High prevalence of Clostridiodes diffiicle PCR ribotypes 001 and 126 in Iran.
Adolescent
Adult
Aged
Aged, 80 and over
Anti-Bacterial Agents
/ pharmacology
Bacterial Proteins
/ genetics
Child
Child, Preschool
Clostridioides difficile
/ classification
Clostridium Infections
/ epidemiology
Community-Acquired Infections
/ epidemiology
Cross Infection
/ epidemiology
Diarrhea
/ microbiology
Drug Resistance, Bacterial
Feces
/ microbiology
Female
Genotype
Humans
Iran
/ epidemiology
Male
Microbial Sensitivity Tests
Middle Aged
Prevalence
Ribotyping
/ methods
Young Adult
Journal
Scientific reports
ISSN: 2045-2322
Titre abrégé: Sci Rep
Pays: England
ID NLM: 101563288
Informations de publication
Date de publication:
13 03 2020
13 03 2020
Historique:
received:
24
09
2019
accepted:
25
02
2020
entrez:
15
3
2020
pubmed:
15
3
2020
medline:
15
12
2020
Statut:
epublish
Résumé
Clostridium difficile is a leading causative agent of hospital-acquired and community-acquired diarrhea in human. This study aims to characterize the predominant C. difficile strains, RT001 and 126, circulating in Iranian hospitals in relation to resistant phenotypes, the antibiotic resistance genes, and their genetic relatedness. A total number of 735 faecal specimens were collected from patients suspected of CDI in Tehran hospitals. Typing and subtyping of the strains were performed using CE-PCR ribotyping and MLVA, respectively, followed by PCR assays for ARGs and indicators of Tns. Minimum inhibitory concentrations (MICs) of five antibiotics were determined by MIC Test Strips. Among 65 strains recovered from CDI patients, RT001 (32.3%) and RT126 (9.2%) were found as the most frequent ribotypes, and 64 MLVA types were identified. Using MLVA, RT001 and RT126 were subtyped into 6 and 4 groups, respectively. The vanA, nim, tetM, gyrA, gyrB genes were detected in 24.6%, 0%, 89.2%, 95.3%, and 92.3% of the strains, respectively. The indicators of Tns including vanHAX, tndX, and int were found in 0%, 3% and 29.2% of the strains, respectively. The most common amino acid (AA) alterations of GyrA and GyrB were related to substitutions of Thr82 → Val and Ser366 → Val, respectively. Resistance rate to metronidazole, vancomycin, tetracycline, ciprofloxacin, and moxifloxacin was 81.5%, 30.7%, 85%, 79%, and 74%, respectively. This study, for the first time revealed the subtypes of circulating RT001 and RT126 in Iran. It is of importance that the majority of the strains belonging to RT001 were multidrug resistant (MDR). This study also pointed to the intra-hospital dissemination of the strains belonging to RT001 and RT126 for short and long periods, respectively, using MLVA. The most important resistance phenotypes observed in this study was vancomycin-resistant phenotypes. Resistance to metronidazole was also high and highlights the need to determine its resistance mechanisms in the future studies.
Identifiants
pubmed: 32170182
doi: 10.1038/s41598-020-61604-z
pii: 10.1038/s41598-020-61604-z
pmc: PMC7070088
doi:
Substances chimiques
Anti-Bacterial Agents
0
Bacterial Proteins
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4658Références
Krutova, M., Matejkova, J., Drevinek, P., Kuijper, E. J. & Nyc, O. Increasing incidence of Clostridium difficile ribotype 001 associated with severe course of the infection and previous fluoroquinolone use in the Czech Republic, 2015. Eur. J. Clin. Microbiol. Infect. Dis. 36, 2251–2258 (2017).
doi: 10.1007/s10096-017-3055-z
Freeman, J. et al. 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, 724–731 (2017).
doi: 10.1016/j.cmi.2017.10.008
Álvarez-Pérez, S., Blanco, J. L., Harmanus, C., Kuijper, E. & García, M. E. Subtyping and antimicrobial susceptibility of Clostridium difficile PCR ribotype 078/126 isolates of human and animal origin. Vet. Microbiol. 199, 15–22 (2017).
doi: 10.1016/j.vetmic.2016.12.001
Furuya-kanamori, L. et al. Comparison of Clostridium difficile ribotypes circulating in Australian hospitals and communities. J. Clin. Microbiol. 55, 216–225 (2017).
