Molecular typing of Clostridium difficile isolates cultured from patient stool samples and gastroenterological medical devices in a single Iranian hospital

Clostridioides difficile epidemiology in the Middle and the Far East

OBJECTIVES

Clostridioides difficile is an important pathogen of healthcare-associated gastrointestinal infections. Recently, an increased number of C. difficile infection (CDI) surveillance data has been reported from Asia. The aim of this review is to summarize the data on the prevalence, distribution and molecular epidemiology of CDI in the Middle and the Far East.

METHODS

Literature was drawn from a search of PubMed up to September 30, 2021.

RESULTS

The meta-analysis of data from 111 studies revealed the pooled CDI prevalence rate in the Middle and the Far East of 12.4% (95% CI 11.4-13.3); 48 studies used PCR for CDI laboratory diagnoses. The predominant types (RT)/sequence type (ST) differ between individual countries (24 studies, 14 countries). Frequently found RTs were 001, 002, 012, 017, 018 and 126; RT017 was predominant in the Far East. The epidemic RT027 was detected in 8 countries (22 studies), but its predominance was reported only in three studies (Israel and Iran). The contamination of vegetable and meat or meat products and/or intestinal carriage of C. difficile in food and companion animals have been reported; the C. difficile RTs/STs identified overlapped with those identified in humans.

CONCLUSIONS

A large number of studies on CDI prevalence in humans from the Middle and the Far East have been published; countries with no available data were identified. The number of studies on C. difficile from non-human sources is limited. Comparative genomic studies of isolates from different sources are needed.

Involvement of Pseudomonas aeruginosa in the occurrence of community and hospital acquired diarrhea, and its virulence diversity among the stool and the environmental samples

Transmission of Pseudomonas aeruginosa along the food chain could cause gastrointestinal infections. To show this involvement, the prevalence, putative virulence genotype, and antibiotic resistance phenotype of P. aeruginosa isolates from stool of 1482 patients with community and hospital acquired diarrhea were compared with 87 isolates from the environmental samples. The results showed infection with P. aeruginosa in 3.4% of the cases, while 57.4% of vegetable samples were contaminated. Significantly higher frequency of lasB (98%), aprA (98%), exoY (98%), and exoS (90%), but lower rate of exoT (39.2%), was detected among the stool isolates. Multi-drug resistance (MDR) phenotype was detected in 25.5% and 4% of the stool and vegetable isolates, respectively. A higher rate of studied virulence genes was detected among the MDR strains vs non-MDR strains. These results indicate P. aeruginosa as a causative agent of diarrhea either among the hospitalized patients and those with community-acquired diarrhea.

Phenotypical and Genotypical Comparison of Clostridium difficile Isolated from Clinical Samples: Homebrew DNA Fingerprinting versus Antibiotic Susceptibility Testing (AST) and Clostridial Toxin Genes

Background

Clostridium (Clostridioides) difficile is recognized as the major cause of healthcare antibiotic-associated diarrhea. We surveyed a molecular epidemiological correlation between the clinical isolates from two general hospitals in Iran through clustering toxigenic types and antibiotic susceptibility testing (AST) accuracy.

Methods

Study population included 460 diarrhoeic specimens from inpatients with a history of antibiotic therapy. All samples underwent enriched anaerobic culture, confirmed by detection of gluD gene with PCR. Toxin status and AST were assessed by the disk diffusion method (DDM) and minimal inhibitory concentrations (MICs) of metronidazole, vancomycin, and rifampin. C. difficile outbreak was analyzed through conventional PCR by tracing toxin genes and Homebrew pulsed-field gel electrophoresis (PFGE) for characterizing isolates within our healthcare systems.

Results

A total of 29 C. difficile strains were isolated by enriched anaerobic culture from the clinical samples. Among them, 22 (4.8%) toxigenic profiles yielded toxins A and B (tcdA, tcdB) and binary toxins (cdtA, cdtB). The minimum inhibitory concentration (MIC) was 18.1% and 9% for vancomycin and metronidazole, and all isolates were susceptible to rifampicin and its minimum inhibitory concentration was at <0.003 μg/mL. The most dominant toxigenic and antibiotic-resistant “pulsotype F” was detected through PFGE combined with multiple Clostridial toxigenic pattern and AST.

