Genomic islands and molecular mechanisms relating to drug-resistance in <i>Clostridioides</i> (<i>Clostridium</i>) <i>difficile</i> PCR ribotype 176

To analyse characteristics of <i>Clostridioides difficile</i> PCR ribotype 176 clinical isolates from Poland, the Czech Republic and Slovakia with regard to the differences in its epidemiology. Antimicrobial susceptibility testing and whole genome sequencing were performed on a selected group of 22 clonally related isolates as determined by multilocus variable-number tandem repeat analysis (n = 509). Heterologous expression and functional analysis of the newly identified methyltransferase were performed. Core genome multilocus sequence typing found 10–37 allele differences. All isolates were resistant to fluoroquinolones (<i>gyr</i>A_p. T82I), aminoglycosides with <i>aac</i>(6’)-<i>Ie-aph</i>(2'’)-<i>Ia</i> in six isolates. Erythromycin resistance was detected in 21/22 isolates and 15 were also resistant to clindamycin with <i>erm</i>B gene. Fourteen isolates were resistant to rifampicin with <i>rpo</i>B_p. R505K or p. R505K/H502N, and five to imipenem with <i>pbp</i>1_p. P491L and <i>pbp</i>3_p. N537K. P<i>nim</i>B^G together with <i>nim</i>B_p. L155I were detected in all isolates but only five were resistant to metronidazole on chocolate agar. The <i>cfr</i>E, <i>van</i>Z1 and <i>cat</i>-like genes were not associated with linezolid, teicoplanin and chloramphenicol resistance, respectively. The genome comparison identified six transposons carrying antimicrobial resistance genes. The <i>erm</i>B gene was carried by new Tn<i>7808</i>, Tn<i>6189</i> and Tn<i>6218</i>-like. The <i>aac</i>(6’)-<i>Ie-aph</i>(2'’)-<i>Ia</i> were carried by Tn<i>6218</i>-like and new Tn<i>7806</i> together with <i>cfr</i>E gene. New Tn<i>7807</i> carried a <i>cat</i>-like gene. Tn<i>6110</i> and new Tn<i>7806</i> contained an RlmN-type 23S rRNA methyltransferase, designated MrmA, associated with high-level macrolide resistance in isolates without <i>erm</i>B gene. Multidrug-resistant <i>C. difficile</i> PCR ribotype 176 isolates carry already described and unique transposons. A novel mechanism for erythromycin resistance in <i>C. difficile</i> was identified.