Abstract
Antimicrobial resistance (AMR) in Clostridioides difficile remains a significant threat to global healthcare systems, not just for the treatment of C. difficile infection (CDI), but as a reservoir of AMR genes that could be potentially transferred to other pathogens. The mechanisms of resistance for several antimicrobials such as metronidazole and MLSB-class agents are only beginning to be elucidated, and increasingly, there is evidence that previously unconsidered mechanisms such as plasmid-mediated resistance may play an important role in AMR in this bacterium. In this review, the genetics of AMR in C. difficile will be described, along with a discussion of the factors contributing to the difficulty in clearly determining the true burden of AMR in C. difficile and how it affects the treatment of CDI.
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10096-021-04311-5/MediaObjects/10096_2021_4311_Fig1_HTML.png)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10096-021-04311-5/MediaObjects/10096_2021_4311_Fig2_HTML.png)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10096-021-04311-5/MediaObjects/10096_2021_4311_Fig3_HTML.png)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10096-021-04311-5/MediaObjects/10096_2021_4311_Fig4_HTML.png)
Similar content being viewed by others
Data availability
Not applicable.
Code availability
Not applicable.
References
O’Neill J (2016) Tackling drug-resistant infections globally: final report and recommendations. The review on antimicrobial resistance. Web citation: https://amr-review.org/. Accessed 20 Apr 2021
Centers for Disease Control and Prevention (2013) CDC antibiotic resistance threats in the United States, 2013. Web citation: http://www.cdc.gov/drugresistance/threat-report-2013/. Accessed 20 Apr 2021
Centers for Disease Control and Prevention (2019) CDC antibiotic resistance threats in the United States, 2019. Web citation: https://www.cdc.gov/drugresistance/biggest-threats.html. Accessed 20 Apr 2021
Peng Z, ** D, Kim HB, Stratton CW, Wu B, Tang YW, Sun X (2017) Update on antimicrobial resistance in Clostridium difficile: resistance mechanisms and antimicrobial susceptibility testing. J Clin Microbiol 55(7):1998–2008
Saha S, Kapoor S, Tariq R, Schuetz AN, Tosh PK, Pardi DS, S K, (2019) Increasing antibiotic resistance in Clostridioides difficile: a systematic review and meta-analysis. Anaerobe 58:35–46
Spigaglia P, Mastrantonio P, Barbanti F (2018) Antibiotic resistances of Clostridium difficile. Springer International Publishing, Cham, pp 137–159
Slimings C, Riley TV (2014) Antibiotics and hospital-acquired Clostridium difficile infection: update of systematic review and meta-analysis. J Antimicrob Chemother 69(4):881–891
Sholeh M, Krutova M, Forouzesh M, Mironov S, Sadeghifard N, Molaeipour L, Maleki A, Kouhsari E (2020) Antimicrobial resistance in Clostridioides (Clostridium) difficile derived from humans: a systematic review and meta-analysis. Antimicrob Resist Infect Control 9(1):158
Hong S, Knight DR, Riley TV (2019) The impact of antimicrobial resistance on induction, transmission and treatment of Clostridium difficile infection. Microbiol Aust 40(2):77–81
Deshpande A, Pasupuleti V, Thota P, Pant C, Rolston DDK, Sferra TJ, Hernandez AV, Donskey CJ (2013) Community-associated Clostridium difficile infection and antibiotics: a meta-analysis. J Antimicrob Chemother 68(9):1951–1961
Baines SD, Wilcox MH (2015) Antimicrobial resistance and reduced susceptibility in Clostridium difficile: potential consequences for induction, treatment, and recurrence of C. difficile infection. Antibiotics (Basel) 4(3):267–298
Rao K, Malani PN (2020) Diagnosis and treatment of Clostridioides (Clostridium) difficile infection in adults in 2020. J Am Med Assoc 323(14):1403–1404
McDonald LC, Gerding DN, Johnson S, Bakken JS, Carroll KC, Coffin SE, Dubberke ER, Garey KW, Gould CV, Kelly C, Loo V, Shaklee Sammons J, Sandora TJ, Wilcox MH (2018) Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin Infect Dis 66(7):e1–e48
