Table 3 Antibiotics resistance-related genes of C. difficile strains based on the CARD

C. difficile 23S rRNA with mutation conferring resistance to erythromycin and clindamycin

23S rRNA with mutation conferring resistance to macrolide antibiotics

Macrolide, lincosamide

Antibiotic target alteration

All 60 strains

ErmB

Erm 23S ribosomal RNA methyltransferase

Macrolide, lincosamide, streptogramin

Antibiotic target alteration

CBA7201–CBA7203, CBA7205, CBA7207, CBA7209, 630, DSM 27639, DSM 29745, DSM 29688, DSM 28666, W0023a, R0104a, CD161, DSM 28669, M68

vanRG

Glycopeptide resistance gene cluster, vanR

Glycopeptide

Antibiotic target alteration

CBA7201–CBA7209, 630, DSM 27639, DSM 29745, DSM 2,688, W0022a, DSM 29632, 08ACD0030, BR81, Mta-79, DSM 28666, DSM 29637, W0023a, FDAARGOS267, DH/NAP11/106/ST-42, W0003a, 20477, 20709, QCD-63q42, DSM 1296^T, DSM 27638, DSM 27640, CD-17-01474, R0104a, 08-00495, 10–00253, 12-00011, 09-00072, 10-00078, 10-00071, 12-00008, CD-10-–00484, CD196, QCD-66c26

vanXYG

Glycopeptide resistance gene cluster, vanXY

Glycopeptide

Antibiotic target alteration

CBA7201, CBA7203–CBA7209, 630, DSM 27639, DSM 29745, DSM 29688, W0022a, DSM 29632, 08ACD0030, BR81, Mta-79, DSM 28666, DSM 29637, W0023a, FDAARGOS267, DH/NAP11/106/ST-42, W0003a, 20477, 20709, QCD-63q42, DSM 1296^T, DSM 27,638, DSM 27,640, CD-17–01,474, R0104a, 08-00495, 10-00253, 12-00011, 09-00072, 10-00078, 10-00071, 12-00008, CD-10-00484, CD196, QCD-66c26

Clostridioides difficile gyrA conferring resistance to fluoroquinolones

Fluoroquinolone resistant gyrA

Fluoroquinolone

Antibiotic target alteration

CBA7201–CBA7203, CBA7205–CBA7207, CBA7209, DSM 29745, QCD-63q42, DSM 27638, DSM 27,640, CD-17-01474, R0104a, 08-00495, 10-00253, 12-00011, 10-00078, 10–00,071, 12-00008, CD-10-00484, QCD-66c26, VL 0104, VL 0391, CDT4, CD161, DSM 29747

cdeA

Multidrug and toxic compound extrusion (MATE) transporter

Fluoroquinolone, acridine dye

Antibiotic efflux

CBA7209, 630, DSM 29745

APH (2'')-If

APH(2'')

Aminoglycoside

Antibiotic inactivation

CBA7201–CBA7203, CBA7205, CBA7207, CBA7209, DSM 27638, DSM 27640

AAC(6')-Ie-APH(2'')-Ia

APH(2''), AAC(6')

Aminoglycoside

Antibiotic inactivation

630, ZJCDC-S82, CD161, M68

aad(6)

ANT(6)

Aminoglycoside

Antibiotic inactivation

DSM 29020

ANT(6)-Ia

ANT(6)

Aminoglycoside

Antibiotic inactivation

M120

ANT(6)-Ib

ANT(6)

Aminoglycoside

Antibiotic inactivation

M120

APH(3')-IIIa

APH(3')

Aminoglycoside

Antibiotic inactivation

CD21062

catI

Chloramphenicol acetyltransferase (CAT)

Phenicol

Antibiotic inactivation

CD21062

SAT-4

Streptothricin acetyltransferase (SAT)

Nucleoside

Antibiotic inactivation

DSM 29020

tet(40)

Major facilitator superfamily (MFS) antibiotic efflux pump

Tetracycline

Antibiotic efflux

DSM 29747, DSM 29020

tet(44)

Tetracycline-resistant ribosomal protection protein

Tetracycline

Antibiotic target protection

M120

tet(W/N/W)

Tetracycline-resistant ribosomal protection protein

Tetracycline

Antibiotic target protection

630

tetB(P)

Tetracycline-resistant ribosomal protection protein

Tetracycline

Antibiotic target protection

DSM 28669

tetM

Tetracycline-resistant ribosomal protection protein

Tetracycline

Antibiotic target protection

DSM 28666, CDT4, DSM 29627, CD161, M68, DSM 29747, M120, CD21062, DSM 29020

tetO

Tetracycline-resistant ribosomal protection protein

Tetracycline

Antibiotic target protection

CD21062