doi: 10.1128/JCM.01779-16
Arvand, M., Hauri, A. M., Zaiß, H., Witte, W. & Bettge-Weller, G. Clostridium difficile ribotypes 001, 017, and 027 are associated with lethal C. difficile infection in Hesse, Germany. Eurosurveillance 14, 19047–53 (2009).
doi: 10.2807/ese.14.45.19403-en
van Dorp, S. M. et al. Standardised surveillance of Clostridium difficile infection in European acute care hospitals: a pilot study, 2013. Eurosurveillance 21, 30293 (2016).
doi: 10.2807/1560-7917.ES.2016.21.29.30293
Davies, K. A. et al. Diversity of Clostridium difficile PCR ribotypes in Europe: Results from the European, multicentre, prospective, biannual, point-prevalence study of Clostridium difficile infection in hospitalised patients with diarrhoea (EUCLID), 2012 and 2013. Eurosurveillance 21, 1–11 (2016).
doi: 10.2807/1560-7917.ES.2016.21.29.30294
Fawley, W. N. et al. Development and validation of an internationally-standardized, high-resolution capillary gel-based electrophoresis PCR-ribotyping protocol for Clostridium difficile. PLoS One 10, 1–14 (2015).
Karlowsky, J. A. et al. PCR ribotyping and antimicrobial susceptibility testing of isolates of Clostridium difficile cultured from toxin-positive diarrheal stools of patients receiving medical care in Canadian hospitals: the Canadian Clostridium difficile surveillance study. Diagn. Microbiol. Infect. Dis. 91, 105–111 (2018).
doi: 10.1016/j.diagmicrobio.2018.01.017
Baines, S. & Wilcox, M. Antimicrobial resistance and reduced susceptibility in Clostridium difficile: potential consequences for induction, treatment, and recurrence of C. difficile infection. Antibiotics 4, 267–298 (2015).
doi: 10.3390/antibiotics4030267
pubmed: 4790285
pmcid: 4790285
Barkin, J. A., Sussman, D. A., Fifadara, N. & Barkin, J. S. Clostridium difficile infection and patient-specific antimicrobial resistance testing reveals a high metronidazole resistance rate. Dig. Dis. Sci. 62, 1035–1042 (2017).
doi: 10.1007/s10620-017-4462-9
Leeds, J. A., Sachdeva, M., Mullin, S., Barnes, S. W. & Ruzin, A. In vitro selection, via serial passage, of Clostridium difficile mutants with reduced susceptibility to fidaxomicin or vancomycin. J. Antimicrob. Chemother. 69, 41–44 (2013).
doi: 10.1093/jac/dkt302
Cetinkaya, Y., Falk, P. & Mayhall, C. G. Vancomycin-resistant enterococci. Clin. Microbiol. Rev. 13, 686–707 (2000).
doi: 10.1128/CMR.13.4.686
pubmed: 11023964
pmcid: 11023964
Dingle, K. E. et al. A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078. bioRxiv 262352 (2018).
Chopra, I. & Roberts, M. Tetracycline antibiotics: mode of action, applications, molecular biology, and epidemiology of bacterial resistance. Microbiol. Mol. Biol. Rev. 65, 232–260 (2001).
doi: 10.1128/MMBR.65.2.232-260.2001
pubmed: 11381101
pmcid: 11381101
Azimirad, M. et al. Molecular typing of Clostridium difficile isolates cultured from patient stool samples and gastroenterological medical devices in a single Iranian hospital. Anaerobe 47, 125–128 (2017).
doi: 10.1016/j.anaerobe.2017.05.004
pubmed: 28501554
pmcid: 28501554
Fawley, W. N. et al. Use of highly discriminatory fingerprinting to analyze clusters of Clostridium difficile infection cases due to epidemic ribotype 027 strains. J. Clin. Microbiol. 46, 954–960 (2008).
doi: 10.1128/JCM.01764-07
pubmed: 18216211
pmcid: 18216211
Al-Thani, A. A., Hamdi, W. S., Al-Ansari, N. A. & Doiphode, S. H. Polymerase chain reaction ribotyping of Clostridium difficile isolates in Qatar: a hospital-based study. BMC Infect. Dis. 14, 502 (2014).
