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Nhu NTQ, Lin H, Pigli Y, Sia JK, Kuhn P, Snitkin ES, Young V, Kamboj M, Pamer EG, Rice PA, Shen A, Dong Q. Flagellar switch inverted repeat impacts flagellar invertibility and varies Clostridioides difficile RT027/MLST1 virulence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.22.546185. [PMID: 39386689 PMCID: PMC11463649 DOI: 10.1101/2023.06.22.546185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Clostridioides difficile RT027 strains cause infections that vary in severity from asymptomatic to lethal, but the molecular basis for this variability is poorly understood. Through comparative analyses of RT027 clinical isolates, we determined that isolates that exhibit greater variability in their flagellar gene expression exhibit greater virulence in vivo . C. difficile flagellar genes are phase-variably expressed due to the site-specific inversion of the flgB 5'UTR region, which reversibly generates ON vs. OFF orientations for the flagellar switch. We found that longer inverted repeat (IR) sequences in this switch region correlate with greater disease severity, with RT027 strains carrying 6A/6T IR sequences exhibiting greater phenotypic heterogeneity in flagellar gene expression (60%-75% ON) and causing more severe disease than those with shorter IRs (> 99% ON or OFF). Taken together, our results reveal that phenotypic heterogeneity in flagellar gene expression may contribute to the variable disease severity observed in C. difficile patients.
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2
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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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3
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Di Bella S, Sanson G, Monticelli J, Zerbato V, Principe L, Giuffrè M, Pipitone G, Luzzati R. Clostridioides difficile infection: history, epidemiology, risk factors, prevention, clinical manifestations, treatment, and future options. Clin Microbiol Rev 2024; 37:e0013523. [PMID: 38421181 PMCID: PMC11324037 DOI: 10.1128/cmr.00135-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024] Open
Abstract
SUMMARYClostridioides difficile infection (CDI) is one of the major issues in nosocomial infections. This bacterium is constantly evolving and poses complex challenges for clinicians, often encountered in real-life scenarios. In the face of CDI, we are increasingly equipped with new therapeutic strategies, such as monoclonal antibodies and live biotherapeutic products, which need to be thoroughly understood to fully harness their benefits. Moreover, interesting options are currently under study for the future, including bacteriophages, vaccines, and antibiotic inhibitors. Surveillance and prevention strategies continue to play a pivotal role in limiting the spread of the infection. In this review, we aim to provide the reader with a comprehensive overview of epidemiological aspects, predisposing factors, clinical manifestations, diagnostic tools, and current and future prophylactic and therapeutic options for C. difficile infection.
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Affiliation(s)
- Stefano Di Bella
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
| | - Gianfranco Sanson
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
| | - Jacopo Monticelli
- Infectious Diseases
Unit, Trieste University Hospital
(ASUGI), Trieste,
Italy
| | - Verena Zerbato
- Infectious Diseases
Unit, Trieste University Hospital
(ASUGI), Trieste,
Italy
| | - Luigi Principe
- Microbiology and
Virology Unit, Great Metropolitan Hospital
“Bianchi-Melacrino-Morelli”,
Reggio Calabria, Italy
| | - Mauro Giuffrè
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
- Department of Internal
Medicine (Digestive Diseases), Yale School of Medicine, Yale
University, New Haven,
Connecticut, USA
| | - Giuseppe Pipitone
- Infectious Diseases
Unit, ARNAS Civico-Di Cristina
Hospital, Palermo,
Italy
| | - Roberto Luzzati
- Clinical Department of
Medical, Surgical and Health Sciences, Trieste
University, Trieste,
Italy
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4
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Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Burnham CAD, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. mBio 2024; 15:e0330023. [PMID: 38329369 PMCID: PMC10936198 DOI: 10.1128/mbio.03300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and the genomic determinants of disease outcomes. Across two wards over 6 months, we selectively cultured C. difficile from patients (n = 384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n = 79), 19 (24%) patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤2 core gene single nucleotide polymorphisms; two of these networks contain strains from different patients. Strain networks were temporally linked (P < 0.0001). To understand the genomic correlates of the disease, we conducted WGS on an additional cohort of C. difficile (n = 102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR, nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes (tcdABER and cdtR) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate that toxigenic and nontoxigenic C. difficile contamination persist in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease. IMPORTANCE Clostridioides difficile infection remains a leading cause of hospital-associated diarrhea, despite increased antibiotic stewardship and transmission prevention strategies. This suggests a changing genomic landscape of C. difficile. Our study provides insight into the nature of prevalent C. difficile strains in a hospital setting and transmission patterns among carriers. Longitudinal sampling of surfaces and patient stool revealed that both toxigenic and nontoxigenic strains of C. difficile clade 1 dominate these two wards. Moreover, quantification of transmission in carriers of these clade 1 isolates underscores the need to revisit infection prevention measures in this patient group. We identified unique genetic signatures associated with virulence in this clade. Our data highlight the complexities of preventing transmission of this pathogen in a hospital setting and the need to investigate the mechanisms of in vivo persistence and virulence of prevalent lineages in the host gut microbiome.
