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Young MK, Leslie JL, Madden GR, Lyerly DM, Carman RJ, Lyerly MW, Stewart DB, Abhyankar MM, Petri WA. Binary Toxin Expression by Clostridioides difficile Is Associated With Worse Disease. Open Forum Infect Dis 2022; 9:ofac001. [PMID: 35146046 PMCID: PMC8825761 DOI: 10.1093/ofid/ofac001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 01/07/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The incidence of Clostridioides difficile infection (CDI) has increased over the past 2 decades and is considered an urgent threat by the Centers for Disease Control and Prevention. Hypervirulent strains such as ribotype 027, which possess genes for the additional toxin C. difficile binary toxin (CDT), are contributing to increased morbidity and mortality. METHODS We retrospectively tested stool from 215 CDI patients for CDT by enzyme-linked immunosorbent assay (ELISA). Stratifying patients by CDT status, we assessed if disease severity and clinical outcomes correlated with CDT positivity. Additionally, we completed quantitative PCR (PCR) DNA extracted from patient stool to detect cdtB gene. Lastly, we performed 16 S rRNA gene sequencing to examine if CDT-positive samples had an altered fecal microbiota. RESULTS We found that patients with CdtB, the pore-forming component of CDT, detected in their stool by ELISA, were more likely to have severe disease with higher 90-day mortality. CDT-positive patients also had higher C. difficile bacterial burden and white blood cell counts. There was no significant difference in gut microbiome diversity between CDT-positive and -negative patients. CONCLUSIONS Patients with fecal samples that were positive for CDT had increased disease severity and worse clinical outcomes. Utilization of PCR and testing for C. difficile toxins A and B may not reveal the entire picture when diagnosing CDI; detection of CDT-expressing strains is valuable in identifying patients at risk of more severe disease.
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Affiliation(s)
- Mary K Young
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Jhansi L Leslie
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Gregory R Madden
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | | | | | | | - David B Stewart
- Department of Surgery, Southern Illinois University School of Medicine, Springfield, Illinois, USA
| | - Mayuresh M Abhyankar
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
| | - William A Petri
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia Health System, Charlottesville, Virginia, USA
- Department of Microbiology, Immunology and Cancer Biology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Pathology, University of Virginia School of Medicine, Charlottesville, Virginia, USA
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Mutai WC, Mureithi MW, Anzala O, Revathi G, Kullin B, Burugu M, Kyany'a C, Odoyo E, Otieno P, Musila L. High Prevalence of Multidrug-Resistant Clostridioides difficile Following Extensive Use of Antimicrobials in Hospitalized Patients in Kenya. Front Cell Infect Microbiol 2021; 10:604986. [PMID: 33628744 PMCID: PMC7897694 DOI: 10.3389/fcimb.2020.604986] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/14/2020] [Indexed: 01/02/2023] Open
Abstract
Introduction Clostridioides difficile is a neglected pathogen in many African countries as it is generally not regarded as one of the major contributors toward the diarrheal disease burden in the continent. However, several studies have suggested that C. difficile infection (CDI) may be underreported in many African settings. The aim of this study was to determine the prevalence of CDI in hospitalized patients, evaluate antimicrobial exposure, and detect toxin and antimicrobial resistance profiles of the isolated C. difficile strains. Methods In this cross-sectional study, 333 hospitalized patients with hospital-onset diarrhoea were selected. The stool samples were collected and cultured on cycloserine-cefoxitin egg yolk agar (CCEY). Isolates were presumptively identified by phenotypic characteristics and Gram stain and confirmed by singleplex real-time PCR (qPCR) assays detecting the species-specific tpi gene, toxin A (tcdA) gene, toxin B (tcdB) gene, and the binary toxin (cdtA/cdtB) genes. Confirmed C. difficile isolates were tested against a panel of eight antimicrobials (vancomycin, metronidazole, rifampicin, ciprofloxacin, tetracycline, clindamycin, erythromycin, and ceftriaxone) using E-test strips. Results C. difficile was detected in 57 (25%) of diarrheal patients over the age of two, 56 (98.2%) of whom received antimicrobials before the diarrheal episode. Amongst the 71 confirmed isolates, 69 (97.1%) harbored at least one toxin gene. More than half of the toxigenic isolates harbored a truncated tcdA gene. All isolates were sensitive to vancomycin, while three isolates (2.1%) were resistant to metronidazole (MIC >32 mg/L). High levels of resistance were observed to rifampicin (65/71, 91.5%), erythromycin (63/71, 88.7%), ciprofloxacin (59/71, 83.1%), clindamycin (57/71, 80.3%), and ceftriaxone (36/71, 50.7.8%). Among the resistant isolates, 61 (85.9%) were multidrug-resistant. Conclusion Multidrug-resistant C. difficile strains were a significant cause of healthcare facility-onset C. difficile infections in patients with prior antimicrobial exposure in this Kenyan hospital.
