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Kunishima H, Ichiki K, Ohge H, Sakamoto F, Sato Y, Suzuki H, Nakamura A, Fujimura S, Matsumoto K, Mikamo H, Mizutani T, Morinaga Y, Mori M, Yamagishi Y, Yoshizawa S. Japanese Society for infection prevention and control guide to Clostridioides difficile infection prevention and control. J Infect Chemother 2024; 30:673-715. [PMID: 38714273 DOI: 10.1016/j.jiac.2024.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/25/2024] [Accepted: 03/26/2024] [Indexed: 05/09/2024]
Affiliation(s)
- Hiroyuki Kunishima
- Department of Infectious Diseases. St. Marianna University School of Medicine, Japan.
| | - Kaoru Ichiki
- Department of Infection Control and Prevention, Hyogo Medical University Hospital, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Japan
| | - Fumie Sakamoto
- Quality Improvement and Safety Center, Itabashi Chuo Medical Center, Japan
| | - Yuka Sato
- Department of Infection Control and Nursing, Graduate School of Nursing, Aichi Medical University, Japan
| | - Hiromichi Suzuki
- Department of Infectious Diseases, University of Tsukuba School of Medicine and Health Sciences, Japan
| | - Atsushi Nakamura
- Department of Infection Prevention and Control, Graduate School of Medical Sciences, Nagoya City University, Japan
| | - Shigeru Fujimura
- Division of Clinical Infectious Diseases and Chemotherapy, Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Japan
| | - Kazuaki Matsumoto
- Division of Pharmacodynamics, Faculty of Pharmacy, Keio University, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University, Japan
| | | | - Yoshitomo Morinaga
- Department of Microbiology, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Japan
| | - Minako Mori
- Department of Infection Control, Hiroshima University Hospital, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Kochi Medical School, Kochi University, Japan
| | - Sadako Yoshizawa
- Department of Laboratory Medicine/Department of Microbiology and Infectious Diseases, Faculty of Medicine, Toho University, Japan
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Boyle BL, Khanna S. Fecal microbiota live - jslm (Rebyota™/RBL) for management of recurrent Clostridioides difficile infection. Future Microbiol 2024:1-9. [PMID: 38989699 DOI: 10.1080/17460913.2024.2364583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 06/03/2024] [Indexed: 07/12/2024] Open
Abstract
There is an unmet need for effective treatments of Clostridioides difficile infection, an emerging health crisis in the United States. The management of C. difficile infection should include treatment of active infection and a strategy to prevent recurrence. Current gold standard therapy includes oral antibiotics which predispose patients to gut dysbiosis and increase the risk of recurrent infection. Addressing dysbiosis via fecal microbiota transplantation is an active and promising area of research, but studies have lacked standardization which makes outcome and safety data difficult to interpret. Rebyota™, formerly known as RBX2660, is a live biotherapeutic product designed using a standardized protocol and manufacturing process that has been shown to be effective for preventing recurrent C. difficile infection.
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Affiliation(s)
| | - Sahil Khanna
- Division of Gastroenterology & Hepatology, Mayo Clinic, Rochester, MN 55905, USA
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Mubaraki MA, Hussain M, Hassan FU, Munir S, Fozia F, Ahmad I, Bibi F, Sultan S, Zialluh Z. Antimicrobial Resistance and Associated Risk Factors for Clostridium difficile in Patients Attending Tertiary Care Settings. J Trop Med 2024; 2024:6613120. [PMID: 38784112 PMCID: PMC11115991 DOI: 10.1155/2024/6613120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 03/31/2024] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
To determine the incidence of antimicrobial-resistant emerging pathogens, Clostridium difficile, and its associated risk factors in tertiary care setups of Pakistan. This cross-sectional prospective study was conducted from January 2019 to December 2020, to determine the prevalence and antimicrobial resistance patterns of C. difficile strains isolated from 450 stool specimens of patients suffering from diarrhea hospitalized in tertiary care hospitals in Peshawar, Pakistan. The stool samples of the patients were processed for culture and detection of toxin A and toxin B by enzyme-linked immunosorbent assay (ELISA) and tpi PCR. The drug sensitivity test was performed for antibiotics including ampicillin, cefixime, cefepime, amoxicillin, nalidixic acid, sulpha/TMP (SXT), chloramphenicol, metronidazole, vancomycin, ciprofloxacin, levofloxacin, and imipenem. Of 450 stool specimens, 108 (24%) were positive for C. difficile by stool culture, whereas 115 (25.5%) were only positive for C. difficile toxins based on ELISA and PCR (128 (28.6%). Of 108, 90.7% (n = 98) isolates were resistant to one antibiotic, and 90 (83.4%) were resistant to three or more antimicrobials. The highest resistance rates were found against penicillin (83.3%) followed by amoxicillin (70%), nalidixic acid (61%), and metronidazole (38%), and the lowest resistance was found against vancomycin (6.4%) and imipenem (3.7%). CDI was statistically significantly correlated with increased age, use of antibiotics, abdominal surgeries, use of proton pump inhibitors and H2a, and presence of comorbidities. The high frequency of C. difficile in Peshawar, Pakistan, indicates that CDI is an important nosocomial infection in different hospitals. The results will be helpful for clinicians to redesign control and therapeutic strategies in hospitals.
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Affiliation(s)
- Murad A. Mubaraki
- Clinical Laboratory Sciences Department, College of Applied Medical Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Mubbashir Hussain
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Faaiz Ul Hassan
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | | | - Fozia Fozia
- Department of Biochemistry, KMU Institute of Dental Sciences, Kohat 26000, Pakistan
| | - Ijaz Ahmad
- Department of Chemistry, Kohat University of Science and Technology, Kohat, Pakistan
| | - Fatima Bibi
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan
| | - Samia Sultan
- Department of Zoology, Abdul Wali Khan University, Mardan, Pakistan
| | - Ziaullah Zialluh
- College of Professional Studies, Northeastern University, Boston, MA, USA
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Fachi JL, Vinolo MAR, Colonna M. Reviewing the Clostridioides difficile Mouse Model: Insights into Infection Mechanisms. Microorganisms 2024; 12:273. [PMID: 38399676 PMCID: PMC10891951 DOI: 10.3390/microorganisms12020273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/16/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Clostridioides difficile is an anaerobic, spore-forming bacterium associated with intestinal infection, manifesting a broad spectrum of gastrointestinal symptoms, ranging from mild diarrhea to severe colitis. A primary risk factor for the development of C. difficile infection (CDI) is antibiotic exposure. Elderly and immunocompromised individuals are particularly vulnerable to CDI. A pivotal aspect for comprehending the complexities of this infection relies on the utilization of experimental models that mimic human CDI transmission, pathogenesis, and progression. These models offer invaluable insights into host-pathogen interactions and disease dynamics, and serve as essential tools for testing potential therapeutic approaches. In this review, we examine the animal model for CDI and delineate the stages of infection, with a specific focus on mice. Our objective is to offer an updated description of experimental models employed in the study of CDI, emphasizing both their strengths and limitations.
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Affiliation(s)
- José L. Fachi
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Marco A. R. Vinolo
- Department of Genetics and Evolution, Microbiology and Immunology, Institute of Biology, University of Campinas, Campinas 13083-862, SP, Brazil;
| | - Marco Colonna
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA;
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Spigaglia P, Mastrantonio P, Barbanti F. Antibiotic Resistances of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:169-198. [PMID: 38175476 DOI: 10.1007/978-3-031-42108-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The rapid evolution of antibiotic resistance in Clostridioides difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are a matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances, and most of the epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways or biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Paola Mastrantonio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Fabrizio Barbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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Spigaglia P, Barbanti F, Faccini S, Vescovi M, Criscuolo EM, Ceruti R, Gaspano C, Rosignoli C. Clostridioides difficile in Pigs and Dairy Cattle in Northern Italy: Prevalence, Characterization and Comparison between Animal and Human Strains. Microorganisms 2023; 11:1738. [PMID: 37512910 PMCID: PMC10383565 DOI: 10.3390/microorganisms11071738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
It has been observed that novel strains of Clostridioides difficile can rapidly emerge and move between animal and human hosts. The aim of this study was to investigate the prevalence of C. difficile in pigs and dairy cattle in northern Italy and to characterize and compare C. difficile animal strains with those from patients from the same geographical area. The C. difficile strains were isolated from animals from farms and slaughterhouses (cross-sectional studies) and from neonatal animals with enteric disorders in routine diagnostic investigations (passive surveillance). Samples positive for C. difficile were found in 87% of the pig farms and in 40% of the cattle farms involved in the cross-sectional studies, with a 20% prevalence among suckling piglets and 6.7% prevalence in neonatal calves, with no significant difference between animals with and without diarrheal symptoms. The prevalence of C. difficile in older animal categories was significantly lower. This result suggests that young age is an important risk factor for C. difficile colonization. In cross-sectional studies at slaughterhouses, in both the heavy pigs and dairy cows examined, only 2% of the intestinal content samples were positive for C. difficile and no contamination was found on the surface of the carcasses. Considering passive surveillance, the prevalence rates of positive samples were 29% in piglets and 1.4% in calves. Overall, 267 strains of animal origin and 97 from humans were collected. In total, 39 ribotypes (RTs) were identified, with RT 078 and RT 018 being predominant among animals and humans, respectively. Several RTs overlapped between animals and patients. In particular, RT 569 was identified as an emergent type in our country. Resistance to erythromycin and moxifloxacin was widely diffused among C. difficile strains, regardless of origin. This study supports C. difficile as a pathogen of one-health importance and highlights the need for a collaborative approach between physicians and veterinarians to control and prevent infections that are able to cross species and geographical barriers.
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Affiliation(s)
- Patrizia Spigaglia
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Fabrizio Barbanti
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Silvia Faccini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Sede Territoriale di Mantova, 46100 Mantova, Italy
| | - Mariella Vescovi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Sede Territoriale di Mantova, 46100 Mantova, Italy
| | | | - Rossella Ceruti
- Servizio di Medicina di Laboratorio, ASST Ospedale "Carlo Poma", 46100 Mantova, Italy
| | - Clara Gaspano
- Servizio di Medicina di Laboratorio, ASST Ospedale "Carlo Poma", 46100 Mantova, Italy
| | - Carlo Rosignoli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Sede Territoriale di Mantova, 46100 Mantova, Italy
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High Prevalence of Clostridioides difficile Ribotype 176 in the University Hospital in Kosice. Pathogens 2023; 12:pathogens12030430. [PMID: 36986352 PMCID: PMC10055383 DOI: 10.3390/pathogens12030430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/03/2023] [Accepted: 03/04/2023] [Indexed: 03/11/2023] Open
Abstract
Dysbiosis of the gut microbiota, caused by antibiotics, plays a key role in the establishment of Clostridioides difficile CD). Toxin-producing strains are involved in the pathogenesis of Clostridioides difficile infection (CDI), one of the most common hospital-acquired infections. We cultured a total of 84 C. difficile isolates from stool samples of patients hospitalized at Louis Pasteur University Hospital in Kosice, Slovakia, that were suspected of CDI and further characterized by molecular methods. The presence of genes encoding toxin A, toxin B, and binary toxin was assessed by toxin-specific PCR. CD ribotypes were detected using capillary-based electrophoresis ribotyping. A total of 96.4% of CD isolates carried genes encoding toxins A and B, and 54.8% of them were positive for the binary toxin. PCR ribotyping showed the presence of three major ribotypes: RT 176 (n = 40, 47.6%); RT 001 (n = 23, 27.4%); and RT 014 (n = 7, 8.3%). Ribotype 176 predominated among clinical CD isolates in our hospital. The proportion of RT 176 and RT 001 in four hospital departments with the highest incidence of CDI cases was very specific, pointing to local CDI outbreaks. Based on our data, previous use of antibiotics represents a significant risk factor for the development of CDI in patients over 65 years of age.