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Affiliation(s)
- Erin P. Newcomer
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Skye R. S. Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kailun Zhang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Candice Cass
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Zainab H. Iqbal
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Emily L. Struttmann
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erik R. Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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5
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Douchant K, He SM, Noordhof C, Greenlaw J, Vancuren S, Schroeter K, Allen-Vercoe E, Sjaarda C, Vanner SJ, Petrof EO, Sheth PM, Guzman M. Defined microbial communities and their soluble products protect mice from Clostridioides difficile infection. Commun Biol 2024; 7:135. [PMID: 38280981 PMCID: PMC10821944 DOI: 10.1038/s42003-024-05778-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 01/03/2024] [Indexed: 01/29/2024] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated infectious diarrhea. The development of C.difficile infection is tied to perturbations of the bacterial community in the gastrointestinal tract, called the gastrointestinal microbiota. Repairing the gastrointestinal microbiota by introducing lab-designed bacterial communities, or defined microbial communities, has recently shown promise as therapeutics against C.difficile infection, however, the mechanisms of action of defined microbial communities remain unclear. Using an antibiotic- C.difficile mouse model, we report the ability of an 18-member community and a refined 4-member community to protect mice from two ribotypes of C.difficile (CD027, CD078; p < 0.05). Furthermore, bacteria-free supernatant delivered orally to mice from the 4-member community proteolyzed C.difficile toxins in vitro and protected mice from C.difficile infection in vivo (p < 0.05). This study demonstrates that bacteria-free supernatant is sufficient to protect mice from C.difficile; and could be further explored as a therapeutic strategy against C.difficile infection.
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Affiliation(s)
- Katya Douchant
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
| | - Shu-Mei He
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Curtis Noordhof
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Jill Greenlaw
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Sarah Vancuren
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Kathleen Schroeter
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Emma Allen-Vercoe
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, N1G2W1, ON, Canada
| | - Calvin Sjaarda
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
- Division of Microbiology, Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Stephen J Vanner
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada
| | - Elaine O Petrof
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
| | - Prameet M Sheth
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada.
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston, K7L3N6, ON, Canada.
- Division of Microbiology, Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada.
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, K7L3N6, ON, Canada.
| | - Mabel Guzman
- The Gastrointestinal Disease Research Unit (GIDRU), Kingston Health Sciences Center, Kingston, K7L2V7, ON, Canada
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6
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Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.26.23295023. [PMID: 38105952 PMCID: PMC10723495 DOI: 10.1101/2023.09.26.23295023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and genomic determinants of disease outcomes. Across two wards over six months, we selectively cultured C. difficile from patients (n=384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n=79), 19 (24%) of patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤ 2 core gene SNPs; 2 of these networks contain strains from different patients. Strain networks were temporally linked (p<0.0001). To understand genomic correlates of disease, we conducted WGS on an additional cohort of C. difficile (n=102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR , nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes ( tcdABER and cdtR ) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate toxigenic and nontoxigenic C. difficile contamination persists in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease.
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7
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Soldavini Pelichotti PC, Cejas D, Fernández-Caniggia L, Trejo FM, Pérez PF. Characterization of a Clostridioides difficile ST-293 isolate from a recurrent infection in Argentina. Rev Argent Microbiol 2023:S0325-7541(22)00102-X. [PMID: 36599754 DOI: 10.1016/j.ram.2022.09.004] [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: 04/08/2022] [Revised: 06/30/2022] [Accepted: 09/27/2022] [Indexed: 01/03/2023] Open
Abstract
Clostridioides difficile is an opportunistic spore-forming pathogen responsible for antibiotic-associated diarrhea in humans. C. difficile produces two main toxins: TcdA and TcdB as well as a third toxin named binary toxin (CDT) that is also involved in virulence. The present study aimed at characterizing the C. difficile isolate ALCD3 involved in a relapse episode of nosocomial infection. Molecular characterization showed that isolate ALCD3 belongs to toxinotype 0/v and the MLST analysis demonstrated allelic profile adk:91, atpA:1, dxr:2, glyA: 1, recA:27, sodA: 1 and tpi:1 which corresponds to ST293 (MLST clade: 1). During growth, isolate ALCD3 showed an early increase in the sporulation ratio as well as maximal values of heat resistant forms after 2 days of incubation. Both sporulation kinetics and production of heat resistant forms were faster for isolate ALCD3 than for the reference strain VPI 10463. Germination in the presence of the natural germinant taurocholate was faster for isolate ALCD3 than for strain VPI 10463, which indicates that isolate ALCD3 starts cortex hydrolysis earlier than strain VPI 10463. Furthermore, the co-germinant glycine, induces rapid release of dipicolinic acid (DPA) in isolate ALCD3. These findings indicate that isolate ALCD3 is particularly efficient in both sporulation and germination. The present work represents the first report of the circulation of C. difficile ST293 in Argentina. The ability of isolate ALCD3 to produce toxins and its high sporulation/germination capacity are key features compatible with a microorganism with high dissemination potential and the possibility of inducing recurrent infections.