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Affiliation(s)
- Winnie C Mutai
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Marianne W Mureithi
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya
| | - Gunturu Revathi
- Department of Pathology, Division of Medical Microbiology, Aga Khan University Hospital, Nairobi, Kenya
| | - Brian Kullin
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
| | - Magdaline Burugu
- Department of Medical Microbiology, School of Medicine, University of Nairobi, Nairobi, Kenya
| | | | - Erick Odoyo
- US Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Peter Otieno
- US Army Medical Research Directorate-Africa, Nairobi, Kenya
| | - Lillian Musila
- US Army Medical Research Directorate-Africa, Nairobi, Kenya
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Fujimoto K, Kimura Y, Shimohigoshi M, Satoh T, Sato S, Tremmel G, Uematsu M, Kawaguchi Y, Usui Y, Nakano Y, Hayashi T, Kashima K, Yuki Y, Yamaguchi K, Furukawa Y, Kakuta M, Akiyama Y, Yamaguchi R, Crowe SE, Ernst PB, Miyano S, Kiyono H, Imoto S, Uematsu S. Metagenome Data on Intestinal Phage-Bacteria Associations Aids the Development of Phage Therapy against Pathobionts. Cell Host Microbe 2020; 28:380-389.e9. [PMID: 32652061 DOI: 10.1016/j.chom.2020.06.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/12/2020] [Accepted: 06/10/2020] [Indexed: 02/08/2023]
Abstract
The application of bacteriophages (phages) is proposed as a highly specific therapy for intestinal pathobiont elimination. However, the infectious associations between phages and bacteria in the human intestine, which is essential information for the development of phage therapies, have yet to be fully elucidated. Here, we report the intestinal viral microbiomes (viromes), together with bacterial microbiomes (bacteriomes), in 101 healthy Japanese individuals. Based on the genomic sequences of bacteriomes and viromes from the same fecal samples, the host bacteria-phage associations are illustrated for both temperate and virulent phages. To verify the usefulness of the comprehensive host bacteria-phage information, we screened Clostridioides difficile-specific phages and identified antibacterial enzymes whose activity is confirmed both in vitro and in vivo. These comprehensive metagenome analyses reveal not only host bacteria-phage associations in the human intestine but also provide vital information for the development of phage therapies against intestinal pathobionts.
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Affiliation(s)
- Kosuke Fujimoto
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; Division of Metagenome Medicine, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yasumasa Kimura
- Division of Systems Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Masaki Shimohigoshi
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Takeshi Satoh
- Division of Systems Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Shintaro Sato
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; Mucosal Vaccine Project, BIKEN Innovative Vaccine Research Alliance Laboratories, Research Institute for Microbial Diseases, Osaka University, Osaka 565-0871, Japan
| | - Georg Tremmel
- Laboratory of DNA Information Analysis, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Miho Uematsu
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Yunosuke Kawaguchi
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Yuki Usui
- Division of Systems Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshiko Nakano
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Tetsuya Hayashi
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Koji Kashima
- Division of Mucosal Immunology, Department of Microbiology and Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yoshikazu Yuki
- Division of Mucosal Immunology, Department of Microbiology and Immunology, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Kiyoshi Yamaguchi
- Division of Clinical Genome Research, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yoichi Furukawa
- Division of Clinical Genome Research, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Masanori Kakuta
- Laboratory of DNA Information Analysis, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Yutaka Akiyama
- Department of Computer Science, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Rui Yamaguchi
- Laboratory of DNA Information Analysis, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Sheila E Crowe
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Peter B Ernst
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California, San Diego, La Jolla, CA 92093, USA; Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Center for Veterinary Sciences and Comparative Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Hiroshi Kiyono
- Division of Gastroenterology, Department of Medicine, CU-UCSD Center for Mucosal Immunology, Allergy and Vaccines, University of California, San Diego, La Jolla, CA 92093, USA; Division of Comparative Pathology and Medicine, Department of Pathology, University of California, San Diego, La Jolla, CA 92093, USA; Department of Mucosal Immunology, IMSUT Distinguished Professor Unit, The Institute of Medical Sciences, The University of Tokyo, Tokyo 108-8639, Japan; International Research and Development Center for Mucosal Vaccines, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan
| | - Seiya Imoto
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.
| | - Satoshi Uematsu
- Department of Immunology and Genomics, Osaka City University Graduate School of Medicine, Osaka 545-8585, Japan; Division of Metagenome Medicine, Human Genome Center, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Division of Innate Immune Regulation, International Research and Development Center for Mucosal Vaccines, the Institute of Medical Sciences, the University of Tokyo, Tokyo 108-8639, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo 113-8657, Japan.