Conclusions

DNA fingerprinting studies represent a powerful tool in surveying hypervirulent C. difficile strains in clinical settings. Resistance to vancomycin and metronidazole, as first-line antibiotics, necessitate accomplishment of proper control strategies and also prescription of tigecycline as a more appropriate option.

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

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.

Phenotypic and Genotypic Characteristics of Clostridium difficile Isolates in Patients with Type 2 Diabetes in Iran

Purpose

This study aimed to investigate the phenotypic and genotypic characterization of Clostridium difficile isolates in type 2 diabetes patients with hospital-acquired diarrhea in four teaching hospitals in Isfahan, Iran.

Patients and Methods

A total of 104 hospitalized patients with type 2 diabetes and nosocomial diarrhea were included in the current study over a 2-year period (2015–2017). C. difficile isolates were characterized by conventional microbiological methods including the presence of toxin genes, antibiotic resistance testing and molecular methods including multilocus sequence typing (MLST) and random amplification of polymorphic DNA (RAPD).

Results

All 21 C. difficile isolates (20.2%) were detected from 104 studied patients. All isolates were susceptible to metronidazole and vancomycin. The antimicrobial resistance rates were distinctly higher for clindamycin and for moxifloxacin. Based on PCR amplification of tcdA and tcdB, 13 isolates (12.5%) carried both of these genes and were considered toxigenic. Thirteen toxigenic C. difficile strains were classified into two sequence types (STs), that is, ST54 and ST2 types. The RAPD-PCR amplification patterns of the detected toxigenic C. difficile revealed three distinct but related RAPD clusters. RAPD cluster 1 had the highest similarity with RAPD types 2 and 3.

Conclusion

A relatively high rate of CDI was observed in patients with type 2 diabetes and was associated with poorer health outcomes. These patients were exposed to multiple antibiotics and other therapeutic agents. We recommend close screening for the coexistence of CDI and type 2 diabetes in patients with diarrhea using a combination of conventional and molecular methods.

Isolation and toxin gene detection of Clostridium (Clostridioides) difficile from traditional and commercial quail farms and packed quail meat for market supply - Short communication

Clostridium (Clostridioides) difficile is a Gram-positive anaerobic rod-shaped bacterium and the main cause of nosocomial diarrhoea in humans. In recent years, the transmission of C. difficile from environmental reservoirs (e.g. food) to humans has become a major focus of research. The aim of this study was to investigate the prevalence and corresponding toxin genes of C. difficile in faecal samples and meat of quails. Thirty samples of packed quail meat in Mashhad, Iran and 500 faecal samples (pooled to n = 5) were collected on quail farms in the Northeastern Khorasan region for further investigation. Of 100 pooled quail faecal samples 10% showed cultural growth of C. difficile. In meat samples two out of 30 specimens (7%) showed cultural growth. In six of ten isolates from faecal samples toxin genes (tcdB and tcdA) were present, while four isolates harboured no toxin genes. However, in meat isolates no toxin genes were present. Mutations in the tcdC gene were not detected, indicating that 'hypervirulent' strains such as RT027 and RT078 were not present. The data suggest that quail and quail products might hold a potential for the spread of C. difficile.

A Two-Step Approach for Diagnosing Glutamate Dehydrogenase Genes by Conventional Polymerase Chain Reaction from Clostridium difficile Isolates

BACKGROUND

Clostridium difficile is the major causative agent of nosocomial antibiotic-associated colitis. The gold standard for C. difficile detection is stool culture followed by cytotoxic assay, although it is laborious and time-consuming. We developed a screening test based on a two-step conventional polymerase chain reaction (PCR) approach to detect gluD, the glutamate dehydrogenase (GDH) enzyme gene, which is a marker for screening of C. difficile. Targeting gluD comparing to the conserved stable genetic element of pathogenicity locus (PaLoc), with an accessory gene of Cdd3, was an effective method for the detection of this pathogen from patients with enterocolitis.

METHODS

Fresh fecal samples of the patients who were clinically suspicious for antibiotic-associated colitis were collected. Stool specimens were cultured on the cycloserine-cefoxitin fructose agar (CCFA) in an anaerobic condition, following alcohol shock treatment and enrichment in Clostridium difficile Brucella broth (CDBB). On confirmed colonies, PCR was carried out for detection of PaLoc subsidiary gene, Cdd3, and toxicogenic genes, tcdA and tcdB. The gluD that is GDH gene detection was performed by conventional PCR on the extracted DNA from 578 fresh stool samples.