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Affiliation(s)
- P Cecilia Soldavini Pelichotti
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, La Plata, Argentina; Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP, 47 y 116 (s/n), La Plata B1900AJI, Argentina
| | - Daniela Cejas
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Ciudad Autónoma de Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Liliana Fernández-Caniggia
- Laboratorio de Microbiología, Hospital Alemán, Av. Pueyrredón 1640, Ciudad Autónoma de Buenos Aires, Argentina
| | - Fernando M Trejo
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, La Plata, Argentina
| | - Pablo F Pérez
- Cátedra de Microbiología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 47 y 115, La Plata, Argentina; Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CCT La Plata, CONICET-UNLP, 47 y 116 (s/n), La Plata B1900AJI, Argentina.
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8
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Zeng J, Wang H, Dong M, Tian GB. Clostridioides difficile spore: coat assembly and formation. Emerg Microbes Infect 2022; 11:2340-2349. [PMID: 36032037 PMCID: PMC9542656 DOI: 10.1080/22221751.2022.2119168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Clostridioides difficile (C. difficile) is a Gram-positive, spore-forming, toxin-producing, obligate anaerobic bacterium. C. difficile infection (CDI) is the leading cause of healthcare-associated infective diarrhoea. The infection is mediated by the spore, a metabolically inactive form of C. difficile. The spore coat acts as a physical barrier to defend against chemical insults from hosts and natural environments. The composition of spore coat has already been revealed; therefore, the interactive networks of spore coat proteins and the dynamic process of coat assembly are the keys to design strategies to control and cure CDI. This review gives a brief discussion of the signal processing and transcriptional regulation of C. difficile sporulation initiation. Following the discussion, the spore formation is also introduced. Finally, this review mainly focuses on the spore coat assembly, a poorly understood process in C. difficile, and important proteins that have been studied.
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Affiliation(s)
- Ji Zeng
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Hao Wang
- School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou, Guangdong 510006, China
| | - Min Dong
- Department of Microbiology, Harvard Medical School, Boston, MA, USA
- Department of Urology, Boston Children’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Guo-Bao Tian
- Department of Microbiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangdong 510080, China
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Key Laboratory of Tropical Diseases Control (Sun Yat-sen University), Ministry of Education, Guangzhou 510080, China
- School of Medicine, Xizang Minzu University, Xianyang, Shaanxi 712082, China
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9
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Abstract
The severity of Clostridioides difficile infections (CDI) has increased over the last few decades. Patient age, white blood cell count, and creatinine levels as well as C. difficile ribotype and toxin genes have been associated with disease severity. However, it is unclear whether specific members of the gut microbiota are associated with variations in disease severity. The gut microbiota is known to interact with C. difficile during infection. Perturbations to the gut microbiota are necessary for C. difficile to colonize the gut. The gut microbiota can inhibit C. difficile colonization through bile acid metabolism, nutrient consumption, and bacteriocin production. Here, we sought to demonstrate that members of the gut bacterial communities can also contribute to disease severity. We derived diverse gut communities by colonizing germfree mice with different human fecal communities. The mice were then infected with a single C. difficile ribotype 027 clinical isolate, which resulted in moribundity and histopathologic differences. The variation in severity was associated with the human fecal community that the mice received. Generally, bacterial populations with pathogenic potential, such as Enterococcus, Helicobacter, and Klebsiella, were associated with more-severe outcomes. Bacterial groups associated with fiber degradation and bile acid metabolism, such as Anaerotignum, Blautia, Lactonifactor, and Monoglobus, were associated with less-severe outcomes. These data indicate that, in addition to the host and C. difficile subtype, populations of gut bacteria can influence CDI disease severity.