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Gargis AS, Karlsson M, Paulick AL, Anderson KF, Adamczyk M, Vlachos N, Kent AG, McAllister G, McKay SL, Halpin AL, Albrecht V, Campbell D, Korhonen LC, Elkins CA, Rasheed JK, Guh AY, McDonald LC, Lutgring JD. Reference Susceptibility Testing and Genomic Surveillance of Clostridioides difficile, United States, 2012-17. Clin Infect Dis 2023; 76:890-896. [PMID: 36208202 PMCID: PMC10839785 DOI: 10.1093/cid/ciac817] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/26/2022] [Accepted: 10/05/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Antimicrobial susceptibility testing (AST) is not routinely performed for Clostridioides difficile and data evaluating minimum inhibitory concentrations (MICs) are limited. We performed AST and whole genome sequencing (WGS) for 593 C. difficile isolates collected between 2012 and 2017 through the Centers for Disease Control and Prevention's Emerging Infections Program. METHODS MICs to 6 antimicrobial agents (ceftriaxone, clindamycin, meropenem, metronidazole, moxifloxacin, and vancomycin) were determined using the reference agar dilution method according to Clinical and Laboratory Standards Institute guidelines. Whole genome sequencing was performed on all isolates to detect the presence of genes or mutations previously associated with resistance. RESULTS Among all isolates, 98.5% displayed a vancomycin MIC ≤2 μg/mL and 97.3% displayed a metronidazole MIC ≤2 μg/mL. Ribotype 027 (RT027) isolates displayed higher vancomycin MICs (MIC50: 2 μg/mL; MIC90: 2 μg/mL) than non-RT027 isolates (MIC50: 0.5 μg/mL; MIC90: 1 μg/mL) (P < .01). No vanA/B genes were detected. RT027 isolates also showed higher MICs to clindamycin and moxifloxacin and were more likely to harbor associated resistance genes or mutations. CONCLUSIONS Elevated MICs to antibiotics used for treatment of C. difficile infection were rare, and there was no increase in MICs over time. The lack of vanA/B genes or mutations consistently associated with elevated vancomycin MICs suggests there are multifactorial mechanisms of resistance. Ongoing surveillance of C. difficile using reference AST and WGS to monitor MIC trends and the presence of antibiotic resistance mechanisms is essential.
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Affiliation(s)
- Amy S Gargis
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Maria Karlsson
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Goldbelt C6, LLC, Chesapeake, Virginia, USA
| | - Ashley L Paulick
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Karen F Anderson
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Michelle Adamczyk
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nicholas Vlachos
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alyssa G Kent
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Gillian McAllister
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Susannah L McKay
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison L Halpin
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Valerie Albrecht
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Davina Campbell
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lauren C Korhonen
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Christopher A Elkins
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J Kamile Rasheed
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alice Y Guh
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - L Clifford McDonald
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joseph D Lutgring
- Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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9
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Stojanovic P, Harmanus C, Kuijper EJ. Community-onset Clostridioides difficile infection in south Serbia. Anaerobe 2023; 79:102669. [PMID: 36455757 DOI: 10.1016/j.anaerobe.2022.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/15/2022] [Accepted: 11/20/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Data from the past decade indicates that Clostridioides difficile infection (CDI) is not only a nosocomial infection but is also increasingly recognized as a disease in the community. OBJECTIVE We aimed to study community-onset (CO) CDI in the various age groups in south Serbia with its clinical characteristics, risk factors and microbiological characterization. METHODS The study group included 93 patients with CO-CDI (median age 62). The control group consisted of 186 patients with community-onset diarrhea and stool samples negative tested for CDI. RESULTS Of all CDI cases diagnosed with a community onset, 74.19% had a previous contact with a healthcare facility in the previous 12 weeks, but 34.40% have no record on hospitalization in the previous 12 months. Using a multivariate statistical regression model, the following risk factors for CO-CDI development were found; antacid usage (OR = 0.267, 95%C.I.:0.10-0.291, p < 0.01), chronic kidney disease (OR = 0.234, 95%C.I.:0.10-0.51, p < 0.01) and antibiotic use during the prior 2 months (OR = 0.061, 95%C.I.:0.02-0.17, p < 0.01), especially tetracycline's (OR = 0.146, 95% C.I.:0.07-0.22, p < 0.01) and cephalosporin's (OR = 0.110, 95%C.I.:0.14-0.42, p < 0.01). The most common ribotypes (RTs) detected in patients with CO-CDI were RT001 (32.3%) and RT027 (24.7%). All tested toxin producing C. difficile isolates were sensitive to metronidazole, vancomycin and tigecycline. A high rate of resistance to moxifloxacin (73.11%) and rifampicin (23.65%) was found. CONCLUSION Patients with CO-CDI had frequently contact with healthcare facility in the previous 12 weeks. Restriction of antacid usage and of high-risk antibiotics in the community may help reduce the incidence of CO-CDI.
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Affiliation(s)
- Predrag Stojanovic
- Faculty of Medicine, University of Niš, Zorana Đinđića 50, 18000, Niš, Serbia; Institute for Public Health Nis, Center of Microbiology, 18000, Niš, Serbia(1).
| | - Celine Harmanus
- Department of Medical Microbiology, Center for Infectious Diseases, National Expertise Center for Clostridioides difficile infections, National Institute of Public Health and the Environment, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, the Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Center for Infectious Diseases, National Expertise Center for Clostridioides difficile infections, National Institute of Public Health and the Environment, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, the Netherlands
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Dost I, Abdel-Glil M, Schmoock G, Menge C, Berens C, González-Santamarina B, Wiegand E, Neubauer H, Schwarz S, Seyboldt C. Clostridioides difficile in South American Camelids in Germany: First Insights into Molecular and Genetic Characteristics and Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:antibiotics12010086. [PMID: 36671289 PMCID: PMC9854998 DOI: 10.3390/antibiotics12010086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
Little is known about zoonotic pathogens and their antimicrobial resistance in South American camelids (SAC) in Germany including Clostridioides (C.) difficile. The aim of this study was to investigate prevalence, molecular characteristics and antimicrobial resistance of C. difficile in SAC. Composite SAC faecal samples were collected in 43 husbandries in Central Germany and cultured for C. difficile. Toxinotyping and ribotyping was done by PCR. Whole genome sequencing was performed with Illumina® Miseq™. The genomes were screened for antimicrobial resistance determinants. Genetic relatedness of the isolates was investigated using core genome multi locus sequence typing (cgMLST) and single nucleotide polymorphism analysis. Antimicrobial susceptibility testing was done using the Etest® method. Eight C. difficile isolates were recovered from seven farms. The isolates belonged to different PCR ribotypes. All isolates were toxinogenic. cgMLST revealed a cluster containing isolates recovered from different farms. Seven isolates showed similar resistance gene patterns. Different phenotypic resistance patterns were found. Agreement between phenotypic and genotypic resistance was identified only in some cases. Consequently, SAC may act as a reservoir for C. difficile. Thus, SAC may pose a risk regarding zoonotic transmission of toxinogenic, potentially human-pathogenic and resistant C. difficile isolates.
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Affiliation(s)
- Ines Dost
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
- Correspondence: ; Tel.: +49-3641-804-2488
| | - Mostafa Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Gernot Schmoock
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Christian Menge
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Christian Berens
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Belén González-Santamarina
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Elisabeth Wiegand
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
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11
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Fecal pharmacokinetics/pharmacodynamics characteristics of fidaxomicin and vancomycin against Clostridioides difficile infection elucidated by in vivo feces-based infectious evaluation models. Clin Microbiol Infect 2022; 29:616-622. [PMID: 36574949 DOI: 10.1016/j.cmi.2022.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 11/26/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022]
Abstract
OBJECTIVES The pharmacokinetics (PK)/pharmacodynamics (PD; PK/PD) characteristics of fidaxomicin (FDX) and vancomycin (VCM) against Clostridioides difficile infection (CDI) are yet to be elucidated because of the lack of an established PK/PD analysis method for intestinal infections and unabsorbed oral drugs. Here, we developed a feces-based PK/PD analysis method and determined the fecal PK/PD index, with target values of FDX and VCM against CDI. METHODS The antimicrobial susceptibility, time-kill curves, and post-antibiotic effects (PAEs) of FDX and VCM against C. difficile were determined in vitro. The optimal fecal PK/PD indices, with target values, were determined from the results of PK and PD studies involving 5-week-old female C57BL/6J mice infected with C. difficile ATCC® 43255. The minimum inhibitory concentration (MIC) breakpoints for C. difficile were estimated based on clinical data concerning fecal antibiotic concentrations in patients with CDI. RESULTS FDX and VCM inhibited C. difficile growth via time-dependent antibacterial activity and exerted PAEs. In the CDI mouse model experiments, the changes in C. difficile load and clinical cures (72-hour survival rates and clinical sickness score grading) were most highly correlated with the ratio of area under the fecal drug concentration-time curve to MIC (AUC0→∞/MIC). The target AUC0→∞/MIC values of FDX and VCM for 3 log10 reduction in C. difficile load was 13,173 and 8,308, respectively. The MIC breakpoints of FDX and VCM for C. difficile was estimated to be 1.0 and 2.0 μg/mL, respectively. CONCLUSIONS The developed in vivo feces-based PK/PD analysis method elucidated the optimal fecal PK/PD index, with target values of FDX and VCM against CDI.
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12
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Make It Less difficile: Understanding Genetic Evolution and Global Spread of Clostridioides difficile. Genes (Basel) 2022; 13:genes13122200. [PMID: 36553467 PMCID: PMC9778335 DOI: 10.3390/genes13122200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection can lead to fulminant colitis associated with shock, hypotension, megacolon, and, in severe cases, death. It is therefore of the utmost urgency to fully characterize this pathogen and better understand its spread, in order to reduce infection rates and improve therapy success. This review aims to provide a state-of-the-art overview of the genetic variation of C. difficile, with particular regard to pathogenic genes and the correlation with clinical issues of its infection. We also summarize the current typing techniques and, based on them, the global distribution of the most common ribotypes. Finally, we discuss genomic surveillance actions and new genetic engineering strategies as future perspectives to make it less difficile.