Trubiano JA, Cheng AC, Korman TM, Roder C, Campbell A, May MLA, Blyth CC, Ferguson JK, Blackmore TK, Riley TV, Athan E (2016) Australasian Society of Infectious Diseases updated guidelines for the management of Clostridium difficile infection in adults and children in Australia and New Zealand. J Intern Med 46(4):479–493
Debast SB, Bauer MP, Kuijper EJ (2014) European Society of Clinical Microbiology and Infectious Diseases: update of the treatment guidance document for Clostridium difficile infection. Clin Microbiol Infect 20:1–26
Carlson TJ, Gonzales-Luna AJ (2020) Antibiotic treatment pipeline for Clostridioides difficile infection (CDI): a wide array of narrow-spectrum agents. Curr Infect Dis Rep 22(8):20
Pu M, Cho JM, Cunningham SA, Behera G, Becker S, Amjad T, Greenwood-Quaintance KE, Mendes-Soares H, Jones-Hall Y, Jeraldo PR, Chen J, Dunny G, Patel R, Kashyap PC (2020) Plasmid acquisition alters vancomycin susceptibility in Clostridioides difficile. Gastroenterology 160(3):941–945
The European Committee on Antimicrobial Susceptibility Testing (2021) Breakpoint tables for interpretation of MICs and zone diameters. Web citation: https://eucast.org/clinical_breakpoints/?debug=1. Accessed 02 Mar 2021
Woods E, Wetzel D, Mukerjee M, McBride S (2018) Examination of the Clostridioides (Clostridium) difficile VanZ ortholog, CD1240. Anaerobe 53:108–115
Ammam F, Marvaud J, Lambert T (2012) Distribution of the vanG-like gene cluster in Clostridium difficile clinical isolates. Can J Microbiol 58:547–551
Shen WJ, Deshpande A, Hevener KE, Endres BT, Garey KW, Palmer KL, Hurdle JG (2020) Constitutive expression of the cryptic vanGCd operon promotes vancomycin resistance in Clostridioides difficile clinical isolates. J Antimicrob Chemother 75(4):859–867
Knight DR, Androga GO, Ballard SA, Howden BP, Riley TV (2016) A phenotypically silent vanB2 operon carried on a Tn1549-like element in Clostridium difficile. mSphere 1(4):e00177-00116
Harnvoravongchai P, Pipatthana M, Chankhamhaengdecha S, Janvilisri T (2017) Insights into drug resistance mechanisms in Clostridium difficile. Essays Biochem 61(1):81–88
Jarrad AM, Blaskovich MAT, Prasetyoputri A, Karoli T, Hansford KA, Cooper MA (2018) Detection and investigation of eagle effect resistance to vancomycin in Clostridium difficile with an ATP-bioluminescence assay. Front Microbiol 9:1420
Tickler IA, Obradovich AE, Goering RV, Fang FC, Tenover FC, Consortium TH, Consortium HAI (2019) Changes in molecular epidemiology and antimicrobial resistance profiles of Clostridioides (Clostridium) difficile strains in the United States between 2011 and 2017. Anaerobe 60:102050
Krutova M, Capek V, Nycova E, Vojackova S, Balejova M, Geigerova L, Tejkalova R, Havlinova L, Vagnerova I, Cermak P, Ryskova L, Jezek P, Zamazalova D, Vesela D, Kucharova A, Nemcova D, Curdova M, Nyc O, Drevinek P (2020) The association of a reduced susceptibility to moxifloxacin in causative Clostridium (Clostridioides) difficile strain with the clinical outcome of patients. Antimicrob Resist Infect Control 9(1):98
Freeman J, Vernon J, Pilling S, Morris K, Nicholson S, Shearman S, Longshaw C, Wilcox MH (2018) The ClosER study: results from a three-year pan-European longitudinal surveillance of antibiotic resistance among prevalent Clostridium difficile ribotypes, 2011–2014. Clin Microbiol Infect 24(7):724–731
Freeman J, Vernon J, Morris K, Nicholson S, Todhunter S, Longshaw C, Wilcox MH (2015) Pan-European longitudinal surveillance of antibiotic resistance among prevalent Clostridium difficile ribotypes. Clin Microbiol Infect 21(3):248.e249-248.e216
Dingsdag SA, Hunter N (2017) Metronidazole: an update on metabolism, structure–cytotoxicity and resistance mechanisms. J Antimicrob Chemother 73(2):265–279
Boekhoud IM, Hornung BVH, Sevilla E, Harmanus C, Bos-Sanders I, Terveer EM, Bolea R, Corver J, Kuijper EJ, Smits WK (2020) Plasmid-mediated metronidazole resistance in Clostridioides difficile. Nat Commun 11(1):598