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10
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Saund K, Pirani A, Lacy DB, Hanna PC, Snitkin E. Strain Variation in Clostridioides difficile Cytotoxicity Associated with Genomic Variation at Both Pathogenic and Nonpathogenic Loci. mSphere 2022; 7:e0017422. [PMID: 35766503 PMCID: PMC9241522 DOI: 10.1128/msphere.00174-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 04/13/2022] [Indexed: 11/20/2022] Open
Abstract
Clinical disease from Clostridioides difficile infection can be mediated by two toxins and their neighboring regulatory genes located within the five-gene pathogenicity locus (PaLoc). We provide several lines of evidence that the cytotoxicity of C. difficile may be modulated by genomic variants outside the PaLoc. We used a phylogenetic tree-based approach to demonstrate discordance between cytotoxicity and PaLoc evolutionary history, an elastic net method to show the insufficiency of PaLoc variants alone to model cytotoxicity, and a convergence-based bacterial genome-wide association study (GWAS) to identify correlations between non-PaLoc loci and changes in cytotoxicity. Combined, these data support a model of C. difficile disease wherein cytotoxicity may be strongly affected by many non-PaLoc loci. Additionally, we characterize multiple other in vitro phenotypes relevant to human infections, including germination and sporulation. These phenotypes vary greatly in their clonality, variability, convergence, and concordance with genomic variation. Finally, we highlight the intersection of loci identified by the GWAS for different phenotypes and clinical severity. This strategy to identify overlapping loci can facilitate the identification of genetic variation linking phenotypic variation to clinical outcomes. IMPORTANCE Clostridioides difficile has two major disease-mediating toxins, A and B, encoded within the pathogenicity locus (PaLoc). In this study, we demonstrate via multiple approaches that genomic variants outside the PaLoc are associated with changes in cytotoxicity. These genomic variants may provide new avenues of exploration in the hunt for novel disease-modifying interventions. Additionally, we provide insight into the evolution of several additional phenotypes also critical for clinical infection, such as sporulation, germination, and growth rate. These in vitro phenotypes display a range of responses to evolutionary pressures and, as such, vary in their appropriateness for certain bacterial genome-wide association study approaches. We used a convergence-based association method to identify the genomic variants most correlated with both changes in these phenotypes and disease severity. These overlapping loci may be important for both bacterial function and human clinical disease.
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Affiliation(s)
- Katie Saund
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
| | - D. Borden Lacy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- The Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee, USA
| | - Philip C. Hanna
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Evan Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
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11
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Redding LE, Tu V, Abbas A, Alvarez M, Zackular JP, Gu C, Bushman FD, Kelly DJ, Barnhart D, Lee JJ, Bittinger KL. Genetic and phenotypic characteristics of Clostridium (Clostridioides) difficile from canine, bovine, and pediatric populations. Anaerobe 2022; 74:102539. [PMID: 35217150 PMCID: PMC9359814 DOI: 10.1016/j.anaerobe.2022.102539] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/02/2022] [Accepted: 02/17/2022] [Indexed: 12/15/2022]
Abstract
Objectives: Carriage of Clostridioides difficile by different species of animals has led to speculation that animals could represent a reservoir of this pathogen for human infections. The objective of this study was to compare C. difficile isolates from humans, dogs, and cattle from a restricted geographic area. Methods: C. difficile isolates from 36 dogs and 15 dairy calves underwent whole genome sequencing, and phenotypic assays assessing growth and virulence were performed. Genomes of animal-derived isolates were compared to 29 genomes of isolates from a pediatric population as well as 44 reference genomes. Results: Growth rates and relative cytotoxicity of isolates were significantly higher and lower, respectively, in bovine-derived isolates compared to pediatric- and canine-derived isolates. Analysis of core genes showed clustering by host species, though in a few cases, human strains co-clustered with canine or bovine strains, suggesting possible interspecies transmission. Geographic differences (e.g., farm, litter) were small compared to differences between species. In an analysis of accessory genes, the total number of genes in each genome varied between host species, with 6.7% of functional orthologs differentially present/absent between host species and bovine-derived strains having the lowest number of genes. Canine-derived isolates were most likely to be non-toxigenic and more likely to carry phages. A targeted study of episomes identified in local pediatric strains showed sharing of a methicillin-resistance plasmid with dogs, and historic sharing of a wide range of episomes across hosts. Bovine-derived isolates harbored the widest variety of antibiotic-resistance genes, followed by canine Conclusions: While C. difficile isolates mostly clustered by host species, occasional co-clustering of canine and pediatric-derived isolates suggests the possibility of interspecies transmission. The presence of a pool of resistance genes in animal-derived isolates with the potential to appear in humans given sufficient pressure from antibiotic use warrants concern.