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13
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Li Y, Liao J, Jian Z, Li H, Chen X, Liu Q, Liu P, Wang Z, Liu X, Yan Q, Liu W. Molecular epidemiology and clinical characteristics of
Clostridioides difficile
infection in patients with inflammatory bowel disease from a teaching hospital. J Clin Lab Anal 2022; 36:e24773. [DOI: 10.1002/jcla.24773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/03/2022] [Accepted: 11/04/2022] [Indexed: 11/21/2022] Open
Affiliation(s)
- Yan‐ming Li
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Jing‐zhong Liao
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Zi‐juan Jian
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Hong‐ling Li
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Xia Chen
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Qing‐xia Liu
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Pei‐lin Liu
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Zhi‐qian Wang
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Xuan Liu
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
- National Clinical Research Center for Geriatric Disorders Xiangya Hospital Changsha China
| | - Wen‐en Liu
- Department of Clinical Laboratory, Xiangya Hospital Central South University Changsha China
- National Clinical Research Center for Geriatric Disorders Xiangya Hospital Changsha China
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14
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Giuliani A, Lerco S, Manani SM, Marcello M, Tantillo I, Nicolin R, Ronco C, Zanella M. Clostridium difficile colitis and peritoneal dialysis associated peritonitis: ‘Difficile’ treatment considerations. ARCH ESP UROL 2022; 43:182-185. [PMID: 36350040 DOI: 10.1177/08968608221132431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Peritoneal dialysis (PD) associated peritonitis is the leading cause of PD discontinuation and haemodialysis transfer. Current guidelines strongly recommend prompt initiation of empiric broad-spectrum intraperitoneal antibiotics, with suspected peritonitis. Clostridium difficile colitis is one of the most common healthcare-associated infections, with increased morbidity and mortality among end-stage kidney disease patients. Clinical presentation is mainly characterised by diarrhoea of varying severity, which may eventually evolve into toxic megacolon and paralytic ileus. However, PD patients with Clostridium difficile infection (CDI) may also have colitis-triggered peritonitis, presenting challenging scenario for antibiotic treatment strategy, since broad-spectrum antibiotics against peritonitis may worsen CDI-related colitis, while inappropriate or discontinuation of antibiotic therapy may worsen peritonitis. Currently, guidelines on peritonitis management do not include such challenging clinical situations, although increasingly common. We herein describe a case of a patient, with culture-negative PD associated peritonitis and CDI, presenting with diarrhoea, abdominal pain and cloudy effluent.
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Affiliation(s)
- Anna Giuliani
- Department of Nephrology Dialysis and Transplantation, San Bortolo Hospital, Vicenza, Italy
- International Renal Research Institute Vicenza (IRRIV), Italy
| | - Silvia Lerco
- International Renal Research Institute Vicenza (IRRIV), Italy
- Department of Medicine, Nephrology, Dialysis and Transplantation Unit, University of Padova, Italy
| | - Sabrina Milan Manani
- Department of Nephrology Dialysis and Transplantation, San Bortolo Hospital, Vicenza, Italy
- International Renal Research Institute Vicenza (IRRIV), Italy
| | - Matteo Marcello
- International Renal Research Institute Vicenza (IRRIV), Italy
- Libera Università Vita e Salute San Raffaele, Milano, Italy
| | - Ilaria Tantillo
- Department of Nephrology Dialysis and Transplantation, San Bortolo Hospital, Vicenza, Italy
- International Renal Research Institute Vicenza (IRRIV), Italy
| | - Roberto Nicolin
- Department of Infectious Diseases, St. Bortolo Hospital, Vicenza, Italy
| | - Claudio Ronco
- International Renal Research Institute Vicenza (IRRIV), Italy
- Department of Medicine (DIMED), University of Padova, Italy
| | - Monica Zanella
- Department of Nephrology Dialysis and Transplantation, San Bortolo Hospital, Vicenza, Italy
- International Renal Research Institute Vicenza (IRRIV), Italy
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15
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Smits WK, Harmanus C, Sanders IMJG, Bry L, Blackwell GA, Ducarmon QR, de Oliveira Ferreira E, Kuijper EJ. Sequence-Based Identification of Metronidazole-Resistant Clostridioides difficile Isolates. Emerg Infect Dis 2022; 28:2308-2311. [PMID: 36286226 PMCID: PMC9622256 DOI: 10.3201/eid2811.220615] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2024] Open
Abstract
The plasmid pCD-METRO confers metronidazole resistance in Clostridioides difficile. We showed high sequence similarity among pCD-METRO plasmids from different isolates and identified pCD-METRO and associated metronidazole-resistant isolates in clinical and veterinary reservoirs in the Americas. We recommend using PCR or genomic assays to detect pCD-METRO in metronidazole-resistant C. difficile.
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16
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Oliver MB, Vaughn BP. Fidaxomicin Use in the Pediatric Population with Clostridioides difficile. Clin Pharmacol 2022; 14:91-98. [PMID: 36177387 PMCID: PMC9514785 DOI: 10.2147/cpaa.s273318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 09/15/2022] [Indexed: 11/23/2022] Open
Abstract
Clostridioides difficile infection (CDI) remains a devastating infection both in hospital settings and in the community. While a number of antibiotics have anti-C. difficile activity, fidaxomicin is unique as a minimally absorbed antibiotic with narrow spectrum of activity. These features make it an appealing option for pediatric CDI to balance safety and efficacy. The purpose of this structured review was to outline the clinical evidence for safety and efficacy of fidaxomicin for pediatric CDI. A structured literature search was performed to identify relevant clinical data. Fidaxomicin is similarly effective to oral vancomycin with a lower rate of recurrent CDI. There were no serious safety signals reported with fidaxomicin. In conclusion, fidaxomicin is a safe and effective treatment option for pediatric CDI.
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Affiliation(s)
- Meredith B Oliver
- M Health Fairview, Masonic Children’s Hospital, Minneapolis, MN, USA
| | - Byron P Vaughn
- Division of Gastroenterology, Hepatology, and Nutrition, University of Minnesota, Minneapolis, MN, USA
- Correspondence: Byron P Vaughn, Department of Medicine, 1-205 Philips Wangensteen Building, 516 Delaware Street S.E, MMC36, Minneapolis, MN, 55455, Tel +1 612 625 8999, Fax +1 612 625 5620, Email
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17
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Antibiotic Resistance Profile of RT 027/176 Versus Other Clostridioides difficile Isolates in Silesia, Southern Poland. Pathogens 2022; 11:pathogens11080949. [PMID: 36015069 PMCID: PMC9416131 DOI: 10.3390/pathogens11080949] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/12/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Clostridioides difficile is an important health care-associated pathogen. The aim of this study was to analyze the antibiotic susceptibility of C. difficile isolates from feces of patients from 13 hospitals in Silesia, Poland. The incidence of CDI per 100.000 people in Silesia in 2018−2019 was higher than the average in Poland (39.3−38.7 vs. 30.2−29.5, respectively). The incidence doubled from 26.4 in 2020 to 55.1 in 2021. Two hundred and thirty stool samples tested positive for GDH (glutamate dehydrogenase) and toxins were cultured anaerobically for C. difficile. The isolates were characterized, typed, and tested for susceptibility to 11 antibiotics by E-test (EUCAST, 2021). The genes of toxins A/B and binary were detected by mPCR. Of 215 isolates, 166 (77.2%) were classified as RT 027 and 6 (2.8%) as related RT 176. Resistance to ciprofloxacin (96.7%), moxifloxacin (79.1%), imipenem (78.1%), penicillin (67%), and rifampicin (40.5%) was found. The ermB gene was detected in 79 (36.7%) strains. Multidrug resistance (MDR) was confirmed in 50 (23.3%) strains of RT 027 (94%). We concluded that a high prevalence of MDR among hypervirulent RT 027/176 C. difficile was found in the Silesian region of Poland, emphasizing the need to enhance regional infection control on CDI and antibiotic stewardships.
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Abdrabou AMM, Bischoff M, Mellmann A, von Müller L, Margardt L, Gärtner BC, Berger FK, Haase G, Häfner H, Hoffmann R, Simon V, Stappmanns H, Hischebeth GT, Büchler C, Rößler S, Hochauf-Stange K, Pfeffer K, MacKenzie C, Kunz C, Alsalameh R, Dziobaka J, le Chapot VS, Sanabria E, Hogardt M, Komp J, Imirzalioglu C, Schmiedel J, Pararas M, Sommer F, Groß U, Bohne W, Kekulé AS, Dagwadordsch U, Löffler B, Rödel J, Walker SV, Tobys D, Weikert-Asbeck S, Hauswaldt S, Kaasch AJ, Zautner AE, Joß N, Siegel E, Kehr K, Schaumburg F, Schoeler S, Hamprecht A, Hellkamp J, Hagemann JB, Kubis J, Hering S, Warnke P. Implementation of a Clostridioides difficile sentinel surveillance system in Germany: First insights for 2019–2021. Anaerobe 2022; 77:102548. [DOI: 10.1016/j.anaerobe.2022.102548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 03/08/2022] [Accepted: 03/14/2022] [Indexed: 11/01/2022]
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19
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Xu T, Zhou F, Wang L, Wu S, Huang H. Metronidazole-Resistant Clostridioides difficile: Genomic and Transcriptomic Traits Acquired under In vitro Metronidazole Induction. Int J Antimicrob Agents 2022; 59:106570. [DOI: 10.1016/j.ijantimicag.2022.106570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/02/2022] [Accepted: 03/06/2022] [Indexed: 11/05/2022]
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20
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Perumalsamy S, Lim SC, Riley TV. Clostridioides (Clostridium) difficile isolated from paediatric patients in Western Australia 2019-2020. Pathology 2022; 54:460-465. [PMID: 35125203 DOI: 10.1016/j.pathol.2021.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/09/2021] [Accepted: 10/17/2021] [Indexed: 11/17/2022]
Abstract
Less is understood about the epidemiology of Clostridioides difficile infection (CDI) in children compared to adults, and its impact is complicated by variations in the natural development of infection in paediatric patients. The interplay of rising CDI incidence in hospitalised paediatric patients, emergence of hypervirulent strains and community associated CDI (CA-CDI) in the past decade is a potential threat in both hospital and community settings. Research in Australia regarding paediatric CDI is limited. Here, we report the molecular characterisation of C. difficile isolated from paediatric patients at a tertiary hospital in Perth, Western Australia. A total of 427 stool samples was collected from patients aged from <1 to 17 years being investigated for diarrhoea from July 2019 to June 2020. Stool specimens were cultured and isolates of C. difficile characterised by ribotyping and toxin gene profiling. Clostridioides difficile was recovered from 84/427 (19.7%) samples tested. The most prevalent PCR ribotypes (RTs) were RT 002 (12.4%), a toxigenic strain, and RT 009 (15.7%), a non-toxigenic strain. Interestingly, C. difficile RT 078 and RT 017, strains that are not endemic in Australia, were isolated from a 1- and 4-year-old child, respectively. Clostridioides difficile RT 106, a strain of emerging importance in Australia, was recovered from two cases (5.3%). Resistance to metronidazole, fidaxomicin, amoxicillin, rifaximin and meropenem was not detected, however, 45 isolates (50.6%) showed resistance to at least one agent, and multidrug resistance was observed in 13.3% of the resistant isolates (6/45). This study provides a baseline for future surveillance of paediatric CDI in Australia. Given that young children can be asymptomatically colonised with toxigenic C. difficile strains, they represent a potential reservoir of strains causing CDI in adults.