Moura I, Monot M, Tani C, Spigaglia P, Barbanti F, Norais N, Dupuy B, Bouza E, Mastrantonio P (2014) Multidisciplinary analysis of a nontoxigenic Clostridium difficile strain with stable resistance to metronidazole. Antimicrob Agents Chemother 58(8):4957–4960
Chong PM, Lynch T, McCorrister S, Kibsey P, Miller M, Gravel D, Westmacott GR, Mulvey MR, the Canadian Nosocomial Infection Surveillance P (2014) Proteomic analysis of a NAP1 Clostridium difficile clinical isolate resistant to metronidazole. Plos One 9(1):e82622
Deshpande A, Wu X, Huo W, Palmer KL, Hurdle JG (2020) Chromosomal resistance to metronidazole in Clostridioides difficile can be mediated by epistasis between iron homeostasis and oxidoreductases. Antimicrob Agents Chemother 64(8):e00415-00420
Boekhoud IM, Sidorov I, Nooij S, Harmanus C, Bos-Sanders IMJG, Viprey V, Spittal W, Clark E, Davies K, Freeman J, Kuijper EJ, Smits WK, Consortium C-C (2021) Haem is crucial for medium-dependent metronidazole resistance in clinical isolates of Clostridioides difficile. J Antimicrob Chemother:dkab097 76(7):1731–1740. https://doi.org/10.1093/jac/dkab097
Spigaglia P, Barbanti F, Mastrantonio P, on behalf of the European Study Group on Clostridium difficile, Ackermann G, Balmelli C, Barbut F, Bouza E, Brazier J, Delmée M, Drudy D, Kuijper E, Ladas H, Mastrantonio P, Nagy E, Pituch H, Poxton I, Rupnik M, Wullt M, Yücesoy M (2011) Multidrug resistance in European Clostridium difficile clinical isolates. J Antimicrob Chemother 66(10):2227–2234
Lynch T, Chong P, Zhang J, Hizon R, Du T, Graham MR, Beniac DR, Booth TF, Kibsey P, Miller M, Gravel D, Mulvey MR, Canadian Nosocomial Infection Surveillance Program (2013) Characterization of a stable, metronidazole-resistant Clostridium difficile clinical isolate. PLoS One 8(1):e53757
Peláez T, Cercenado E, Alcalá L, Marín M, Martín-López A, Martínez-Alarcón J, Catalán P, Sánchez-Somolinos M, Bouza E (2008) Metronidazole resistance in Clostridium difficile is heterogeneous. J Clin Microbiol 46(9):3028–3032
Krutova A, Kinross P, Barbut F, Hajdu A, Wilcox MH, Kuijper EJ (2017) How to: surveillance of Clostridium difficile infections. Clin Microbiol Infect 24:469–475
Artsimovitch I, Seddon J, Sears P (2012) Fidaxomicin is an inhibitor of the initiation of bacterial RNA synthesis. Clin Infect Dis 55(Suppl 2):S127–S131
Kuehne SA, Dempster AW, Collery MM, Joshi N, Jowett J, Kelly ML, Cave R, Longshaw CM, Minton NP (2018) Characterization of the impact of rpoB mutations on the in vitro and in vivo competitive fitness of Clostridium difficile and susceptibility to fidaxomicin. J Antimicrob Chemother 73(4):973–980
Sears P, Crook DW, Louie TJ, Miller MA, Weiss K (2012) Fidaxomicin attains high fecal concentrations with minimal plasma concentrations following oral administration in patients with Clostridium difficile infection. Clin Infect Dis 55:S116–S120
Schwanbeck J, Riedel T, Laukien F, Schober I, Oehmig I, Zimmermann O, Overmann J, Groß U, Zautner AE, Bohne W (2019) Characterization of a clinical Clostridioides difficile isolate with markedly reduced fidaxomicin susceptibility and a V1143D mutation in rpoB. J Antimicrob Chemother 74(1):6–10
Nelson RL, Suda KJ, Evans CT (2017) Antibiotic treatment for Clostridium difficile‐associated diarrhoea in adults. Cochrane Database Syst Rev 3(3):CD004610
Lew T, Putsathit P, Sohn KM, Wu Y, Ouchi K, Ishii Y, Tateda K, Riley TV, Collins DA (2020) Antimicrobial susceptibilities of Clostridium difficile isolates from 12 Asia-Pacific countries in 2014 and 2015. Antimicrob Agents Chemother 64(7):e00296-e220
Mascio CT, Chesnel L, Thorne G, Silverman JA (2014) Surotomycin demonstrates low in vitro frequency of resistance and rapid bactericidal activity in Clostridium difficile, Enterococcus faecalis, and Enterococcus faecium. Antimicrob Agents Chemother 58(7):3976–3982
Imwattana K, Kiratisin P, Riley TV, Knight DR (2020) Genomic basis of antimicrobial resistance in non-toxigenic Clostridium difficile in Southeast Asia. Anaerobe 66:102290