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Affiliation(s)
- L E Redding
- Department of Clinical Studies-New Bolton Center, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, PA, 19348, USA.
| | - V Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, PA, 19104, USA
| | - A Abbas
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - M Alvarez
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - J P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - C Gu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - F D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - D J Kelly
- Department of Clinical Studies-New Bolton Center, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, PA, 19348, USA
| | - D Barnhart
- Department of Clinical Studies-New Bolton Center, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, PA, 19348, USA
| | - J J Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, PA, 19104, USA
| | - K L Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, PA, 19104, USA
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12
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Shen A. Clostridioides difficile Spore Formation and Germination: New Insights and Opportunities for Intervention. Annu Rev Microbiol 2021; 74:545-566. [PMID: 32905755 DOI: 10.1146/annurev-micro-011320-011321] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Spore formation and germination are essential for the bacterial pathogen Clostridioides difficile to transmit infection. Despite the importance of these developmental processes to the infection cycle of C. difficile, the molecular mechanisms underlying how this obligate anaerobe forms infectious spores and how these spores germinate to initiate infection were largely unknown until recently. Work in the last decade has revealed that C. difficile uses a distinct mechanism for sensing and transducing germinant signals relative to previously characterized spore formers. The C. difficile spore assembly pathway also exhibits notable differences relative to Bacillus spp., where spore formation has been more extensively studied. For both these processes, factors that are conserved only in C. difficile or the related Peptostreptococcaceae family are employed, and even highly conserved spore proteins can have differential functions or requirements in C. difficile compared to other spore formers. This review summarizes our current understanding of the mechanisms controlling C. difficile spore formation and germination and describes strategies for inhibiting these processes to prevent C. difficile infection and disease recurrence.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA;
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13
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Miles-Jay A, Young VB, Pamer EG, Savidge TC, Kamboj M, Garey KW, Snitkin ES. A multisite genomic epidemiology study of Clostridioides difficile infections in the USA supports differential roles of healthcare versus community spread for two common strains. Microb Genom 2021; 7. [PMID: 34180789 PMCID: PMC8461479 DOI: 10.1099/mgen.0.000590] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Clostridioides difficile is the leading cause of healthcare-associated infectious diarrhoea. However, it is increasingly appreciated that healthcare-associated infections derive from both community and healthcare environments, and that the primary sites of C. difficile transmission may be strain-dependent. We conducted a multisite genomic epidemiology study to assess differential genomic evidence of healthcare vs community spread for two of the most common C. difficile strains in the USA: sequence type (ST) 1 (associated with ribotype 027) and ST2 (associated with ribotype 014/020). We performed whole-genome sequencing and phylogenetic analyses on 382 ST1 and ST2 C. difficile isolates recovered from stool specimens collected during standard clinical care at 3 geographically distinct US medical centres between 2010 and 2017. ST1 and ST2 isolates both displayed some evidence of phylogenetic clustering by study site, but clustering was stronger and more apparent in ST1, consistent with our healthcare-based study more comprehensively sampling local transmission of ST1 compared to ST2 strains. Analyses of pairwise single-nucleotide variant (SNV) distance distributions were also consistent with more evidence of healthcare transmission of ST1 compared to ST2, with 44 % of ST1 isolates being within two SNVs of another isolate from the same geographical collection site compared to 5.5 % of ST2 isolates (P-value=<0.001). Conversely, ST2 isolates were more likely to have close genetic neighbours across disparate geographical sites compared to ST1 isolates, further supporting non-healthcare routes of spread for ST2 and highlighting the potential for misattributing genomic similarity among ST2 isolates to recent healthcare transmission. Finally, we estimated a lower evolutionary rate for the ST2 lineage compared to the ST1 lineage using Bayesian timed phylogenomic analyses, and hypothesize that this may contribute to observed differences in geographical concordance among closely related isolates. Together, these findings suggest that ST1 and ST2, while both common causes of C. difficile infection in hospitals, show differential reliance on community and hospital spread. This conclusion supports the need for strain-specific criteria for interpreting genomic linkages and emphasizes the importance of considering differences in the epidemiology of circulating strains when devising interventions to reduce the burden of C. difficile infections.