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Affiliation(s)
- Sicilia Perumalsamy
- The University of Western Australia, School of Biomedical Sciences, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
| | - Su Chen Lim
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Thomas V Riley
- The University of Western Australia, School of Biomedical Sciences, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia; PathWest Laboratory Medicine, Department of Microbiology, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia.
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21
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Imwattana K, Rodríguez C, Riley TV, Knight DR. A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile. Microb Genom 2021; 7. [PMID: 34793295 PMCID: PMC8743556 DOI: 10.1099/mgen.0.000696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few ‘epidemic’ strains in specific geographical regions. Here, through detailed analysis of 10 330 publicly-available C. difficile genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in C. difficile. Of the 10 330 C. difficile genomes, 4532 (43.9 %) in 89 STs across clades 1–5 carried at least one genotypic AMR determinant, with 901 genomes (8.7 %) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades. C. difficile from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (P<0.0001). Based on the phylogenetic clade, AMR prevalence was higher in clades 2 (84.3 %), 4 (81.5 %) and 5 (64.8 %) compared to other clades (collectively 26.9 %) (P<0.0001). MDR prevalence was highest in clade 4 (61.6 %) which was over three times higher than in clade 2, the clade with the second-highest MDR prevalence (18.3 %). There was a strong association between specific AMR determinants and three major epidemic C. difficile STs: ST1 (clade 2) with fluoroquinolone resistance (mainly T82I substitution in GyrA) (P<0.0001), ST11 (clade 5) with tetracycline resistance (various tet-family genes) (P<0.0001) and ST37 (clade 4) with macrolide-lincosamide-streptogramin B (MLSB) resistance (mainly ermB) (P<0.0001) and MDR (P<0.0001). A novel and previously overlooked tetM-positive transposon designated Tn6944 was identified, predominantly among clade 2 strains. This study provides a comprehensive review of AMR in the global C. difficile population which may aid in the early detection of drug-resistant C. difficile strains, and prevention of their dissemination worldwide.
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Affiliation(s)
- Korakrit Imwattana
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V Riley
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia
| | - Daniel R Knight
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia
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22
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Harrison MA, Kaur H, Wren BW, Dawson LF. Production of p-cresol by Decarboxylation of p-HPA by All Five Lineages of Clostridioides difficile Provides a Growth Advantage. Front Cell Infect Microbiol 2021; 11:757599. [PMID: 34778108 PMCID: PMC8588808 DOI: 10.3389/fcimb.2021.757599] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/05/2021] [Indexed: 11/19/2022] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and is capable of causing severe symptoms, such as pseudomembranous colitis and toxic megacolon. An unusual feature of C. difficile is the distinctive production of high levels of the antimicrobial compound para-cresol. p-Cresol production provides C. difficile with a competitive colonization advantage over gut commensal species, in particular, Gram-negative species. p-Cresol is produced by the conversion of para-hydroxyphenylacetic acid (p-HPA) via the actions of HpdBCA decarboxylase coded by the hpdBCA operon. Host cells and certain bacterial species produce p-HPA; however, the effects of p-HPA on the viability of C. difficile and other gut microbiota are unknown. Here we show that representative strains from all five C. difficile clades are able to produce p-cresol by two distinct mechanisms: (i) via fermentation of p-tyrosine and (ii) via uptake and turnover of exogenous p-HPA. We observed strain-specific differences in p-cresol production, resulting from differential efficiency of p-tyrosine fermentation; representatives of clade 3 (CD305) and clade 5 (M120) produced the highest levels of p-cresol via tyrosine metabolism, whereas the toxin A-/B+ isolate from clade 4 (M68) produced the lowest level of p-cresol. All five lineages share at least 97.3% homology across the hpdBCA operon, responsible for decarboxylation of p-HPA to p-cresol, suggesting that the limiting step in p-cresol production may result from tyrosine to p-HPA conversion. We identified that elevated intracellular p-HPA, modulated indirectly via CodY, controls p-cresol production via inducing the expression of HpdBCA decarboxylase ubiquitously in C. difficile populations. Efficient turnover of p-HPA is advantageous to C. difficile as p-HPA has a deleterious effect on the growth of C. difficile and other representative Gram-negative gut bacteria, transduced potentially by the disruption of membrane permeability and release of intracellular phosphate. This study provides insights into the importance of HpdBCA decarboxylase in C. difficile pathogenesis, both in terms of p-cresol production and detoxification of p-HPA, highlighting its importance to cell survival and as a highly specific therapeutic target for the inhibition of p-cresol production across C. difficile species.
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Affiliation(s)
- Mark A. Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Harparkash Kaur
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan W. Wren
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Lisa F. Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
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23
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Novakova E, Stofkova Z, Sadlonova V, Hleba L. Diagnostic Methods of Clostridioides difficile Infection and Clostridioides difficile Ribotypes in Studied Sample. Antibiotics (Basel) 2021; 10:antibiotics10091035. [PMID: 34572617 PMCID: PMC8466394 DOI: 10.3390/antibiotics10091035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/26/2021] [Accepted: 08/19/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Clostridioides (Clostridium) difficile is the most common nosocomial pathogen and antibiotic-related diarrhea in health-care facilities. Over the last few years, there was an increase in the incidence rate of C. difficile infection cases in Slovakia. In this study, the phenotypic (toxigenicity, antimicrobial susceptibility) and genotypic (PCR ribotypes, genes for binary toxins) patterns of C. difficile isolates from patients with CDI were analyzed, from July to August 2016, taken from hospitals in the Horne Povazie region of northern Slovakia. The aim of the study was also to identify hypervirulent strains (e.g., the presence of RT027 or RT176). METHODS The retrospective analysis of biological samples suspected of CDI were analyzed by GDH, anaerobic culture, enzyme immunoassay on toxins A/B, multiplex "real-time" PCR and PCR capillary-based electrophoresis ribotyping, and by MALDI TOF MS. RESULTS C. difficile isolates (n = 44) were identified by PCR ribotyping, which revealed five different ribotypes (RT001, 011, 017, 081, 176). The presence of hypervirulent RT027 was not identified. The C. difficile isolates (RT001, 011, 081, 176) were susceptible to metronidazole and vancomycin. One isolate RT017 had reduced susceptibility to vancomycin. A statistically significant difference between the most prevalent PCR ribotypes, RT001 and RT176, regarding variables such as albumin, CRP, creatinine, the length of hospitalization (p = 0.175), and glomerular filtration (p = 0.05) was not found. CONCLUSION The results of PCR capillary-based electrophoresis ribotyping in the studied samples showed a high prevalence of RT176 and 001.
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Affiliation(s)
- Elena Novakova
- Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4A, 03601 Martin, Slovakia; (E.N.); (V.S.)
| | - Zuzana Stofkova
- Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4A, 03601 Martin, Slovakia; (E.N.); (V.S.)
- Correspondence:
| | - Vladimira Sadlonova
- Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4A, 03601 Martin, Slovakia; (E.N.); (V.S.)
| | - Lukas Hleba
- Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, A. Hlinku 610/4, 94901 Nitra, Slovakia;
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24
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O’Grady K, Knight DR, Riley TV. Antimicrobial resistance in Clostridioides difficile. Eur J Clin Microbiol Infect Dis 2021; 40:2459-2478. [DOI: 10.1007/s10096-021-04311-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023]
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25
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The Integrity of Heme Is Essential for Reproducible Detection of Metronidazole-Resistant Clostridioides difficile by Agar Dilution Susceptibility Tests. J Clin Microbiol 2021; 59:e0058521. [PMID: 34132582 DOI: 10.1128/jcm.00585-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Metronidazole resistance in clinical Clostridioides difficile is often described as unstable, since resistant strains reportedly appear susceptible following freezer storage or brief passage. This has presented a conundrum for adopting susceptibility testing to accurately evaluate the connection between metronidazole resistance and decreased clinical efficacy of metronidazole in patients with C. difficile infections (CDIs). We discovered that supplementation of microbiological media with the metalloporphyrin heme is crucial for detection of metronidazole-resistant C. difficile using the agar dilution susceptibility testing method. Known metronidazole-resistant strains appeared susceptible to metronidazole in media lacking heme. Similarly, these resistant strains exhibited increased susceptibility to metronidazole when tested on heme-containing agars that were exposed to room light for more than 1 day, likely due to heme photodecomposition. In parallel experiments, resistance was reproducibly detected when heme-containing agars were either prepared and used on the same day or protected from light and then used on subsequent days. Notably, heme did not influence the susceptibilities of drug-susceptible strains that were of the same ribotype as the resistant strains. These findings firmly show that the consistent detection of metronidazole-resistant C. difficile is dependent upon heme and its protection from light. Studies are warranted to determine the extent to which this heme-associated metronidazole-resistant phenotype affects the clinical efficacy of metronidazole in CDI and the underlying genetic and biochemical mechanisms.
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Antimicrobial resistance progression in the United Kingdom: A temporal comparison of Clostridioides difficile antimicrobial susceptibilities. Anaerobe 2021; 70:102385. [PMID: 34048922 DOI: 10.1016/j.anaerobe.2021.102385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/29/2021] [Accepted: 05/17/2021] [Indexed: 01/31/2023]
Abstract
OBJECTIVES Clostridioides difficile (CD) is widely reported as one of the most prevalent multi-drug resistant (MDR) organisms. Assessment of temporally disparate isolate collections can give valuable epidemiological data to further the understanding of antimicrobial resistance progression. METHODS A collection of 75 CD isolates (1980-86) was characterised by PCR ribotyping, cell cytotoxicity assay and susceptibility testing with a panel of 16 antimicrobials and compared to a modern surveillance collection consisting of 416 UK isolates (2012-2016). Agar-incorporation was performed to ascertain susceptibility data for vancomycin, metronidazole, rifampicin, fidaxomicin, moxifloxacin, clindamycin, imipenem, chloramphenicol, tigecycline, linezolid, ciprofloxacin, piperacillin/tazobactam, ceftriaxone, amoxicillin, tetracycline and erythromycin. Genomes were obtained using Illumina HiSeq3000 sequencing and assembled using CLC Genomics Workbench. Resistance genes were identified using the Comprehensive Antibiotic Research Database's Resistance Gene Identifier and ResFinder3.0. RESULTS Twenty-six known and one previously unobserved ribotype (RT) were detected. RT015 and RT020 dominated; 21.3% and 17.3%, respectively. Three moxifloxacin resistant (16-32 mg/L) RT027 isolates were recovered, pre-dating the earliest reports of this phenotype/genotype. Phenotypic resistance was observed to moxifloxacin (9.3% of isolates), ciprofloxacin (100%), erythromycin (17.3%), tetracycline (9.3%), linezolid and chloramphenicol (4.0%). Phenotypic comparisons with modern strains revealed increasing minimum inhibitory concentrations (MIC), with MIC50 elevations of one doubling-dilution for the majority of compounds, excluding clindamycin and imipenem. Moxifloxacin MIC90 comparisons revealed a two doubling-dilution increase between temporal isolate collections. Historical genomes revealed twenty different resistance determinants, including ermB (8.0% of isolates), tetM (9.3%), cfr (5.3%) and gyrA substitution Thr-82→Ile (9.3%). Seventeen isolates (22.7%) were resistant to ≥3 compounds (MDR), demonstrating ten different combinations. Intra-RT diversity was observed. CONCLUSIONS Antibiotic resistance in CD has increased since the early 1980s, across the majority of classes. Moxifloxacin resistance determinants may pre-date its introduction.