Carman RJ, Boone JH, Grover H, Wickham KN, Chen L (2012) In vivo selection of rifamycin-resistant Clostridium difficile during rifaximin therapy. Antimicrob Agents Chemother 56(11):6019–6020
World Health Organisation (2020) Global Tuberculosis Report 2020. Web citation: https://www.who.int/teams/global-tuberculosis-programme/tb-reports/global-tuberculosisreport-2020. Accessed 10 May 2021
Chatedaki C, Voulgaridi I, Kachrimanidou M, Hrabak J, Papagiannitsis CC, Petinaki E (2019) Antimicrobial susceptibility and mechanisms of resistance of Greek Clostridium difficile clinical isolates. J Glob Antimicrob Resist 16:53–58
Carlson TJ, Endres BT, Bassères E, Gonzales-Luna AJ, Garey KW (2019) Ridinilazole for the treatment of Clostridioides difficile infection. Expert Opin Investig Drugs 28(4):303–310
Vickers RJ, Tillotson GS, Nathan R, Hazan S, Pullman J, Lucasti C, Deck K, Yacyshyn B, Maliakkal B, Pesant Y, Tejura B, Roblin D, Gerding DN, Wilcox MH, Dsg Co (2017) Efficacy and safety of ridinilazole compared with vancomycin for the treatment of Clostridium difficile infection: a phase 2, randomised, double-blind, active-controlled, non-inferiority study. Lancet Infect Dis 17(7):735–744
Adams HM, Li X, Mascio C, Chesnel L, Palmer KL (2015) Mutations associated with reduced surotomycin susceptibility in Clostridium difficile and Enterococcus species. Antimicrob Agents Chemother 59(7):4139–4147
Oliphant CM, Green GM (2002) Quinolones: a comprehensive review. Am Fam Physician 65(3):455–464
Imwattana K, Knight DR, Kullin B, Collins DA, Putsathit P, Kiratisin P, Riley TV (2020) Antimicrobial resistance in Clostridium difficile ribotype 017. Expert Rev Anti Infect Ther 18(1):17–25
Spigaglia P (2016) Recent advances in the understanding of antibiotic resistance in Clostridium difficile infection. Ther Adv Infect Dis 3(1):23–42
Mackin KE, Elliott B, Kotsanas D, Howden BP, Carter GP, Korman TM, Riley TV, Rood JI, Jenkin GA, Lyras D (2015) Molecular characterization and antimicrobial susceptibilities of Clostridium difficile clinical isolates from Victoria, Australia. Anaerobe 34:80–83
Wasels F, Kuehne S, Cartman S, Spigaglia P, Barbanti F, Minton N, Mastrantonio P (2014) Fluoroquinolone resistance does not impose a cost on the fitness of Clostridium difficile in vitro. Antimicrob Agents Chemother 59(3):1794–1796
Mac Aogáin M, Kilkenny S, Walsh C, Lindsay S, Moloney G, Morris T, Jones S, Rogers TR (2015) Identification of a novel mutation at the primary dimer interface of GyrA conferring fluoroquinolone resistance in Clostridium difficile. J Glob Antimicrob Resist 3(4):295–299
Pellissery AJ, Vinayamohan PG, Yin H-B, Mooyottu S, Venkitanarayanan K (2019) In vitro efficacy of sodium selenite in reducing toxin production, spore outgrowth and antibiotic resistance in hypervirulent Clostridium difficile. J Med Microbiol 68(7):1118–1128
Linder JA, Huang ES, Steinman MA, Gonzales R, Stafford RS (2005) Fluoroquinolone prescribing in the United States: 1995 to 2002. Am J Med 118(3):259–268
Niederman MS, Mandell LA, Anzueto A, Bass JB, Broughton WA, Campbell GD, Dean N, File T, Fine MJ, Gross PA, Martinez F, Marrie TJ, Plouffe JF, Ramirez J, Sarosi GA, Torres A, Wilson R, Yu VL (2001) Guidelines for the management of adults with community-acquired pneumonia. Am J Respir Crit Care Med 163(7):1730–1754
Knight DR, Riley TV (2016) Clostridium difficile clade 5 in Australia: antimicrobial susceptibility profiling of PCR ribotypes of human and animal origin. J Antimicrob Chemother 71(8):2213–2217
Knight DR, Giglio S, Huntington PG, Korman TM, Kotsanas D, Moore CV, Paterson DL, Prendergast L, Huber CA, Robson J, Waring L, Wehrhahn MC, Weldhagen GF, Wilson RM, Riley TV (2015) Surveillance for antimicrobial resistance in Australian isolates of Clostridium difficile, 2013–14. J Antimicrob Chemother 70(11):2992–2999
Australian Commission on Safety and Quality in Health Care (2018) Clostridium difficile infection. Monitoring the national burden of Clostridium difficile. Sydney. Web citation: https://www.safetyandquality.gov.au/publications-and-resources/resource-library/monitoringnational-burden-clostridium-difficileinfection. Accessed 21 Oct 2021