RESULTS

57 (9.8%) strains of C. difficile were approved by conventional PCR for gluD and Cdd3 genes, in which 37 (6.4%) colonies had tcdA+/tcdB+ genotype, 2 (0.3%) tcdA+/tcdB-, 4 (0.7%) tcdA-/ tcdB+ and the remaining 14 (2.4%) colonies were tcdA and tcdB negative.

CONCLUSION

These results demonstrate that targeting gluD by PCR is quite promising for rapid detection of C. difficile from fresh fecal samples. Furthermore, the multiple-gene analysis for tcdA and tcdB assay proved a reliable approach for diagnosing of toxigenic strains among clinical samples.

The emergence of metronidazole and vancomycin reduced susceptibility in Clostridium difficile isolates in Iran

OBJECTIVES

Clostridium difficile (C. difficile) is the main causative agent of antibiotic-associated diarrhoea (AAD) and pseudomembranous colitis. The accumulation of antimicrobial resistance in C. difficile strains can drive C. difficile infection (CDI) epidemiology. This study was undertaken to evaluate the antimicrobial resistance patterns of toxigenic C. difficile isolates cultured from diarrhoeal stool samples of hospitalised patients with suspected CDI in three tertiary care hospitals in Tehran, Iran.

METHODS

Two hundred and fifty diarrhoeal stool samples were investigated by toxigenic culture using cycloserine-cefoxitin-fructose agar and the VERO cell line. Antimicrobial susceptibility to metronidazole, vancomycin, clindamycin, tetracycline, and moxifloxacin was performed by disk diffusion and Etest methods on Brucella Blood Agar supplemented with hemin and vitamin K.

RESULTS

Thirty-five stool samples (14.0%) proved positive using C. difficile toxigenic culture. According to Clinical and Laboratory Standards Institute breakpoints, the following resistance was identified in C. difficile isolates: metronidazole (2 of 35); moxifloxacin (7 of 35); clindamycin (18 of 35); and tetracycline (5 of 35). Using European Committee on Antimicrobial Susceptibility Testing breakpoints, three of 35 isolates showed reduced-susceptibility for vancomycin and 14 of 35 for metronidazole. In addition, the results showed a good correlation between the inhibition zone diameter (disk diffusion) and MIC values (Etest); Pearson correlation coefficient 0.7400.95 (P< 0.001).

CONCLUSIONS

Multidrug resistance was observed in Iranian clinical toxigenic C. difficile isolates, including reduced susceptibility to first-line CDI treatment drugs. In addition, disk diffusion can be used as a cost-effective option for the antimicrobial susceptibility testing of C. difficile isolates.

Molecular typing of Clostridioides difficile isolates from clinical and non-clinical samples in Iran

Clostridioides difficile is a major cause of nosocomial infectious diarrhea in hospitalized patients throughout the world. We aimed to characterize C. difficile isolates among hospitalized patients, hospital staffs, and hospital environment samples obtained in three tertiary care hospitals of Iran with regard to their molecular types between June 2016 and November 2017. The toxigenicity of C. difficile isolates was determined by toxigenic culture and multiplex-PCR. Toxigenic C. difficile isolates collected were ribotyped using capillary gel electrophoresis-based PCR and the database of WEBRIBO (http://webribo.ages.at). Of 500 clinical and non-clinical samples, toxigenic C. difficile were identified in 35 of 250 stool samples (14%) and in 3 of 250 swabs (1.2%). The most frequently found ribotypes (RTs) were 039, AI-12, and AI-21 (15.8, 10.52, and 10.52% of all isolates, respectively). Further RTs were: 017, 001, AI-3, AI-15, AI-18, AI-10, AI-4, and PR21195 (as new ribotype). The epidemic RTs (027 and 078) seen in the Europe, North America, and Asia were completely absent in this study.

Clostridium difficile-associated Diarrhea in Developing Countries: A Systematic Review and Meta-Analysis

Introduction

The prevalence of Clostridium difficile infection is rapidly increasing worldwide, but prevalence is difficult to estimate in developing countries where awareness, diagnostic resources, and surveillance protocols are limited. As diarrhea is the hallmark symptom, we conducted a systematic review and meta-analysis to determine the prevalence and incidence of C. difficile infection in patients in these regions who presented with diarrhea.