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Wickramage I, Spigaglia P, Sun X. Mechanisms of antibiotic resistance of Clostridioides difficile. J Antimicrob Chemother 2021; 76:3077-3090. [PMID: 34297842 DOI: 10.1093/jac/dkab231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile (CD) is one of the top five urgent antibiotic resistance threats in USA. There is a worldwide increase in MDR of CD, with emergence of novel strains which are often more virulent and MDR. Antibiotic resistance in CD is constantly evolving with acquisition of novel resistance mechanisms, which can be transferred between different species of bacteria and among different CD strains present in the clinical setting, community, and environment. Therefore, understanding the antibiotic resistance mechanisms of CD is important to guide optimal antibiotic stewardship policies and to identify novel therapeutic targets to combat CD as well as other bacteria. Epidemiology of CD is driven by the evolution of antibiotic resistance. Prevalence of different CD strains and their characteristic resistomes show distinct global geographical patterns. Understanding epidemiologically driven and strain-specific characteristics of antibiotic resistance is important for effective epidemiological surveillance of antibiotic resistance and to curb the inter-strain and -species spread of the CD resistome. CD has developed resistance to antibiotics with diverse mechanisms such as drug alteration, modification of the antibiotic target site and extrusion of drugs via efflux pumps. In this review, we summarized the most recent advancements in the understanding of mechanisms of antibiotic resistance in CD and analysed the antibiotic resistance factors present in genomes of a few representative well known, epidemic and MDR CD strains found predominantly in different regions of the world.
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Affiliation(s)
- Ishani Wickramage
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Down Blvd, Tampa, FL 33612, USA
| | - Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Down Blvd, Tampa, FL 33612, USA
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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. Haem is crucial for medium-dependent metronidazole resistance in clinical isolates of Clostridioides difficile. J Antimicrob Chemother 2021; 76:1731-1740. [PMID: 33876817 PMCID: PMC8212768 DOI: 10.1093/jac/dkab097] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
Background Until recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Objectives To identify factors that contribute to plasmid-independent metronidazole resistance of C. difficile. Methods Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile using a combination of antimicrobial susceptibility testing on different solid agar media and WGS of selected isolates. Results We find that nearly all isolates demonstrate a haem-dependent increase in the MIC of metronidazole, which in some cases leads to isolates qualifying as resistant (MIC >2 mg/L). Moreover, we find an SNP in the haem-responsive gene hsmA, which defines a metronidazole-resistant lineage of PCR ribotype 010/MLST ST15 isolates that also includes pCD-METRO-containing strains. Conclusions Our data demonstrate that haem is crucial for medium-dependent metronidazole resistance in C. difficile.
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Affiliation(s)
- Ilse M Boekhoud
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Igor Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Céline Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Virginie Viprey
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - William Spittal
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Emma Clark
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Kerrie Davies
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Jane Freeman
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland.,National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
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Seth-Smith HMB, Biggel M, Roloff T, Hinic V, Bodmer T, Risch M, Casanova C, Widmer A, Sommerstein R, Marschall J, Tschudin-Sutter S, Egli A. Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile. Front Cell Infect Microbiol 2021; 11:681518. [PMID: 34141631 PMCID: PMC8204696 DOI: 10.3389/fcimb.2021.681518] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Clostridioides difficile causes nosocomial outbreaks which can lead to severe and even life-threatening colitis. Rapid molecular diagnostic tests allow the identification of toxin-producing, potentially hypervirulent strains, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for C. difficile.
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Affiliation(s)
- Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Tim Roloff
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Vladimira Hinic
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Thomas Bodmer
- Clinical Microbiology, Labormedizinisches Zentrum Dr Risch, Liebefeld, Switzerland
| | - Martin Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr Risch, Liebefeld, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andreas Widmer
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Rami Sommerstein
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.,Infectious Diseases, Hirslanden Central Switzerland, Lucerne, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland
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Imwattana K, Putsathit P, Knight DR, Kiratisin P, Riley TV. Molecular Characterization of, and Antimicrobial Resistance in, Clostridioides difficile from Thailand, 2017-2018. Microb Drug Resist 2021; 27:1505-1512. [PMID: 33956520 DOI: 10.1089/mdr.2020.0603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI). Many antimicrobials, such as fluoroquinolones, have been associated with outbreaks of CDI globally. This study characterized AMR among clinical C. difficile strains in Thailand, where antimicrobial use remains inadequately regulated. Stool samples were screened for tcdB and positives were cultured. C. difficile isolates were characterized by toxin profiling and PCR ribotyping. Antimicrobial susceptibility testing was performed by agar incorporation, and whole-genome sequencing and AMR genotyping were performed on a subset of strains. There were 321 C. difficile strains isolated from 326 stool samples. The most common toxigenic ribotype (RT) was RT 017 (18%), followed by RTs 014 (12%) and 020 (7%). Resistance to clindamycin, erythromycin, moxifloxacin, and rifaximin was common, especially among RT 017 strains. AMR genotyping revealed a strong correlation between resistance genotype and phenotype for moxifloxacin and rifaximin. The presence of erm-class genes was associated with high-level clindamycin and erythromycin resistance. Point substitutions in the penicillin-binding proteins were not sufficient to confer meropenem resistance, but a Y721S substitution in PBP3 was associated with a 4.37-fold increase in meropenem minimal inhibitory concentration. No resistance to metronidazole, vancomycin, or fidaxomicin was observed.
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Affiliation(s)
- Korakrit Imwattana
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia.,Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Papanin Putsathit
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Daniel R Knight
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia
| | | | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia
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Molecular epidemiology and antimicrobial resistance of Clostridioides difficile in Germany, 2014-2019. Int J Med Microbiol 2021; 311:151507. [PMID: 33915347 DOI: 10.1016/j.ijmm.2021.151507] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 03/12/2021] [Accepted: 04/15/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile is a Gram positive spore-forming rod and mainly responsible for nosocomial diarrhea in developed nations. Molecular and antimicrobial surveillance is important for monitoring the strain composition including genotypes of high epidemiological importance such as ribotype 027 (RT027) and corresponding resistance patterns. 1535 isolates obtained from samples sent between 2014 and 2019 to the German National Reference Center (NRC) for diagnostic reasons (NRC strain set), and 1143 isolates from a Tertiary Care University Center in Saarland, Germany (non-NRC strain set), were evaluated using antibiotic susceptibility testing and ribotyping. In the NRC strain set, RT027 overtook RT001, the main RT found in the preceding studies, and dominated with 36.2%, followed by RT001 (13.3%), and RT014 (8.5%). Of note, since 2016 a constant decrease of RT027 could be noticed. In the non-NRC strain set a large strain diversity was present with RT014 (18%) and RT001 (8.9%) being most prevalent. In NRC samples, resistance towards metronidazole, vancomycin, moxifloxacin, clarithromycin and rifampicin was 2.7%, 0%, 57.1%, 53.2% and 19.2%, respectively. Metronidazole resistance was almost exclusively found in RT027 isolates. Rifampicin resistance was also observed predominantly in isolates of RT027, constituting an almost four-fold increase, when compared to preceeding studies in this region. In conclusion these data demonstrate that RT027 is a driver for rifampicin and metronidazole resistance, underlining the importance of continuous surveillance efforts.
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Global Landscape of Clostridioides Difficile Phylogeography, Antibiotic Susceptibility, and Toxin Polymorphisms by Post-Hoc Whole-Genome Sequencing from the MODIFY I/II Studies. Infect Dis Ther 2021; 10:853-870. [PMID: 33751421 PMCID: PMC8116447 DOI: 10.1007/s40121-021-00426-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/26/2021] [Indexed: 12/31/2022] Open
Abstract
INTRODUCTION Clostridioides (Clostridium) difficile infection, the leading cause of healthcare-associated diarrhea, represents a significant burden on global healthcare systems. Despite being a global issue, information on C. difficile from a global perspective is lacking. The aim of this study is to model the global phylogeography of clinical C. difficile. METHODS Using samples collected from the MODIFY I and II studies (NCT01241552, NCT01513239), we performed whole-genome sequencing of 1501 clinical isolates including 37 novel sequence types (STs), representing the largest worldwide collection to date. RESULTS Our data showed ribotypes, multi-locus sequence typing clades, and whole-genome phylogeny were in good accordance. The clinical C. difficile genome was found to be more conserved than previously reported (61% core genes), and modest recombination rates of 1.4-5.0 were observed across clades. We observed a significant continent distribution preference among five C. difficile clades (Benjamini-Hochberg corrected Fisher's exact test P < 0.01); moreover, weak association between geographic and genetic distance among ribotypes suggested sources beyond healthcare-related transmission. Markedly different trends of antibiotic susceptibility among lineages and regions were identified, and three novel mutations (in pyridoxamine 5'-phosphate oxidase family protein: Tyr130Ser, Tyr130Cys, and a promoter SNP) associated with metronidazole-reduced susceptibility were discovered on a nim-related gene and its promotor by genome-wide association study. Toxin gene polymorphisms were shown to vary within and between prevalent ribotypes, and novel severe mutations were found on the tcdC toxin regulator protein. CONCLUSION Our systematic characterization of a global set of clinical trial C. difficile isolates from infected individuals demonstrated the complexity of the genetic makeup of this pathogenic organism. The geographic variability of clades, variability in toxin genes, and mutations associated with antibiotic susceptibility indicate a highly complex interaction of C. difficile between host and environment. This dataset will provide a useful resource for validation of findings and future research of C. difficile.