Alyousef AA (2018) Clostridium difficile: epidemiology, pathogenicity, and an update on the limitations of and challenges in its diagnosis. J AOAC Int 101(4):1119–1126
Li H, Li W-G, Zhang W-Z, Yu S-B, Liu Z-J, Zhang X, Wu Y, Lu J-X (2019) Antibiotic resistance of clinical isolates of Clostridioides difficile in China and its association with geographical regions and patient age. Anaerobe 60:102094
Banawas SS (2018) Clostridium difficile infections: a global overview of drug sensitivity and resistance mechanisms. Biomed Res Int 2018:8414257
Schmidt C, Loffler B, Ackermann G (2007) Antimicrobial phenotypes and molecular basis in clinical strains of Clostridium difficile. Diagn Microbiol Infect Dis 59(1):1–5
Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Marwick CA, Coia J, Brown D, Buchanan S, Ijaz UZ, Goswami C, Douce G, Fawley WN, Wilcox MH, Peto TEA, Walker AS, Crook DW (2019) A role for tetracycline selection in recent evolution of agriculture-associated Clostridium difficile PCR ribotype 078. mBio 10(2):e02790-02718
Dong D, Zhang L, Chen X, Jiang C, Yu B, Wang X, Peng Y (2013) Antimicrobial susceptibility and resistance mechanisms of clinical Clostridium difficile from a Chinese tertiary hospital. Int J Antimicrob Agents 41(1):80–84
Knetsch CW, Kumar N, Forster SC, Connor TR, Browne HP, Harmanus C, Sanders IM, Harris SR, Turner L, Morris T, Perry M, Miyajima F, Roberts P, Pirmohamed M, Songer JG, Weese JS, Indra A, Corver J, Rupnik M, Wren BW, Riley TV, Kuijper EJ, Lawley TD (2018) Zoonotic transfer of Clostridium difficile harboring antimicrobial resistance between farm animals and humans. J Clin Micro 56(3):e01384-e1317
Knetsch CW, Connor TR, Mutreja A, van Dorp SM, Sanders IM, Browne HP, Harris D, Lipman L, Keessen EC, Corver J, Kuijper EJ, Lawley TD (2014) Whole genome sequencing reveals potential spread of Clostridium difficile between humans and farm animals in the Netherlands, 2002 to 2011. Euro Surveill 19(45):20954
Werner A, Mölling P, Fagerström A, Dyrkell F, Arnellos D, Johansson K, Sundqvist M, Norén T (2020) Whole genome sequencing of Clostridioides difficile PCR ribotype 046 suggests transmission between pigs and humans. PLoS One 15(12):e0244227
Knight DR, Squire MM, Collins DA, Riley TV (2017) Genome analysis of Clostridium difficile PCR ribotype 014 lineage in Australian pigs and humans reveals a diverse genetic repertoire and signatures of long-range interspecies transmission. Front Microbiol 7:2138
Vidor CJ, Bulach D, Awad M, D L, (2019) Paeniclostridium sordellii and Clostridioides difficile encode similar and clinically relevant tetracycline resistance loci in diverse genomic locations. BMC Microbiol 19(1):53
Cheknis A, Devaris D, Chesnel L, Dale SE, Nary J, Sambol SP, Citron DM, Goering RV, Johnson S (2020) Characterization of Clostridioides difficile isolates recovered from two phase 3 surotomycin treatment trials by restriction endonuclease analysis, PCR riboty** and antimicrobial susceptibilities. J Antimicrob Chemother 75(11):3120–3125
Begum K, Bassères E, Miranda J, Lancaster C, Gonzales-Luna AJ, Carlson TJ, Rashid T, Eyre DW, Wilcox MH, Alam MJ, Garey KW (2020) In vitro activity of omadacycline, a new tetracycline analog, and comparators against Clostridioides difficile. Antimicrob Agents Chemother 64(8):e00522-e520
Zhao L, Luo Y, Bian Q, Wang L, Ye J, Song X, Jiang J, Tang Y-W, Wang X, ** D (2020) High-level resistance of toxigenic Clostridioides difficile genotype to macrolide-lincosamide-streptogramin B in community acquired patients in Eastern China. Infect Drug Resist 13:171–181
Ramírez-Hernández V, Ramírez-Vargas G (2020) A putative erm gene is present in ΔermB Clostridioides difficile isolates showing high levels of resistance to clindamycin. bioRxiv:2020.2011.2020.391128. https://doi.org/10.1101/2020.11.20.391128
Goh S, Hussain H, Chang BJ, Emmett W, Riley TV, Mullany P (2013) Phage ϕC2 mediates transduction of Tn6215, encoding erythromycin resistance, between strains. mBio 4(6):e00840-00813
