolates;7,8 however, the transferable Tn6218-related transposons has not yet been reported in C. perfringens. Herein, we identified one C. perfringens toxinotype D strain, designated as 21-D-5, harbouring antibiotic resistance gene optrA and Tn6218-like transposons, and further analysed the Tn6218-like transposons and optrA-carrying plasmid p21-D-5b. We collected rectal samples from diarrhoeal Guanzhong diary goats in Weinan city, Shaanxi province in 2021, and one C. perfringens strain 21-D-5 was isolated from the samples. Toxin gene detection indicated 21-D-5 belonged to toxinotype D, positive for toxin genes plc, cpb2, etx and cpe. The broth microdilution method was used to examine the antibiotic resistance of 21-D-5, and strong resistance against clindamycin (MIC > 64 mg/L), florfenicol (MIC > 64 mg/L), chloramphenicol (MIC = 32 mg/L) and linezolid (MIC = 16 mg/L) was observed. WGS of 21-D-5 was then performed with the Nanopore PromethION platform (Biomarker Technologies, Beijing, China). WGS (NCBI BioSample: SAMN28005067) resulted in a total length of 3 650 743 bp, in which two plasmids designated as p21-D-5a (121 548 bp) and p21-D-5b (224 659 bp) were detected.