doi: 10.1186/1471-2334-14-502
pubmed: 4262129
pmcid: 4262129
Jamal, W., Pauline, E. & Rotimi, V. A prospective study of community-associated Clostridium difficile infection in Kuwait: epidemiology and ribotypes. Anaerobe 35, 28–32 (2015).
doi: 10.1016/j.anaerobe.2015.06.006
Sharara, A. et al. Hypervirulent Clostridium difficile strains are rarely associated with nosocomial CDI in adults in Lebanon: results from a prospective study on the incidence, risk factors for relapse, and outcome of nosocomial CDI: 104. Am. J. Gastroenterol. 112, S51 (2017).
doi: 10.14309/00000434-201710001-00104
Marsh, J. W. et al. Multilocus variable-number tandem-repeat analysis and multilocus sequence typing reveal genetic relationships among Clostridium difficile isolates genotyped by restriction endonuclease analysis. J. Clin. Microbiol. 48, 412–418 (2010).
doi: 10.1128/JCM.01315-09
Baines, S. D. et al. Emergence of reduced susceptibility to metronidazole in Clostridium difficile. J. Antimicrob. Chemother. 62, 1046–1052 (2008).
doi: 10.1093/jac/dkn313
Erikstrup, L. T. et al. Antimicrobial susceptibility testing of Clostridium difficile using EUCAST epidemiological cut-off values and disk diffusion correlates. Clin. Microbiol. Infect. 18, 266–272 (2012).
doi: 10.1111/j.1469-0691.2012.03907.x
Krehelova, M., Nyč, O., Sinajová, E. & Krutova, M. The predominance and clustering of Clostridioides (Clostridium) difficile PCR ribotype 001 isolates in three hospitals in Eastern Slovakia, 2017. Folia Microbiol. (Praha). 1, 1–6 (2018).
Knetsch, C. W. et al. Genetic markers for Clostridium difficile lineages linked to hypervirulence Printed in Great Britain. Microbiology 27, 3113–3123 (2011).
doi: 10.1099/mic.0.051953-0
Hung, Y.-P. et al. Clostridium difficile ribotype 126 in southern Taiwan: a cluster of three symptomatic cases. Anaerobe 30, 188–192 (2014).
doi: 10.1016/j.anaerobe.2014.06.005
Eckert, C. et al. Clinical and microbiological features of Clostridium difficile infections in France: The ICD-RAISIN 2009 national survey. Med. Mal. Infect. 43, 67–74 (2013).
doi: 10.1016/j.medmal.2013.01.004
Freeman, J. et al. Pan-European longitudinal surveillance of antibiotic resistance among prevalent Clostridium difficile ribotypes. Clin. Microbiol. Infect. 21, 248–249 (2015).
doi: 10.1016/j.cmi.2014.09.017
Norén, T., Alriksson, I., Åkerlund, T., Burman, L. G. & Unemo, M. In vitro susceptibility to 17 antimicrobials of clinical Clostridium difficile isolates collected in 1993-2007 in Sweden. Clin. Microbiol. Infect. 16, 1104–1110 (2010).
doi: 10.1111/j.1469-0691.2009.03048.x
Husain, F. et al. Two multidrug-resistant clinical isolates of bacteroides fragilis carry a novel metronidazole resistance nim gene (nimJ). Antimicrob. Agents Chemother. 57, 3767–3774 (2013).
doi: 10.1128/AAC.00386-13
pubmed: 3719759
pmcid: 3719759
Peláez, T. et al. Metronidazole resistance in Clostridium difficile is heterogeneous. J. Clin. Microbiol. 46, 3028–3032 (2008).
doi: 10.1128/JCM.00524-08
pubmed: 2546748
pmcid: 2546748
Boekhoud, I. M. et al. Plasmid-mediated metronidazole resistance in Clostridioides difficile. bioRxiv 643775 (2019).
Spigaglia, P. et al. Fluoroquinolone resistance in Clostridium difficile isolates from a prospective study of C. difficile infections in Europe. J. Med. Microbiol. 57, 784–789 (2008).
doi: 10.1099/jmm.0.47738-0
Huang, H., Weintraub, A., Fang, H. & Nord, C. E. Antimicrobial resistance in Clostridium difficile. Int. J. Antimicrob. Agents 34, 516–522 (2009).
doi: 10.1016/j.ijantimicag.2009.09.012
Spigaglia, P. et al. Multidrug resistance in European Clostridium difficile clinical isolates. J. Antimicrob. Chemother. 66, 2227–2234 (2011).