Isidro J, Menezes J, Serrano M, Borges V, Paixão P, Mimoso M, Martins F, Toscano C, Santos A, Henriques AO, Oleastro M (2018) Genomic study of a Clostridium difficile multidrug resistant outbreak-related clone reveals novel determinants of resistance. Front Microbiol 9(2994):2994
Vester B (2018) The cfr and cfr-like multiple resistance genes. Res Microbiol 169(2):61–66
Candela T, Marvaud JC, Nguyen TK, Lambert T (2017) A cfr-like gene cfr(C) conferring linezolid resistance is common in Clostridium difficile. Int J Antimicrob Agents 50(3):496–500
Stojković V, Ulate MF, Hidalgo-Villeda F, Aguilar E, Monge-Cascante C, Pizarro-Guajardo M, Tsai K, Tzoc E, Camorlinga M, Paredes-Sabja D, Quesada-Gómez C, Fujimori DG, Rodríguez C (2019) cfr(B), cfr(C), and a new cfr-like gene, cfr(E), in Clostridium difficile strains recovered across Latin America. Antimicrob Agents Chemother 64(1):e01074-e1019
Lim S-C, Androga GO, Knight DR, Moono P, Foster NF, Riley TV (2018) Antimicrobial susceptibility of Clostridium difficile isolated from food and environmental sources in Western Australia. Int J Antimicrob Agents 52(3):411–415
Bozdogan B, Appelbaum PC (2004) Oxazolidinones: activity, mode of action, and mechanism of resistance. Int J Antimicrob Agents 23(2):113–119
von der Hartmut Lode N, Höh SZ, KB, Carl Erik Nord, (2001) Ecological effects of linezolid versus amoxicillin/clavulanic acid on the normal intestinal microflora. Scand J Infect Dis 33(12):899–903
Baines SD, Noel AR, Huscroft GS, Todhunter SL, O’Connor R, Hobbs JK, Freeman J, Lovering AM, Wilcox MH (2011) Evaluation of linezolid for the treatment of Clostridium difficile infection caused by epidemic strains using an in vitro human gut model. J Antimicrob Chemother 66(7):1537–1546
Zabel LT, Worm S (2005) Linezolid contributed to Clostridium difficile colitis with fatal outcome. Infection 33(3):155–157
Plattner M, Gysin M, Haldimann K, Becker K, Hobbie SN (2020) Epidemiologic, phenotypic, and structural characterization of aminoglycoside-resistance gene aac(3)-IV. Int J Mol Sci 21(17):6133
Marsh JW, Pacey MP, Ezeonwuka C, Ohm SL, Snyder D, Cooper VS, Harrison LH, Doi Y, Mustapha MM (2019) Clostridioides difficile: a potential source of npmA in the clinical environment. J Antimicrob Chemother 74 (2):521-523
Toth M, Stewart NK, Smith C, Vakulenko SB (2018) Intrinsic class D β-lactamases of Clostridium difficile. mBio 9(6):e01803-01818
Sandhu BK, Edwards AN, Anderson SE, Woods EC, McBride SM (2019) Regulation and anaerobic function of the Clostridioides difficile β-lactamase. Antimicrob Agents Chemother 64(1):e01496-e1419
Codjoe FS, Donkor ES (2017) Carbapenem resistance: a review. Med Sci (Basel, Switzerland) 6(1):1
Isidro J, Santos A, Nunes A, Borges V, Silva C, Vieira L, Mendes AL, Serrano M, Henriques AO, Gomes JP, Oleastro M (2018) Imipenem resistance in Clostridium difficile ribotype 017. Portugal Emerging infectious diseases 24(4):741–745
Lopez JME (2017) Characterization of an efflux pump system, the CD_AcrA-AcrB-TolC complex, in Clostridium difficile. Kansas State University, Department of Plant Pathology, p 66
Lebel S, Bouttier S, Lambert T (2004) The cme gene of Clostridium difficile confers multidrug resistance in Enterococcus faecalis. FEMS Microbiol Lett 238(1):93–100
Dridi L, Tankovic J, Petit JC (2004) CdeA of Clostridium difficile, a new multidrug efflux transporter of the MATE family. Microb Drug Resist 10(3):191–196
Ngernsombat C, Sreesai S, Harnvoravongchai P, Chankhamhaengdecha S, Janvilisri T (2017) CD2068 potentially mediates multidrug efflux in Clostridium difficile. Sci Rep 7(1):9982–9982
Knight DR, Kullin B, Androga GO, Barbut F, Eckert C, Johnson S, Spigaglia P, Tateda K, Tsai P-J, Riley TV (2019) Evolutionary and genomic insights into Clostridioides difficile sequence type 11: a diverse zoonotic and antimicrobial-resistant lineage of global one health importance. mBio 10(2):e00446-00419