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Yang J, Yang H. Non-antibiotic therapy for Clostridioides difficile infection: a review. Crit Rev Clin Lab Sci 2019; 56:493-509. [PMID: 31411909 DOI: 10.1080/10408363.2019.1648377] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Clostridioides difficile infection (CDI) is a common infectious disease that is mainly caused by antibiotics. Antibiotic therapy is still the dominant treatment for CDI, although it is accompanied by side effects. Probiotics, fecal microbiota transplantation (FMT), engineered microorganisms, bacteriophages, diet, natural active substances, nanoparticles and compounds are examples of emerging non-antibiotic therapies that have received a great amount of attention. In this review, we collected data about different non-antibiotic therapies for CDI and provided a comprehensive analysis and detailed comparison of these therapies. The mechanism of action, therapeutic efficacy, and the strengths and weaknesses of these non-antibiotic therapies have been investigated to provide a basis for the reasonable alternative of non-antibiotic therapies for CDI. In summary, probiotics and FMT are currently the best choice for non-antibiotic therapy for CDI.
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Affiliation(s)
- Jingpeng Yang
- State Key Laboratory of Microbial Metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University , Shanghai , China
| | - Hong Yang
- State Key Laboratory of Microbial Metabolism, and School of Life Science & Biotechnology, Shanghai Jiao Tong University , Shanghai , China
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Abstract
Multidrug resistance (MDR) in anaerobes is not a well-known topic. Bacteroides fragilis group isolates have numerous resistance determinants such as multidrug efflux pumps, cfiA and nimB genes and activating insertion sequences, and some isolates exhibited extensive drug-resistant patterns. MDR rates in B. fragilis group were from 1.5 to >18% and up to >71% in cfiA and nimB positive isolates carrying insertion sequences. MDR was present in >1/2 of Clostridioides difficile isolates, most often in epidemic/hypervirulent strains and unusually high metronidazole or vancomycin resistance has been reported in single studies. MDR was found in Prevotella spp. (in ≤10% of isolates), Finegoldia magna, Veillonella spp. and Cutibacterium acnes. Resistance in the anaerobes tends to be less predictable and anaerobic microbiology is required in more laboratories. New hopes may be new antibiotics such as eravacycline, cadazolid, surotomycin, ridinilazol or C. difficile toxoid vaccines; however, more efforts are needed to track the MDR in anaerobes.
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Affiliation(s)
- Lyudmila Boyanova
- Department of Medical Microbiology, Medical University of Sofia, Sofia 1431, Bulgaria
| | - Rumyana Markovska
- Department of Medical Microbiology, Medical University of Sofia, Sofia 1431, Bulgaria
| | - Ivan Mitov
- Department of Medical Microbiology, Medical University of Sofia, Sofia 1431, Bulgaria
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Yang J, Yang H. Effect of Bifidobacterium breve in Combination With Different Antibiotics on Clostridium difficile. Front Microbiol 2018; 9:2953. [PMID: 30564210 PMCID: PMC6288195 DOI: 10.3389/fmicb.2018.02953] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 11/16/2018] [Indexed: 12/18/2022] Open
Abstract
While combinations of probiotics with antibiotics have exhibited beneficial and adverse effects in the treatment of Clostridium difficile infection (CDI), no substantive explanation has been provided for these effects. In this study, C. difficile ATCC 9689 (CD) was treated with Bifidobacterium breve (YH68) in combination with five different antibiotics to explore the effects of the different combinations on C. difficile. Cell-free culture supernatant (CFCS) of YH68 was combined with metronidazole (MTR), vancomycin (VAN), clindamycin (CLI), ceftazidime (CAZ) or ampicillin (AMP) to treat CD. The plate counting method was used to determine the growth and spore production of CD, and cell damage was assessed by the measurement of extracellular ATP levels with a luminescence-based kit. The production of toxin A/B was measured with an ELISA kit. The gene expression levels of tcdA and tcdB in CD were evaluated by real-time qPCR. The CFCS of YH68 (3 × 109 CFU/mL) at 0.25 times the minimal inhibitory concentration (MIC) (0.25YH68) in combination with the five antibiotics exerted stronger inhibitory effects on the growth and spore production of CD than the same antibiotics in the absence of 0.25YH68, except 0.25YH68&MTR&, 0.25YH68&MTR&CAZ, and 0.25YH68&VAN&CLI. However, treatment with 0.25YH68&VAN, 0.25YH68&, 0.25YH68&MTR&CAZ, 0.25YH68&VAN&CAZ, 0.25YH68&VAN&, and 0.25YH68&CAZ& resulted in increased cell damage. In addition, the different combinations, except 0.25YH68&CLI, 0.25YH68&MTR& and 0.25YH68&VAN&CLI, dramatically reduced the production of toxin A/B in comparison with the effects of the same antibiotics in the absence of 0.25YH68. The gene expression levels of tcdA and tcdB in CD were lowered upon treatment with 0.25YH68 in combination with MTR, CLI, CAZ, MTR&CAZ, MTR&, CLI&CAZ, and CLI&, whereas the levels were enhanced by 0.25YH68 in combination with VAN, AMP, MTR&CLI, VAN&CLI, VAN&, and CAZ&. In summary, YH68 in combination with specific antibiotics could enhance the inhibitory effects of antibiotics against CD. In addition, the antagonistic effects between some antibiotics could be weakened by YH68.
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Affiliation(s)
| | - Hong Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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