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Bjöersdorff OG, Lindberg S, Kiil K, Persson S, Guardabassi L, Damborg P. Dogs are carriers of Clostridioides difficile lineages associated with human community-acquired infections. Anaerobe 2021; 67:102317. [PMID: 33418077 DOI: 10.1016/j.anaerobe.2020.102317] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/26/2020] [Indexed: 12/19/2022]
Abstract
There is an increasing concern about the role of animals as reservoirs of Clostridioides difficile. In this study, we investigated prevalence, antimicrobial resistance and zoonotic potential of C. difficile in dogs. Two-hundred and twenty-five dog faecal deposits were collected from trashcans in nine public gardens. C. difficile was isolated using selective plating and enrichment culture, identified by MALDI-TOF, tested for susceptibility to seven antibiotics by E-test, and sequenced on an Illumina NextSeq platform. Genome sequences were analysed to determine multilocus sequence types and resistance and toxin gene profiles. Zoonotic potential was assessed by measuring genetic variations of core genome (cg)MLST types between canine isolates and 216 temporally and spatially related human clinical isolates from a national database. C. difficile was isolated from 11 samples (4.9%). Seven isolates were toxigenic (tcdA+, tcdB+, cdtA/B-) and belonged to the sequence types ST2, ST6, ST10 and ST42. The four non-toxigenic isolates were assigned to ST15, ST26 and one novel ST. ST2, corresponding to PCR ribotype RT014/020, was the dominating lineage (n = 4) and, together with ST26 and ST42 isolates, showed close resemblance to human isolates, i.e. 2-5 allelic differences among the 1999 genes analysed by cgMLST. Three non-toxigenic isolates displayed resistance to clindamycin, erythromycin and tetracycline mediated by erm(B) and tet(M). Resistance to metronidazole, moxifloxacine, rifampicin or vancomycin was not detected. In conclusion, a small proportion of faecal deposits contained toxigenic C. difficile such as ST2 (RT014/020), which is a major cause of community-acquired infections. Our finding suggests that pathogenic strains can be exchanged between dogs and humans.
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Affiliation(s)
- Olivia Graaf Bjöersdorff
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sanna Lindberg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Søren Persson
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark.
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Wolf J, Kalocsai K, Fortuny C, Lazar S, Bosis S, Korczowski B, Petit A, Bradford D, Croos-Dabrera R, Incera E, Melis J, van Maanen R. Safety and Efficacy of Fidaxomicin and Vancomycin in Children and Adolescents with Clostridioides (Clostridium) difficile Infection: A Phase 3, Multicenter, Randomized, Single-blind Clinical Trial (SUNSHINE). Clin Infect Dis 2020; 71:2581-2588. [PMID: 31773143 PMCID: PMC7744996 DOI: 10.1093/cid/ciz1149] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 11/26/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Fidaxomicin, a narrow-spectrum antibiotic approved for Clostridioides (Clostridium) difficile infection (CDI) in adults, is associated with lower rates of recurrence than vancomycin; however, pediatric data are limited. This multicenter, investigator-blind, phase 3, parallel-group trial assessed the safety and efficacy of fidaxomicin in children. METHODS Patients aged <18 years with confirmed CDI were randomized 2:1 to 10 days of treatment with fidaxomicin (suspension or tablets, twice daily) or vancomycin (suspension or tablets, 4 times daily). Safety assessments included treatment-emergent adverse events. The primary efficacy end point was confirmed clinical response (CCR), 2 days after the end of treatment (EOT). Secondary end points included global cure (GC; CCR without CDI recurrence) 30 days after EOT (end of study; EOS). Plasma and stool concentrations of fidaxomicin and its active metabolite OP-1118 were measured. RESULTS Of 148 patients randomized, 142 were treated (30 <2 years old). The proportion of participants with treatment-emergent adverse events was similar with fidaxomicin (73.5%) and vancomycin (75.0%). Of 3 deaths in the fidaxomicin arm during the study, none were CDI or treatment related. The rate of CCR at 2 days after EOT was 77.6% (76 of 98 patients) with fidaxomicin and 70.5% (31 of 44) with vancomycin, whereas the rate of GC at EOS was significantly higher in participants receiving fidaxomicin (68.4% vs 50.0%; adjusted treatment difference, 18.8%; 95% confidence interval, 1.5%-35.3%). Systemic absorption of fidaxomicin and OP-1118 was minimal, and stool concentrations were high. CONCLUSIONS Compared with vancomycin, fidaxomicin was well tolerated and demonstrated significantly higher rates of GC in children and adolescents with CDI. CLINICAL TRIALS REGISTRATION NCT02218372.
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Affiliation(s)
- Joshua Wolf
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, USA
| | - Krisztina Kalocsai
- Gyermekinfektológia, Dél-pesti Centrumkórház Országos Haematológiai és Infektológiai Intézet, Budapest, Hungary
| | - Claudia Fortuny
- Department of Paediatric Infectious Diseases, Hospital Sant Joan de Déu, Universitat de Barcelona, Barcelona, Spain
| | - Stefan Lazar
- Department of Pediatrics, Clinical Hospital for Infectious and Tropical Diseases “Dr. Victor Babeș,” Bucharest, Romania
| | - Samantha Bosis
- Pediatric Highly Intensive Care Unit, Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Bartosz Korczowski
- Department of Pediatrics and Pediatric Gastroenterology, University of Rzeszów, Rzeszów, Poland
| | - Arnaud Petit
- Department of Pediatric Hematology and Oncology, Hôpital Trousseau, HUEP, APHP, Paris, France
- Faculty of Medicine, Sorbonne Université, UMRS 938, GRC MyPAC, Paris, France
| | | | | | | | - Joost Melis
- Astellas Pharma B.V., Leiden, the Netherlands
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Marujo V, Arvand M. The largely unnoticed spread of Clostridioides difficile PCR ribotype 027 in Germany after 2010. Infect Prev Pract 2020; 2:100102. [PMID: 34368730 PMCID: PMC8336157 DOI: 10.1016/j.infpip.2020.100102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 10/26/2020] [Indexed: 02/04/2023] Open
Abstract
In recent decades, incidence and severity of Clostridioides difficile infection (CDI) has increased dramatically, coinciding with the emergence of hypervirulent strains such as PCR ribotype 027 (RT027). Data on prevalence of distinct C. difficile strains in random CDI cases in Germany are scarce. The aim of this review was to obtain an overview of prevalence and geographical distribution of RT027 among clinical C. difficile isolates from random cases in non-outbreak settings in hospitals in Germany. For this purpose, we performed a literature review on reported cases of C. difficile RT027 in Germany between 2007 and 2019 in three databases (PubMed, Embase and LIVIVO) and conference proceedings. Studies with selection bias for RT027 (e.g. clinical severity, outbreak reports) were excluded. A total of 304 records were screened, from which 21 were included in this analysis. The nationwide prevalence of RT027 in Germany was <1% prior to 2010 but increased continuously thereafter, reaching 21.7% in 2013. The regional prevalence varied markedly between federal states, higher prevalence was reported from North Rhine-Westphalia (37.4%) and Saxony (31.8%) in 2013-2015. However, data on C. difficile RT027 were not available from almost half of the federal states and were scarce at the national level. Our data suggest a remarkable spread of RT027 in Germany during the past decade, which has remained rather unnoticed so far. A national program for molecular surveillance of C. difficile is required to monitor the changing epidemiology of CDI and to adjust the prevention and control measures.
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Affiliation(s)
- Vanda Marujo
- Robert Koch Institute, Department of Infectious Diseases, Unit for Hospital Hygiene, Infection Prevention and Control, Berlin, Germany
| | - Mardjan Arvand
- Robert Koch Institute, Department of Infectious Diseases, Unit for Hospital Hygiene, Infection Prevention and Control, Berlin, Germany
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Cheknis A, Devaris D, Chesnel L, Dale SE, Nary J, Sambol SP, Citron DM, Goering RV, Johnson S. Characterization of Clostridioides difficile isolates recovered from two Phase 3 surotomycin treatment trials by restriction endonuclease analysis, PCR ribotyping and antimicrobial susceptibilities. J Antimicrob Chemother 2020; 75:3120-3125. [PMID: 32747931 DOI: 10.1093/jac/dkaa297] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVES To investigate the molecular epidemiology and antimicrobial susceptibility of Clostridioides difficile isolates from patients with C. difficile infection (CDI) from two Phase 3 clinical trials of surotomycin. METHODS In both trials [Protocol MK-4261-005 (NCT01597505) conducted across Europe, North America and Israel; and Protocol MK-4261-006 (NCT01598311) conducted across North America, Asia-Pacific and South America], patients with CDI were randomized (1:1) to receive oral surotomycin (250 mg twice daily) or oral vancomycin (125 mg four times per day) for 10 days. Stool samples were collected at baseline and C. difficile isolates were characterized by restriction endonuclease analysis (REA) and PCR ribotyping. Susceptibility testing was performed by agar dilution, according to CLSI recommendations. RESULTS In total, 1147 patients were included in the microbiological modified ITT population. Of 992 recovered isolates, 922 (92.9%) were typed. There was a high association between REA groups and their corresponding predominant PCR ribotype (RT) for BI, DH, G and CF strains. REA group A showed more diverse PCR RTs. Overall, the most common strain was BI/RT027 (20.3%) followed by Y/RT014/020 (15.0%) and DH/RT106 (7.2%). The BI/RT027 strain was particularly prevalent in Europe (29.9%) and Canada (23.6%), with lower prevalence in the USA (16.8%) and Australia/New Zealand (3.4%). Resistance was most prevalent in the BI/RT027 strain, particularly to metronidazole, vancomycin and moxifloxacin. CONCLUSIONS A wide variation in C. difficile strains, both within and across different geographical regions, was documented by both REA and ribotyping, which showed overall good correlation.
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Affiliation(s)
| | | | | | | | - Julia Nary
- ACM Global Laboratories, Rochester, NY, USA
| | | | | | | | - Stuart Johnson
- Edward Hines, Jr. VA Hospital, Hines, IL, USA.,Loyola University Medical Center, Maywood, IL, USA
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Laboratory-Based Surveillance of Clostridium difficile Infection in Australian Health Care and Community Settings, 2013 to 2018. J Clin Microbiol 2020; 58:JCM.01552-20. [PMID: 32848038 DOI: 10.1128/jcm.01552-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 08/22/2020] [Indexed: 11/20/2022] Open
Abstract
In the early 2000s, a binary toxin (CDT)-producing strain of Clostridium difficile, ribotype 027 (RT027), caused extensive outbreaks of diarrheal disease in North America and Europe. This strain has not become established in Australia, and there is a markedly different repertoire of circulating strains there compared to other regions of the world. The C. difficile Antimicrobial Resistance Surveillance (CDARS) study is a nationwide longitudinal surveillance study of C. difficile infection (CDI) in Australia. Here, we describe the molecular epidemiology of CDI in Australian health care and community settings over the first 5 years of the study, 2013 to 2018. Between 2013 and 2018, 10 diagnostic microbiology laboratories from five states in Australia participated in the CDARS study. From each of five states, one private (representing community) and one public (representing hospitals) laboratory submitted isolates of C. difficile or PCR-positive stool samples during two collection periods per year, February-March (summer/autumn) and August-September (winter/spring). C. difficile was characterized by toxin gene profiling and ribotyping. A total of 1,523 isolates of C. difficile were studied. PCR ribotyping yielded 203 different RTs, the most prevalent being RT014/020 (n = 449; 29.5%). The epidemic CDT+ RT027 (n = 2) and RT078 (n = 6), and the recently described RT251 (n = 10) and RT244 (n = 6) were not common, while RT126 (n = 17) was the most prevalent CDT+ type. A heterogeneous C. difficile population was identified. C. difficile RT014/020 was the most prevalent type found in humans with CDI. Continued surveillance of CDI in Australia remains critical for the detection of emerging strain lineages.