Brook I, Wexler HM, Goldstein EJC (2013) Antianaerobic antimicrobials: spectrum and susceptibility testing. Clin Microbiol Rev 26(3):526–546
Skinner AM, Petrella L, Siddiqui F, Sambol SP, Gulvik CA, Gerding DN, Donskey CJ, Johnson S (2020) Unique clindamycin-resistant Clostridioides difficile strain related to fluoroquinolone-resistant epidemic BI/RT027 strain. Emerg Infect Dis 26(2):247–254
Lim SK, Stuart RL, Mackin KE, Carter GP, Kotsanas D, Francis MJ, Easton M, Dimovski K, Elliott B, Riley TV, Hogg G, Paul E, Korman TM, Seemann T, Stinear TP, Lyras D, Jenkin GA (2014) Emergence of a ribotype 244 strain of Clostridium difficile associated with severe disease and related to the epidemic ribotype 027 strain. Clin Infect Dis 58(12):1723–1730
The European Committee on Antimicrobial Susceptibility Testing (2021) EUCAST definitions of clinical breakpoints and epidemiological cut-off values, https://eucast.org/clinical_breakpoints/?debug=1. Accessed 18 Mar 2021
Clinical and Laboratory Standards Institute (CLSI) (2020) Performance standards for antimicrobial susceptibility testing. CLSI supplement M100. Clinical and Laboratory Standards Institute, 950 West Valley Road, Suite 2500, Wayne, Pennsylvania 19087 USA (30th ed). https://standards.globalspec.com/std/14371884/CLSI%20M100
The European Committee on Antimicrobial Susceptibility Testing (2021) Breakpoint tables for interpretation of MICs and zone diameters Version: 11.0. http://www.eucast.org
Cusack TP, Ashley EA, Ling CL, Rattanavong S, Roberts T, Turner P, Wangrangsimakul T, Dance DAB (2019) Impact of CLSI and EUCAST breakpoint discrepancies on reporting of antimicrobial susceptibility and AMR surveillance. Clin Microbiol Infect 25(7):910–911
Elliott B, Androga GO, Knight DR, Riley TV (2017) Clostridium difficile infection: evolution, phylogeny and molecular epidemiology. Infect Genet Evol 49:1–11
Ferguson JK, Cheng AC, Gilbert GL, Gottlieb T, Korman T, McGregor A, Richards M, Roberts S, Robson J, Van Gessel H, Riley TV (2011) Clostridium difficile laboratory testing in Australia and New Zealand: national survey results and Australasian Society for Infectious Diseases recommendations for best practice. Pathology 43(5):482–487
Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV (2020) The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies. bioRxiv:2020.2009.2021.307223
Gerding DN, Sambol SP, Johnson S (2018) Non-toxigenic Clostridioides (formerly Clostridium) difficile for prevention of C. difficile infection: from bench to bedside back to bench and back to bedside. Front Microbiol 9:1700
Spigaglia P, Barbanti F, Mastrantonio P, Brazier JS, Barbut F, Delmée M, Kuijper E, I. RP, on behalf of the European Study Group on Clostridium difficile (2008) Fluoroquinolone resistance in Clostridium difficile isolates from a prospective study of C. difficile infections in Europe. J Med Microbiol 57 (6):784-789
Kuwata Y, Tanimoto S, Sawabe E, Shima M, Takahashi Y, Ushizawa H, Fujie T, Koike R, Tojo N, Kubota T, Saito R (2015) Molecular epidemiology and antimicrobial susceptibility of Clostridium difficile isolated from a university teaching hospital in Japan. Eur J Clin Microbiol Infect Dis 34(4):763–772
Liao CH, Ko WC, Lu JJ, Hsueh PR (2012) Characterizations of clinical isolates of Clostridium difficile by toxin genotypes and by susceptibility to 12 antimicrobial agents, including fidaxomicin (OPT-80) and rifaximin: a multicenter study in Taiwan. Antimicrob Agents Chemother 56(7):3943–3949
Walkty A, Boyd DA, Gravel D, Hutchinson J, McGeer A, Moore D, Simor A, Suh K, Taylor G, Miller M, Mulvey MR (2010) Molecular characterization of moxifloxacin resistance from Canadian Clostridium difficile clinical isolates. Diagn Microbiol Infect Dis 66(4):419–424
Huang H, Weintraub A, Fang H, Nord CE (2009) Antimicrobial resistance in Clostridium difficile. Int J Antimicrob Agents 34(6):516–522
