A novel genomic island harbouring lsa(E), lnu(B) genes and a defective prophage in a Streptococcus pyogenes isolate resistant to lincosamide, streptogramin A and pleuromutilin antibiotics

Dàmaris Berbel (1) , Jordi Càmara (1) , Ernesto García (2) , Fe Tubau (1) , Francois Guerin (3) , Jean-Christophe Giard (4) , M Ángeles Domínguez (1) , Vincent Cattoir (5) , Carmen Ardanuy (1)

1 IDIBELL - Institut d'Investigació Biomèdica de Bellvitge [Barcelone]
2 CIBER-BBN - Centro de Investigación Biomédica en Red en Bioingeniería, Biomateriales y Nanomedicina
3 CHU Caen
4 U2RM - Unité de Recherche Risques Microbiens
5 BRM - ARN régulateurs bactériens et médecine

The lincosamide-resistant and macrolide-susceptible phenotype has not been described to date in Streptococcus pyogenes (group A Streptococcus; GAS). The aim of this study was to characterize a GAS isolate susceptible to macrolides but resistant to lincosamide, streptogramin A and pleuromutilin antibiotics (LSP phenotype). The antimicrobial susceptibility was tested by the microdilution broth method and the resistance phenotype by D-test. The GAS2887HUB isolate was subjected to whole-genome sequencing. The isolate showed a positive Gots' test (clindamycin inactivation). WGS revealed the strain was ST10 and emm93 and had five resistance genes (lnu(B), ant(6)-Ia, aph(3')-III, tet(M), and dfrG). The tet(M) gene was located into a Tn916-like transposon. The lsa(E)-lnu(B)-containing sequence (inserted downstream of the rumA gene) was formed by a 39.6-kb prophage, followed by a gene cluster encoding aminoglycoside-streptothricin resistance [ant(6)Ia-sat4-aph(3')III] and lsa(E)-lnu(B) genes. This structure was not transferred by conjugation. In conclusion, we have described a new genetic element carrying a determinant of lincosamide resistance in a GAS. Further molecular epidemiological surveys are needed to determine the prevalence of this mechanism of resistance in GAS.

Keywords: GAS; L phenotype; LS(A)P phenotype; Streptococcus pyogenes; lnu(B); lsa(E)

Domains: Life Sciences [q-bio]

Dàmaris Berbel, Jordi Càmara, Ernesto García, Fe Tubau, Francois Guerin, et al.. A novel genomic island harbouring lsa(E), lnu(B) genes and a defective prophage in a Streptococcus pyogenes isolate resistant to lincosamide, streptogramin A and pleuromutilin antibiotics. International Journal of Antimicrobial Agents, 2019, 54 (5), pp.647-651. ⟨10.1016/j.ijantimicag.2019.08.019⟩. ⟨hal-02307172⟩