Methods

We conducted a systematic literature search of MEDLINE/PubMed, Scopus, and Latin-American and Caribbean Health Sciences Literature databases to identify and analyze data from recent studies providing prevalence or incidence rates of C. difficile-associated diarrhea in developing countries within four regions: Africa–Middle East, developing Asia, Latin America, and China. Our objectives were to determine the current prevalence and incidence density rates of first episodes of C. difficile-associated diarrhea in developing countries.

Results

Within the regions included in our analysis, prevalence of C. difficile infection in patients with diarrhea was 15% (95% CI 13–17%) (including community and hospitalized patients), with no significant difference across regions. The incidence of C. difficile infection in 17 studies including this information was 8.5 per 10,000 patient-days (95% CI 5.83–12.46). Prevalence was significantly higher in hospitalized patients versus community patients (p  = 0.0227).

Conclusion

Our prevalence estimate of 15% is concerning; however, low awareness and inconsistent diagnostic and surveillance protocols suggest this is markedly underestimated. Enhanced awareness and management of C. difficile infection in patients with diarrhea, along with improvements in infection control and surveillance practices, should be implemented to reduce prevalence of C. difficile-associated diarrhea in developing countries.

Funding

Pfizer Inc.

Electronic supplementary material

The online version of this article (10.1007/s40121-019-0231-8) contains supplementary material, which is available to authorized users.

Molecular epidemiology of Clostridium difficile infection in Iranian hospitals

Background

Clostridium difficile infection (CDI) is known as one of the most important causes of nosocomial infections. The main objective of this study was to evaluate the presence of Clostridium difficile in the stool of hospitalized patients with diarrhea as well as in their environments.

Methods

C. difficile isolates were characterized according to the presence of toxin genes and antibiotic resistance. Multilocus Sequence Typing Analysis (MLST) was applied for finding the genetic polymorphism and relationship among strain lineages.

Results

A total of 821 samples (574 stools and 247 swabs) were collected between April 2015 and May 2017. The prevalence of C. difficile isolates was 28.6% (164/574) in patients and 19% (47/247) in swabs taken from medical devices, hands of healthcare workers and skin patient sites. Finally, 11.5% (66/574) toxigenic C. difficile strains isolated from stool samples of inpatients and 4.4% (11/247) from hands of healthcare workers and skin patient sites. All the toxigenic isolates were inhibited by a low concentration of vancomycin (MIC < 0.5 μg/ml). About 43% (33/77) and 39% of isolates were resistant to Clindamycin and moxifloxacin respectively. All isolates were susceptible to metronidazole. Toxigenic C. difficile strains were analyzed by MLST and were divided into 4 different STs. The detected types were ST-54 (57.9%), followed by ST-2 (31.6. %), ST-15 (5.3%) and ST-37 (5.3%), while none of the isolates were identified as ST-1 or ST-11. Significant risk factors for CDI appear to be advanced age, undergoing chemotherapy, previous surgery, and residence in the nursing home.

Conclusions

CDI is common in Iran and further studies are recommended to monitor its epidemiological variations. Moreover, greater attempts must be made to encourage antibiotic stewardship by healthcare workers and the public.

The frequency of bacterial contamination and diversity of drug resistance patterns in devices and staff of endoscopy and colonoscopy units

Background: This study aimed at analyzing microbial contamination in medical equipment, environment, and staff of a gastroenterology unit.

Methods: Samples of gastrointestinal imaging devices, the environment, and staff were collected using standard swab-rinse technique and biochemical or molecular characteristics of the isolates, their susceptibility to antibiotics, and similarity of the resistance patterns were investigated.

Results: Out of 107 samples, bacterial contamination was detected in the hands of staff (54.1%), imaging devices (56.7%), and in the environment (54.5%). While Pseudomonas spp. were detected only in the imaging devices (13.5%), Bacillus spp. (32.4% and 31.5%), Enterococcus spp. (14.3% and 5.9%), Clostridium difficile (10.8% and 10.5%), and Staphylococcus epidermidis (5.4% and 15.9%) were orderly the most common isolates from samples of the imaging devices and the environment. Nearly, 40% of P. aeruginosa strains were resistant to cefepime, while resistance to cephalosporins and β-lactamase inhibitor was detected in 33% and 75% of S. aureus strains, respectively. Homology of resistance patterns was detected between the imaging devices and hands of the staff.

Conclusion: Our results proposed biofilm and spore forming bacteria as main contaminants of imaging devices in this hospital. Homology of the resistance patterns proposed involvement of staff in contamination of the equipment.