He M, Sebaihia M, Lawley TD, Stabler RA, Dawson LF, Martin MJ, Holt KE, Seth-Smith HM, Quail MA, Rance R, Brooks K, Churcher C, Harris D, Bentley SD, Burrows C, Clark L, Corton C, Murray V, Rose G, Thurston S, van Tonder A, Walker D, Wren BW, Dougan G, Parkhill J (2010) Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A 107(16):7527–7532
Dingle KE, Elliott B, Robinson E, Griffiths D, Eyre DW, Stoesser N, Vaughan A, Golubchik T, Fawley WN, Wilcox MH, Peto TE, Walker AS, Riley TV, Crook DW, Didelot X (2014) Evolutionary history of the Clostridium difficile pathogenicity locus. Genome Biol Evol 6(1):36–52
Wang H, Roberts AP, Lyras D, Rood JI, Wilks M, Mullany P (2000) Characterization of the ends and target sites of the novel conjugative transposon Tn5397 from Clostridium difficile: excision and circularization is mediated by the large resolvase. TndX J Bacteriol 182(13):3775–3783
Roberts AP, Mullany P (2011) Tn916-like genetic elements: a diverse group of modular mobile elements conferring antibiotic resistance. FEMS Microbiol Rev 35(5):856–871
Corver J, Bakker D, Brouwer MSM, Harmanus C, Hensgens MP, Roberts AP, Lipman LJA, Kuijper EJ, van Leeuwen HC (2012) Analysis of a Clostridium difficile PCR ribotype 078 100 kilobase island reveals the presence of a novel transposon, Tn6164. BMC Microbiol 12:130–130
Lyras D, Storie C, Huggins AS, Crellin PK, Bannam TL, Rood JI (1998) Chloramphenicol resistance in Clostridium difficile is encoded on Tn4453 transposons that are closely related to Tn4451 from Clostridium perfringens. Antimicrob Agents Chemother 42(7):1563–1567
O’Connor JR, Galang MA, Sambol SP, Hecht DW, Vedantam G, Gerding DN, Johnson S (2008) Rifampin and rifaximin resistance in clinical isolates of Clostridium difficile. Antimicrob Agents Chemother 52(8):2813–2817
Pecavar V, Blaschitz M, Hufnagl P, Zeinzinger J, Fiedler A, Allerberger F, Maass M, Indra A (2012) High-resolution melting analysis of the single nucleotide polymorphism hot-spot region in the rpoB gene as an indicator of reduced susceptibility to rifaximin in Clostridium difficile. J Med Microbiol 61(Pt 6):780–785
Miller MA, Blanchette R, Spigaglia P, Barbanti F, Mastrantonio P (2011) Divergent rifamycin susceptibilities of Clostridium difficile strains in Canada and Italy and predictive accuracy of rifampin Etest for rifamycin resistance. J Clin Microbiol 49(12):4319–4321
Carman RJ, Genheimer CW, Rafii F, Park M, Hiltonsmith MF, Lyerly DM (2009) Diversity of moxifloxacin resistance during a nosocomial outbreak of a predominantly ribotype ARU 027 Clostridium difficile diarrhea. Anaerobe 15(6):244–248
Curry SR, Marsh JW, Shutt KA, Muto CA, O’Leary MM, Saul MI, Pasculle AW, Harrison LH (2009) High frequency of rifampin resistance identified in an epidemic Clostridium difficile clone from a large teaching hospital. Clin Infect Dis 48(4):425–429
Ackermann G, Tang YJ, Kueper R, Heisig P, Rodloff AC, Silva J Jr, Cohen SH (2001) Resistance to moxifloxacin in toxigenic Clostridium difficile isolates is associated with mutations in gyrA. Antimicrob Agents Chemother 45(8):2348–2353
Dridi L, Tankovic J, Burghoffer B, Barbut F, Petit JC (2002) gyrA and gyrB mutations are implicated in cross-resistance to ciprofloxacin and moxifloxacin in Clostridium difficile. Antimicrob Agents Chemother 46(11):3418–3421
Funding
K.O. is funded by an Australian Government Research Training Program Scholarship. D.R.K. is funded by a Fellowship from the National Health and Medical Research Council (APP1138257) and a grant from the Raine Medical Research Foundation (RPG002-19).
Author information
Authors and Affiliations
Contributions
Not applicable.
Corresponding author
Ethics declarations
Ethics approval
Not applicable.
Consent to participate
Not applicable.
Consent for publication
Not applicable.
Conflict of interest
The authors declare no competing interests.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
O’Grady, K., Knight, D.R. & Riley, T.V. Antimicrobial resistance in Clostridioides difficile. Eur J Clin Microbiol Infect Dis 40, 2459–2478 (2021). https://doi.org/10.1007/s10096-021-04311-5
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10096-021-04311-5