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Affiliation(s)
| | | | - Eric G Pamer
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,The University of Chicago, Chicago, IL, USA
| | | | - Mini Kamboj
- Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Weill Cornell Medical College, New York, NY, USA
| | - Kevin W Garey
- University of Houston College of Pharmacy, Houston, TX, USA
| | - Evan S Snitkin
- University of Michigan Medical School, Ann Arbor, MI, USA
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14
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Clearance of Clostridioides difficile Colonization Is Associated with Antibiotic-Specific Bacterial Changes. mSphere 2021; 6:6/3/e01238-20. [PMID: 33952668 PMCID: PMC8103992 DOI: 10.1128/msphere.01238-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The community of microorganisms, or microbiota, in our intestines prevents pathogens like C. difficile from colonizing and causing infection. However, antibiotics can disturb the gut microbiota, which allows C. difficile to colonize. C. difficile infections (CDI) are primarily treated with antibiotics, which frequently leads to recurrent infections because the microbiota has not yet returned to a resistant state. The gut bacterial community prevents many pathogens from colonizing the intestine. Previous studies have associated specific bacteria with clearing Clostridioides difficile colonization across different community perturbations. However, those bacteria alone have been unable to clear C. difficile colonization. To elucidate the changes necessary to clear colonization, we compared differences in bacterial abundance between communities able and unable to clear C. difficile colonization. We treated mice with titrated doses of antibiotics prior to C. difficile challenge, resulting in no colonization, colonization and clearance, or persistent colonization. Previously, we observed that clindamycin-treated mice were susceptible to colonization but spontaneously cleared C. difficile. Therefore, we investigated whether other antibiotics would show the same result. We found that reduced doses of cefoperazone and streptomycin permitted colonization and clearance of C. difficile. Mice that cleared colonization had antibiotic-specific community changes and predicted interactions with C. difficile. Clindamycin treatment led to a bloom in populations related to Enterobacteriaceae. Clearance of C. difficile was concurrent with the reduction of those blooming populations and the restoration of community members related to the Porphyromonadaceae and Bacteroides. Cefoperazone created a susceptible community characterized by drastic reductions in the community diversity and interactions and a sustained increase in the abundance of many facultative anaerobes. Lastly, clearance in streptomycin-treated mice was associated with the recovery of multiple members of the Porphyromonadaceae, with little overlap in the specific Porphyromonadaceae observed in the clindamycin treatment. Further elucidation of how C. difficile colonization is cleared from different gut bacterial communities will improve C. difficile infection treatments. IMPORTANCE The community of microorganisms, or microbiota, in our intestines prevents pathogens like C. difficile from colonizing and causing infection. However, antibiotics can disturb the gut microbiota, which allows C. difficile to colonize. C. difficile infections (CDI) are primarily treated with antibiotics, which frequently leads to recurrent infections because the microbiota has not yet returned to a resistant state. The recurrent infection cycle often ends when the fecal microbiota from a presumed resistant person is transplanted into the susceptible person. Although this treatment is highly effective, we do not understand the mechanism. We hope to improve the treatment of CDI through elucidating how the bacterial community eliminates CDI. We found that C. difficile colonized susceptible mice but was spontaneously eliminated in an antibiotic treatment-specific manner. These data indicate that each community had different requirements for clearing colonization. Understanding how different communities clear colonization will reveal targets to improve CDI treatments.
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15
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Dudzicz S, Wiecek A, Adamczak M. Clostridioides difficile Infection in Chronic Kidney Disease-An Overview for Clinicians. J Clin Med 2021; 10:E196. [PMID: 33430465 PMCID: PMC7827228 DOI: 10.3390/jcm10020196] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/30/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023] Open
Abstract
Increased incidence of Clostridioides difficile infection (CDI), occurrence of severe and complicated CDI, and more frequent occurrence of drug-resistant, recurrent or non-hospital CDI has become a worldwide clinical problem. CDI is more common in patients with chronic kidney disease (CKD) than in the general population. CDI seems to be associated with frequent hospitalization, frequently used antibiotic therapy, dysbiosis, and abnormalities of the immune system observed in CKD patients. Dysbiosis is a common disorder found in CKD patients. It may be related to insufficient fiber content in the diet, reduced amount of consumed fluids and often reduced physical activity, constipation, impaired gastrointestinal motility, multidrug pharmacotherapy, and uremic milieu in CKD stage 5. In patients with CKD the clinical manifestations of CDI are similar to the general population; however, more frequent recurrence of CDI and higher prevalence of severe CDI are reported. Moreover, the increase in CDI related mortality is observed more in CKD patients than in the general population. The aim of this review paper is to summarize the current knowledge concerning the epidemiology, pathogenesis, clinical picture, and prevention and treatment in CKD patients.
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Affiliation(s)
| | - Andrzej Wiecek
- Department of Nephrology, Transplantation and Internal Medicine, Medical University of Silesia, 40-027 Katowice, Poland; (S.D.); (M.A.)