doi: 10.1093/jac/dkr292
pubmed: 21771851
pmcid: 21771851
Bakker, D. et al. Relatedness of human and animal Clostridium difficile PCR ribotype 078 isolates determined on the basis of multilocus variable-number tandem-repeat analysis and tetracycline resistance. J. Clin. Microbiol. 48, 3744–3749 (2010).
doi: 10.1128/JCM.01171-10
pubmed: 20686080
pmcid: 20686080
Kikuchi, E., Miyamoto, Y., Narushima, S. & Itoh, K. Design of Species‐specific primers to identify 13 species of Clostridium harbored in human intestinal tracts. Microbiol. Immunol. 46, 353–358 (2002).
doi: 10.1111/j.1348-0421.2002.tb02706.x
pubmed: 12139395
pmcid: 12139395
Persson, S., Torpdahl, M. & Olsen, K. E. P. New multiplex PCR method for the detection of Clostridium difficile toxin A (tcdA) and toxin B (tcdB) and the binary toxin (cdtA/cdtB) genes applied to a Danish strain collection. Clin. Microbiol. Infect. 14, 1057–1064 (2008).
doi: 10.1111/j.1469-0691.2008.02092.x
pubmed: 19040478
pmcid: 19040478
Spigaglia, P. & Mastrantonio, P. Molecular analysis of the pathogenicity locus and polymorphism in the putative negative regulator of toxin production (TcdC) among Clostridium difficile clinical isolates. J. Clin. Microbiol. 40, 3470–3475 (2002).
doi: 10.1128/JCM.40.9.3470-3475.2002
pubmed: 12202595
pmcid: 12202595
Kariyama, R., Mitsuhata, R., Chow, J. W., Clewell, B. & Kumon, H. Simple and reliable multiplex PCR assay for surveillance isolates of simple and reliable multiplex PCR assay for surveillance isolates of vancomycin-resistant Enterococci. J. Clin. Microbiol. 38, 3092–3095 (2000).
doi: 10.1128/JCM.38.8.3092-3095.2000
pubmed: 87194
pmcid: 87194
Trinh, S. & Reysset, G. Detection by PCR of the nim genes encoding 5-nitroimidazole resistance in Bacteroides spp. J. Clin. Microbiol. 34, 2078–2084 (1996).
doi: 10.1128/JCM.34.9.2078-2084.1996
pubmed: 229193
pmcid: 229193
Yu, H., Seol, S. & Cho, D. Diversity of Tn1546-like elements in vancomycin-resistant Enterococci isolated from humans and poultry in Korea. J. Clin. Microbiol. 41, 2641–2643 (2003).
doi: 10.1128/JCM.41.6.2641-2643.2003
pubmed: 156543
pmcid: 156543
Marchese, A., Ramirez, M., Schito, G. C. & Tomasz, A. Molecular epidemiology of penicillin-resistant Streptococcus pneumoniae isolates recovered in Italy from 1993 to 1996. J. Clin. Microbiol. 36, 2944–2949 (1998).
doi: 10.1128/JCM.36.10.2944-2949.1998
pubmed: 105092
pmcid: 105092
Gherardi, G. et al. Phenotypic and genotypic characterization of two penicillin-susceptible serotype 6B Streptococcus pneumoniae clones circulating in Italy. J. Clin. Microbiol. 41, 2855–2861 (2003).
doi: 10.1128/JCM.41.7.2855-2861.2003
pubmed: 165367
pmcid: 165367
Spigaglia, P., Carucci, V., Barbanti, F. & Mastrantonio, P. ErmB determinants and Tn916-like elements in clinical isolates of Clostridium difficile. Antimicrob. Agents Chemother. 49, 2550–2553 (2005).
doi: 10.1128/AAC.49.6.2550-2553.2005
pubmed: 1140533
pmcid: 1140533
Marsh, J. W. et al. Multilocus variable-number tandem-repeat analysis for investigation of Clostridium difficile transmission in hospitals. J. Clin. Microbiol. 44, 2558–2566 (2006).
doi: 10.1128/JCM.02364-05
pubmed: 1489528
pmcid: 1489528
Marsh, J. W. et al. Multi-locus variable number tandem repeat analysis for investigation of the genetic association of Clostridium difficile isolates from food, food animals and humans. Anaerobe 17, 156–160 (2011).
doi: 10.1016/j.anaerobe.2011.05.015