Whole genome sequence of Streptococcus pluranimalium SP21–2, a porcine strain harbouring optrA and lsa(E) with chromosomal location

Abstract

ABSTRACT: Objectives: The aim of this study was to characterise the whole genome sequence of multidrug-resistant Streptococcus pluranimalium strain SP21–2 of swine origin in China. Methods: Illumina Miseq (200X coverage) and Nanopore PromethION platform (100X coverage) were used for genome sequencing. Rapid Annotation using Subsystem Technology (RAST) was used to annotate the genome of SP21–2. The antimicrobial resistance genes (ARGs) were identified using ResFinder-4.1. Results: The assembled circular genome of S. pluranimalium SP21–2 was 1,987,058 bp in length with a GC content of 39.54%, and no plasmid sequence was detected. A total of 2086 coding sequences were predicted by RAST. Oxazolidinone-phenicol resistance gene, optrA, and pleuromutilin-lincosamide-streptogramin A resistance gene, lsa(E), are both located on chromosomes, associated with IS1216 and ISS1S, respectively. In addition, SP21–2 harbours lnu(B) (lincosamide), ant (6)-Ia and aac(6’)-aph(2”) (aminoglycoside), erm(B) (macrolide), and tet(O) (tetracycline). Conclusion: We firstly report the oxazolidinone-phenicol gene, optrA, and pleuromutilin-lincosamide-streptogramin A resistance gene, lsa(E), in S. pluranimalium. In this strain, we firstly identified ISS1S and IS1216 carrying ARGs in S. pluranimalium, which will provide a valuable reference to understanding potential transfer mechanisms of ARGs in S. pluranimalium.

Keywords

• Streptococcus pluranimalium
• Optra
• Lsa(E)
• Multiresistance gene cluster