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16
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Orozco-Aguilar J, Alfaro-Alarcón A, Acuña-Amador L, Chaves-Olarte E, Rodríguez C, Quesada-Gómez C. In vivo animal models confirm an increased virulence potential and pathogenicity of the NAP1/RT027/ST01 genotype within the Clostridium difficile MLST Clade 2. Gut Pathog 2020; 12:45. [PMID: 32983262 PMCID: PMC7510272 DOI: 10.1186/s13099-020-00383-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/18/2020] [Indexed: 01/05/2023] Open
Abstract
Background Based on MLST analyses the global population of C. difficile is distributed in eight clades, of which Clade 2 includes the “hypervirulent” NAP1/RT027/ST01 strain along with various unexplored sequence types (STs). Methods To clarify whether this clinically relevant phenotype is a widespread feature of C. difficile Clade 2, we used the murine ileal loop model to compare the in vivo pro-inflammatory (TNF-α, IL-1β, IL-6) and oxidative stress activities (MPO) of five Clade 2 clinical C. difficile isolates from sequence types (STs) 01, 41, 67, and 252. Besides, we infected Golden Syrian hamsters with spores from these strains to determine their lethality, and obtain a histological evaluation of tissue damage, WBC counts, and serum injury biomarkers (LDH, ALT, AST, albumin, BUN, creatinine, Na+, and Cl−). Genomic distances were calculated using Mash and FastANI to explore whether the responses were dictated by phylogeny. Results The ST01 isolate tested ranked first in all assays, as it induced the highest overall levels of pro-inflammatory cytokines, MPO activity, epithelial damage, biochemical markers, and mortality measured in both animal models. Statistically indistinguishable or rather similar outputs were obtained for a ST67 isolate in tests such as tissue damage, neutrophils count, and lethal activity. The results recorded for the two ST41 isolates tested were of intermediate magnitude and the ST252 isolate displayed the lowest pathogenic potential in all animal experiments. This ordering matched the genomic distance of the ST01 isolate to the non-ST01 isolates. Conclusions Despite their close phylogenic relatedness, our results demonstrate differences in pathogenicity and virulence levels in Clade 2 C. difficile strains, confirm the high severity of infections caused by the NAP1/RT027/ST01 strain, and highlight the importance of C. difficile typing.
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Affiliation(s)
- Josué Orozco-Aguilar
- Laboratorio de Ensayos Biológicos (LEBi), Universidad de Costa Rica, San José, Costa Rica.,Facultad de Farmacia, Universidad de Costa Rica, San José, Costa Rica.,Programa de Posgrado en Microbiología, Parasitología, Química Clínica e Inmunología, Universidad de Costa Rica, San José, Costa Rica
| | - Alejandro Alfaro-Alarcón
- Departamento de Patología, Escuela de Medicina Veterinaria, Universidad Nacional, Heredia, Costa Rica
| | - Luis Acuña-Amador
- Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Esteban Chaves-Olarte
- Programa de Posgrado en Microbiología, Parasitología, Química Clínica e Inmunología, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Programa de Posgrado en Microbiología, Parasitología, Química Clínica e Inmunología, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
| | - Carlos Quesada-Gómez
- Laboratorio de Ensayos Biológicos (LEBi), Universidad de Costa Rica, San José, Costa Rica.,Programa de Posgrado en Microbiología, Parasitología, Química Clínica e Inmunología, Universidad de Costa Rica, San José, Costa Rica.,Centro de Investigación en Enfermedades Tropicales and Facultad de Microbiología, Universidad de Costa Rica, San José, Costa Rica
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17
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Hernandez BG, Vinithakumari AA, Sponseller B, Tangudu C, Mooyottu S. Prevalence, Colonization, Epidemiology, and Public Health Significance of Clostridioides difficile in Companion Animals. Front Vet Sci 2020; 7:512551. [PMID: 33062657 PMCID: PMC7530174 DOI: 10.3389/fvets.2020.512551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 08/14/2020] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile, previously Clostrdium difficile, is a major cause of antibiotic-associated enteric disease in humans in hospital settings. Increased incidence of C. difficile infection (CDI) in community settings raises concerns over an alternative source of CDI for humans. The detection of genetically similar and toxigenic C. difficile isolates in companion animals, including asymptomatic pets, suggests the potential role of household pets as a source of community-associated CDI. The close association between companion animals and humans, in addition to the use of similar antibiotics in both species, could provide a selective advantage for the emergence of new C. difficile strains and thus increase the incidental transmission of CDI to humans. Therefore, screening household pets for C. difficile is becoming increasingly important from a public health standpoint and may become a part of routine testing in the future, for the benefit of susceptible or infected individuals within a household. In this review, we analyze available information on prevalence, pathophysiology, epidemiology, and molecular genetics of C. difficile infection, focusing on companion animals and evaluate the risk of pet-borne transmission of CDI as an emerging public health concern. Molecular epidemiological characterization of companion animal C. difficile strains could provide further insights into the interspecies transmission of CDI. The mosaic nature of C. difficile genomes and their susceptibility to horizontal gene transfer may facilitate the inter-mixing of genetic material, which could increase the possibility of the emergence of new community-associated CDI strains. However, detailed genome-wide characterization and comparative genome analysis are warranted to confirm this hypothesis.