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Analysis of C. difficile infection-related outcomes in European participants in the bezlotoxumab MODIFY I and II trials. Eur J Clin Microbiol Infect Dis 2020; 39:1933-1939. [PMID: 32504314 PMCID: PMC7497347 DOI: 10.1007/s10096-020-03935-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/24/2020] [Indexed: 12/04/2022]
Abstract
The MODIFY I/II trials demonstrated that bezlotoxumab, a human monoclonal antibody against Clostridioides difficile toxin B, given during antibiotic treatment for Clostridioides difficile infection (CDI) significantly reduced C. difficile recurrence (rCDI) in adults at high risk for rCDI. Efficacy of CDI-directed intervention may depend on ribotype regional epidemiology, and patient characteristics. This post hoc analysis assessed the efficacy of bezlotoxumab in the subgroup of MODIFY I/II trial participants enrolled in Europe. Data from the bezlotoxumab (10 mg/kg single intravenous infusion) and placebo (0.9% saline) groups from MODIFY I/II were compared to assess initial clinical cure (ICC), rCDI, all-cause, and CDI-associated rehospitalizations within 30 days of discharge, and mortality through 12 weeks post-infusion. Of 1554 worldwide participants, 606 were from Europe (bezlotoxumab n = 313, 51%; placebo n = 292; 48%). Baseline characteristics were generally similar across groups, although there were more immunocompromised participants in the bezlotoxumab group (27.2%) compared with placebo (20.1%). Fifty-five percent of participants were female, and 86% were hospitalized at randomization. The rate of ICC was similar between treatment groups. The rate of rCDI in the bezlotoxumab group was lower compared with placebo among European participants overall, and among those with ≥ 1 risk factor for rCDI. Bezlotoxumab reduced 30-day CDI-associated rehospitalizations compared with placebo. These results are consistent with overall results from the MODIFY trials and demonstrate that bezlotoxumab reduces rCDI and CDI-associated rehospitalizations in European patients with CDI. MODIFY I/II (NCT01241552 and NCT01513239)
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Clostridioides difficile infections in Saudi Arabia: Where are we standing? Saudi Pharm J 2020; 28:1118-1121. [PMID: 32922143 PMCID: PMC7474162 DOI: 10.1016/j.jsps.2020.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/28/2020] [Indexed: 12/12/2022] Open
Abstract
Clostridioides difficile infections (CDIs) are infamous healthcare-associated infections for causing watery diarrhea to long-term hospitalized patients with a high mortality rate. Epidemiological reports from western countries showed up-trending pattern in the number of CDIs cases. It is becoming immensely challenging for routine diagnostic protocols to detect CDIs accurately with short turnaround time. In Saudi Arabia, there is a paucity of data about CDIs’ prevalence, recurrence rate, methods of screening and mortality rate. Nevertheless, a growing number of cases with similar virulence strains and comparable antibiotic resistance pattern to the western countries counterparts reported data were also detected. This review aims to present the status of CDIs’ diagnosis and incidence rate in Saudi Arabia based on current literature.
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Efficacy and mechanism of actions of natural antimicrobial drugs. Pharmacol Ther 2020; 216:107671. [PMID: 32916205 DOI: 10.1016/j.pharmthera.2020.107671] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Microbial infections have significantly increased over the last decades, and the mortality rates remain unacceptably high. The emergence of new resistance patterns and the spread of new viruses challenge the eradication of infectious diseases. The declining efficacy of antimicrobial drugs has become a global public health problem. Natural products derived from natural sources, such as plants, animals, and microorganisms, have significant efficacy for the treatment of infectious diseases accompanied by less adverse effects, synergy, and ability to overcome drug resistance. As the Chinese female scientist Youyou Tu received the Nobel Prize for the antimalarial drug artemisinin, antimicrobial drugs developed from Traditional Chinese Medicine are expected to receive increasing attention again. This review summarizes the antimicrobial agents derived from natural products approved for nearly 20 years and describes their efficacy and mode of action. The aim of this unit is to review the current status of antimicrobial drugs from natural products in order to increase the value of natural products as a source of novel drug candidates for infectious diseases.
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Abstract
PURPOSE OF REVIEW Anaerobic bacteria are implicated in a broad range of infections and can cause significant morbidity and mortality. As such, development of antimicrobial resistance (AMR) increases the risk of worse clinical outcomes and death. RECENT FINDINGS Anaerobe AMR is highly variable according to region and species included in the survey. The overall trend is to increasing resistance, particularly in Europe and Asia, and in the Bacteroides fragilis group and Clostridium sp. Conversely, with the decline in RT027, resistance in Clostridiodes difficile is decreasing. Resistance to moxifloxacin and clindamycin has reached 30-50%, whereas prevalence of metronidazole and carbapenem resistance is generally low. Infections due to multidrug anaerobes have been increasingly reported, with clinical studies demonstrating adverse clinical outcomes, including higher mortality, with anaerobic resistance or inappropriate therapy. The role of antimicrobial stewardship in the setting of increasing anaerobe resistance is yet to be fully elucidated. SUMMARY These findings highlight the importance of continuous surveillance in monitoring emerging trends in anaerobe AMR. Mean inhibitory concentrations should be reported due to variable susceptibility breakpoints and for detection of isolates with reduced susceptibility. At a local level, the clinical microbiology laboratory has a key role in identifying and undertaking susceptibility testing to inform individual patient management, develop local antibiograms and liaise with antimicrobial stewardship teams. A greater understanding of the clinical impact of anaerobic resistance and the role of antimicrobial stewardship in preventing resistance is required.
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Maraki S, Mavromanolaki VE, Stafylaki D, Kasimati A. Antimicrobial susceptibility patterns of clinically significant Gram-positive anaerobic bacteria in a Greek tertiary-care hospital, 2017–2019. Anaerobe 2020; 64:102245. [PMID: 32707228 DOI: 10.1016/j.anaerobe.2020.102245] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/17/2020] [Accepted: 07/18/2020] [Indexed: 12/29/2022]
Affiliation(s)
- Sofia Maraki
- Department of Clinical Microbiology and Microbial Pathogenesis, University Hospital of Heraklion, Crete, Greece.
| | | | - Dimitra Stafylaki
- Department of Clinical Microbiology and Microbial Pathogenesis, University Hospital of Heraklion, Crete, Greece
| | - Anna Kasimati
- Department of Clinical Microbiology and Microbial Pathogenesis, University Hospital of Heraklion, Crete, Greece
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Chromosomal Resistance to Metronidazole in Clostridioides difficile Can Be Mediated by Epistasis between Iron Homeostasis and Oxidoreductases. Antimicrob Agents Chemother 2020; 64:AAC.00415-20. [PMID: 32457109 DOI: 10.1128/aac.00415-20] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/21/2020] [Indexed: 12/17/2022] Open
Abstract
Chromosomal resistance to metronidazole has emerged in clinical Clostridioides difficile isolates, but the genetic mechanisms remain unclear. This is further hindered by the inability to generate spontaneous metronidazole-resistant mutants in the lab to interpret genetic variations in clinical isolates. We therefore constructed a mismatch repair mutator in nontoxigenic ATCC 700057 to survey the mutational landscape for de novo resistance mechanisms. In separate experimental evolutions, the mutator adopted a deterministic path to resistance, with truncation of the ferrous iron transporter FeoB1 as a first-step mechanism of low-level resistance. Deletion of feoB1 in ATCC 700057 reduced the intracellular iron content, appearing to shift cells toward flavodoxin-mediated oxidoreductase reactions, which are less favorable for metronidazole's cellular action. Higher-level resistance evolved from sequential acquisition of mutations to catalytic domains of pyruvate-ferredoxin/flavodoxin oxidoreductase (PFOR; encoded by nifJ), a synonymous codon change to putative xdh (xanthine dehydrogenase; encoded by CD630_31770), likely affecting mRNA stability, and last, frameshift and point mutations that inactivated the iron-sulfur cluster regulator (IscR). Gene silencing of nifJ, xdh, or iscR with catalytically dead Cas9 revealed that resistance involving these genes occurred only when feoB1 was inactivated; i.e., resistance was seen only in the feoB1 deletion mutant and not in the isogenic wild-type (WT) parent. Interestingly, metronidazole resistance in C. difficile infection (CDI)-associated strains carrying mutations in nifJ was reduced upon gene complementation. This observation supports the idea that mutation in PFOR is one mechanism of metronidazole resistance in clinical strains. Our findings indicate that metronidazole resistance in C. difficile is complex, involving multigenetic mechanisms that could intersect with iron-dependent and oxidoreductive metabolic pathways.
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Molecular epidemiology and antimicrobial resistance of Clostridioides difficile detected in chicken, soil and human samples from Zimbabwe. Int J Infect Dis 2020; 96:82-87. [DOI: 10.1016/j.ijid.2020.04.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 01/05/2023] Open
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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. The association of a reduced susceptibility to moxifloxacin in causative Clostridium (Clostridioides) difficile strain with the clinical outcome of patients. Antimicrob Resist Infect Control 2020; 9:98. [PMID: 32605598 PMCID: PMC7325081 DOI: 10.1186/s13756-020-00765-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 06/23/2020] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES To investigate the relationship between Clostridium (Clostridioides) difficile strain characteristics and C. difficile infection (CDI) outcome. METHODS Between October and December 2017, 16 hospitals collected epidemiological data according to the European Centre for Disease Prevention and Control (ECDC) surveillance protocol for CDI. C. difficile isolates were characterized by ribotyping, toxin genes detection and antibiotic susceptibility testing to metronidazole, vancomycin and moxifloxacin. RESULTS The overall mean CDI incidence density was 4.5 [95% CI 3.6-5.3] cases per 10,000 patient-days. From the 433 CDI cases, 330 (76.2%) were healthcare-associated, 52 (12.0%) cases were community-associated or of unknown origin and 51 (11.8%) CDI cases recurrent; a complicated course of CDI was reported in 65 cases (15.0%). Eighty-eight (20.3%) of patients died and 59 of them within 30 days after the CDI diagnosis. From the 379 C. difficile isolates, the most prevalent PCR ribotypes were 001 (n = 127, 33.5%) and 176 (n = 44, 11.6%). A total of 186 (49.1%) isolates showed a reduced susceptibility to moxifloxacin (> 4 mg/L) and 96.4% of them had Thr82Ile in the GyrA. Nineteen isolates revealed reduced susceptibility to metronidazole and two isolates to vancomycin (> 2 mg/L). A fatal outcome was associated with a reduced susceptibility to moxifloxacin, the advanced age of the patients and a complicated course of CDI (p<0.05). No association between ribotype, binary toxin and a reduced susceptibility to moxifloxacin and complicated course or recurrent CDI was found. CONCLUSIONS A reduced susceptibility to moxifloxacin, in causative C. difficile strains was associated with fatal outcome of the patients, therefore it is an important marker in surveillance of CDI.
