High prevalence of Clostridiodes diffiicle PCR ribotypes 001 and 126 in Iran

Abstract

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 vancomycinresistant phenotypes. Resistance to metronidazole was also high and highlights the need to determine its resistance mechanisms in the future studies. Clostridium difficile is a leading causative agent of hospital-acquired (HA) and community-acquired (CA) diarrhea in human 1. Severe C. difficile infections (CDIs) are commonly associated with hypervirulent strains pertaining to PCR ribotypes (RTs) 027 and 078. The C. difficile RT001 is regarded to be a hypervirulent strain as well as RT078 2. C. difficile RT126 is considered as a hypervirulent strain that is genetically close to RT078 (identical patterns of PCR ribotyping) 3,4. The RT078 is one of the most common types of C. difficile isolated from human in Europe 2,3. The RT001 and RT072 associated with lethal CDI, are common in Europe 5,6. The RTs001/072 have almost identical patterns of PCR ribotyping and could be differentiated by multilocus variable-number tandem repeat analysis (MLVA) 7. Capillary electrophoresis (CE)-PCR ribotyping is currently employed as an appropriate alternative to agarose gel-based PCR ribotyping for epidemiological surveillance. However, it needs to be combined with MLVA in order to subtype the strain...

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Loop mediated isothermal amplification of Clostridioides difficile isolates in gastrointestinal patients

“…The result of the culture method showed the 20.0% (n = 10/50) frequency rate for C. difficile . Using culture method, in previous studies by Shoaei et al ( 2019 ) from Isfahan, Iran and Baghani et al ( 2020 ) from Tehran, Iran, a higher (28.6%) and a lower (8.8%) frequency rate was reported for C. difficile , respectively. Also, Putsathit et al ( 2017 ) from Thailand and Plants-Paris et al ( 2019 ) from Kenya reported the C. difficile strains in 23.7% (n = 100/422) and 37.6% of the stool samples using the direct culture method.…”

Molecular characterization of pathogenicity locus (PaLoc) and tcdC genetic diversity among tcdAB Clostridioides difficile clinical isolates in Tehran, Iran

“…In our previous study that used a large collection of C. di cile isolates, RT 001 (12.9%), RT 126 (11.2%), and RT 084 (3.3%) were the most frequent RTs identi ed in CDI patients across different hospitals and medical centers in Tehran [39]. In a recent study by Baghani et al, RT 001 (32.3%) and RT 126 (9.2%) were also reported as the most common RTs isolated from patients with CDI in Tehran [40]. To date, RT 027 isolates have not been reported from Iranian patients.…”