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Affiliation(s)
- Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.
| | - Vaclav Capek
- Bioinformatics centre, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Elka Nycova
- Department of Medical Microbiology, Hospital Bulovka, Prague, Czech Republic
| | - Sabina Vojackova
- Department of Medical Microbiology, University Hospital Brno, Brno, Czech Republic
| | - Magda Balejova
- Department of Medical Microbiology, Hospital Ceske Budejovice, Ceske Budejovice, Czech Republic
| | - Lenka Geigerova
- Department of Medical Microbiology, Faculty of Medicine, Charles University and University Hospital Plzen, Plzen, Czech Republic
| | - Renata Tejkalova
- Department of Medical Microbiology, Faculty of Medicine, Masaryk University and St. Anne's University Hospital, Brno, Czech Republic
| | - Lenka Havlinova
- Department of Medical Microbiology and Immunology, Hospital Liberec, Liberec, Czech Republic
| | - Iva Vagnerova
- Department of Microbiology, Faculty of Medicine and Dentistry, Palacky University Hospital, Olomouc, Czech Republic
| | - Pavel Cermak
- Department of Medical Microbiology, Thomayer's Hospital, Prague, Czech Republic
| | - Lenka Ryskova
- Department of Clinical Microbiology, University Hospital Hradec Kralove, Hradec Kralove, Czech Republic
| | - Petr Jezek
- Department of Clinical Microbiology and Parasitology, Hospital Pribram, Pribram, Czech Republic
| | - Dana Zamazalova
- Department of Clinical Microbiology, Hospital Nove Mesto na Morave, Nove Mesto na Morave, Czech Republic
| | - Denisa Vesela
- Department of Medical Microbiology, Hospital Jindrichuv Hradec, Jindrichuv Hradec, Czech Republic
| | - Alice Kucharova
- Department of Medical Microbiology, Hospital Tabor, Tabor, Czech Republic
| | - Dana Nemcova
- Department of Clinical Microbiology, Institute for Clinical and Experimental Medicine, Prague, Czech Republic
| | - Martina Curdova
- Department of Clinical Microbiology, Military University Hospital, Prague, Czech Republic
| | - Otakar Nyc
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Pavel Drevinek
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
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Antimicrobial Susceptibilities of Clostridium difficile Isolates from 12 Asia-Pacific Countries in 2014 and 2015. Antimicrob Agents Chemother 2020; 64:AAC.00296-20. [PMID: 32393487 DOI: 10.1128/aac.00296-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/02/2020] [Indexed: 01/05/2023] Open
Abstract
Clostridium (Clostridioides) difficile causes toxin-mediated diarrhea and pseudomembranous colitis, primarily among hospital inpatients. Outbreaks of C. difficile infection (CDI) have been caused by strains with acquired antimicrobial resistance, particularly fluoroquinolone resistance, including C. difficile ribotype (RT) 027 in North America and Europe and RT 017, the most common strain in Asia. Despite being the most common cause of hospital-acquired infection in high-income countries, and frequent misuse of antimicrobials in Asia, little is known about CDI in the Asia-Pacific region. We aimed to determine the antimicrobial susceptibility profiles of a collection of C. difficile isolates from the region. C. difficile isolates (n = 414) from a 2014 study of 13 Asia-Pacific countries were tested for susceptibility to moxifloxacin, amoxicillin-clavulanate, erythromycin, clindamycin, rifaximin, metronidazole, vancomycin, and fidaxomicin according to the Clinical and Laboratory Standards Institute's agar dilution method. All isolates were susceptible to metronidazole, vancomycin, amoxicillin-clavulanate, and fidaxomicin. Moxifloxacin resistance was detected in all countries except Australia, all RT 369 and QX 239 strains, and 92.7% of RT 018 and 70.6% of RT 017 strains. All C. difficile RT 012, 369, and QX 239 strains were also resistant to erythromycin and clindamycin. Rifaximin resistance was common in RT 017 strains only (63.2%) and was not detected in Australian, Japanese, or Singaporean isolates. In conclusion, antimicrobial susceptibility of C. difficile varied by strain type and by country. Multiresistance was common in emerging RTs 369 and QX 239 and the most common strain in Asia, RT 017. Ongoing surveillance is clearly warranted.
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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Genovese C, La Fauci V, D'Amato S, Squeri A, Anzalone C, Costa GB, Fedele F, Squeri R. Molecular epidemiology of antimicrobial resistant microorganisms in the 21th century: a review of the literature. ACTA BIO-MEDICA : ATENEI PARMENSIS 2020; 91:256-273. [PMID: 32420962 PMCID: PMC7569612 DOI: 10.23750/abm.v91i2.9176] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/10/2020] [Indexed: 12/26/2022]
Abstract
Healthcare-associated infections (HAIs) are the most frequent and severe complication acquired in healthcare settings with high impact in terms of morbidity, mortality and costs. Many bacteria could be implicated in these infections, but, expecially multidrug resistance bacteria could play an important role. Many microbial typing technologies have been developed until to the the bacterial whole-genome sequencing and the choice of a molecular typing method therefore will depend on the skill level and resources of the laboratory and the aim and scale of the investigation. In several studies the molecular investigation of pathogens involved in HAIs was performed with many microorganisms identified as causative agents such as Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Clostridium difficile, Acinetobacter spp., Enterobacter spp., Enterococcus spp., Staphylococcus aureus and several more minor species. Here, we will describe the most and least frequently reported clonal complex, sequence types and ribotypes with their worldwide geographic distribution for the most important species involved in HAIs.
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Affiliation(s)
- Cristina Genovese
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Vincenza La Fauci
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Smeralda D'Amato
- Postgraduate Medical School in Hygiene and Preventive Medicine, University of Messina, Italy.
| | - Andrea Squeri
- Department of Human Pathology of the adult and developmental age Gaetano Barresi, University of Messina, Messina, Italy.
| | - Carmelina Anzalone
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Gaetano Bruno Costa
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
| | - Francesco Fedele
- Department of Biomedical and Dental Sciences and Morphofunctional Imaging, University of Messina, Messina, Italy.
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Healthcare-associated infections and antimicrobial resistance in Canadian acute care hospitals, 2014-2018. ACTA ACUST UNITED AC 2020; 46:99-112. [PMID: 32558807 DOI: 10.14745/ccdr.v46i05a01] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Background Healthcare-associated infections (HAIs) and antimicrobial resistance (AMR) pose serious threats to the health of Canadians due to increased morbidity, mortality and healthcare costs. Epidemiologic and laboratory surveillance data, collected through the Canadian Nosocomial Infection Surveillance Program, are used to inform infection prevention and control and antimicrobial stewardship programs and policies. The objective of this study was to describe the epidemiologic and laboratory characteristics and trends of HAIs and AMR from 2014 to 2018 using surveillance data provided by Canadian hospitals participating in the Canadian Nosocomial Infection Surveillance Program. Methods Data were collected from 70 Canadian sentinel hospitals between January 1, 2014 and December 31, 2018 for Clostridioides difficile infection (CDI), methicillin-resistant Staphylococcus aureus bloodstream infections, vancomycin-resistant Enterococci bloodstream infections and carbapenemase-producing Enterobacteriaceae. Case counts, rates, outcome data, molecular characterization and antimicrobial resistance profiles are presented. Additionally, hospital-level Escherichia coli antibiogram data were collected and are described. Results Increases in rates per 10,000 patient-days were observed for methicillin-resistant S. aureus bloodstream infections (59%; 0.66-1.05, p=0.023) and vancomycin-resistant Enterococci bloodstream infections (143%; 0.14-0.34, p=0.023). However, CDI rates decreased by 12.5% between 2015 and 2018 (from 6.16-5.39, p=0.042). Carbapenemase-producing Enterobacteriaceae infection rates remained low and stable whereas colonization increased by 375% (0.04-0.19; p=0.014). Conclusion Ongoing efforts to prevent HAIs and reduce AMR in Canada require consistent, standardized surveillance data from acute care hospitals. Increased collaboration with provincial, territorial and international partners in infection prevention and control, as well as antimicrobial stewardship, will be essential in reducing the burden of observed HAIs (including antimicrobial resistant organisms).
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Snydman DR, McDermott LA, Jenkins SG, Goldstein EJC, Patel R, Forbes BA, Johnson S, Gerding DN, Thorpe CM, Walk ST. Epidemiologic trends in Clostridioides difficile isolate ribotypes in United States from 2011 to 2016. Anaerobe 2020; 63:102185. [PMID: 32387171 DOI: 10.1016/j.anaerobe.2020.102185] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 11/26/2022]
Abstract
BACKGROUND Geographic and temporal trends in the distribution of PCR ribotypes for Clostridioides difficile associated diarrheal isolates obtained in the United States (US) are changing. As part of a US national surveillance program of C. difficile susceptibility to fidaxomicin, we quantified the distribution of PCR ribotypes of stool isolates collected from 2011 to 2016. METHODS C. difficile isolates or C. difficile toxin + stools from patients with C. difficile infection (CDI) were submitted for testing to Tufts Medical Center from 6 geographically distinct medical centers. Following isolation and confirmation as C. difficile, approximately 35% of the isolates were randomly sampled, stratified by center, for PCR ribotyping by capillary gel electrophoresis. Toxin gene profiling was performed on all isolates. RESULTS 939 isolates from a total of 2814 (33.4%) isolated over the 6 years were analyzed. Seventy unique ribotypes were observed, including 19 ribotypes observed 10 or more times. Sixteen ribotypes were not previously observed in our data base. Ribotype 027 declined by more than 60% over the 6 years of the survey from 35.3% to 13.1% (p < 0.001). Ribotype 106 was the most common in 2016, followed by 027 and 014-020. There were strong correlations between 027 and binary toxin with the 18 base pair deletion of tcdC and ribotype 078-126 had 100% concordance with the previously described tcdC 39 base pair deletion. CONCLUSIONS The frequency of ribotypes in the US has changed with a marked decline in 027. Each of the geographical areas had variations which differed from each other, but collectively, these results suggest that the changing epidemiology of C. difficile in the US is consistent with what is being seen in Europe. Continued surveillance and monitoring of changes in ribotype distributions of C. difficile are warranted.
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Affiliation(s)
| | | | | | | | - R Patel
- Mayo Clinic, Rochester, MN, USA
| | - B A Forbes
- Virginia Commonwealth, Richmond, VA, USA
| | - S Johnson
- Loyola University Medical Center, Maywood, IL, USA; Edward Hines Jr. VA Hospital, Hines, IL, USA
| | - D N Gerding
- Loyola University Medical Center, Maywood, IL, USA; Edward Hines Jr. VA Hospital, Hines, IL, USA
| | | | - S T Walk
- Montana State University, Bozeman, MT, USA
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