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Affiliation(s)
- Belen G. Hernandez
- Department of Veterinary Pathology, Iowa State University, Ames, IA, United States
| | | | - Brett Sponseller
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Chandra Tangudu
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, United States
| | - Shankumar Mooyottu
- Department of Veterinary Pathology, Iowa State University, Ames, IA, United States
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18
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Menon A, Perry DA, Motyka J, Weiner S, Standke A, Penkevich A, Keidan M, Young VB, Rao K. Changes in the Association between Diagnostic Testing Method, PCR Ribotype, and Clinical Outcomes from Clostridioides difficile Infection: One Institution's Experience. Clin Infect Dis 2020; 73:e2883-e2889. [PMID: 32930705 DOI: 10.1093/cid/ciaa1395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND In patients with Clostridioides difficile infection (CDI), the relationship between clinical, microbial, and temporal/epidemiological trends relate and disease severity and adverse outcomes is incompletely understood. Here, in a follow-up to our study conducted in 2010-2013, we evaluate stool toxin levels and C. difficile PCR ribotypes. We hypothesized that elevated stool toxins and infection with ribotype 027 associate with severe disease and adverse outcomes. METHODS In a cohort of 565 subjects at the University of Michigan with CDI diagnosed by positive testing for toxins A/B by EIA or PCR for the tcdB gene, we quantified stool toxin levels via a modified cell cytotoxicity assay, isolated C. difficile by anaerobic culture, and performed PCR ribotyping. Severe CDI was defined by IDSA criteria, and primary outcomes were all-cause 30-day mortality and a composite of colectomy, ICU admission, and/or death attributable to CDI within 30 days. Analyses included bivariable tests and adjusted logistic regression. RESULTS 199 samples were diagnosed by EIA and 447 were diagnosed by PCR. Toxin positivity associated with IDSA severity, but not primary outcomes. In 2016, compared to 2010-2013, ribotype 106 newly emerged, accounting for 10.6% of strains, ribotype 027 fell from 16.5% to 9.3%, and ribotype 014-027 remained stable at 18.9%. Ribotype 014-020 associated with IDSA severity and 30-day mortality (P=.001). CONCLUSION Toxin positivity by EIA and CCA associated with IDSA severity, but not with subsequent adverse outcomes. The molecular epidemiology of C. difficile has shifted, and this may have implications for the optimal diagnostic strategy for and clinical severity of CDI.
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Affiliation(s)
- Anitha Menon
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - D Alex Perry
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jonathan Motyka
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Shayna Weiner
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Alexandra Standke
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Aline Penkevich
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Micah Keidan
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Vincent B Young
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
| | - Krishna Rao
- Department of Internal Medicine, Division of Infectious Diseases, University of Michigan, Ann Arbor, MI, USA.,University of Michigan Medical School, Ann Arbor, MI, USA
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19
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Smith AB, Soto Ocana J, Zackular JP. From Nursery to Nursing Home: Emerging Concepts in Clostridioides difficile Pathogenesis. Infect Immun 2020; 88:IAI.00934-19. [PMID: 32122939 PMCID: PMC7309631 DOI: 10.1128/iai.00934-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Clostridioides difficile is a Gram-positive, spore-forming, anaerobic bacterium that infects the human gastrointestinal tract, causing a wide range of disorders that vary in severity from mild diarrhea to toxic megacolon and/or death. Over the past decade, incidence, severity, and costs associated with C. difficile infection (CDI) have increased dramatically in both the pediatric and adult populations. The factors driving this rapidly evolving epidemiology remain largely unknown but are likely due in part to previously unappreciated host, microbiota, and environmental factors. In this review, we will cover the risks and challenges of CDI in adult and pediatric populations and examine asymptomatic colonization in infants. We will also discuss the emerging role of diet, pharmaceutical drugs, and pathogen-microbiota interactions in C. difficile pathogenesis, as well as the impact of host-microbiota interactions in the manifestation of C. difficile-associated disease. Finally, we highlight new areas of research and novel strategies that may shed light on this complex infection and provide insights into the future of microbiota-based therapeutics for CDI.
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Affiliation(s)
- Alexander B Smith
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joshua Soto Ocana
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Joseph P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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20
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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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21
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Saund K, Lapp Z, Thiede SN, Pirani A, Snitkin ES. prewas: data pre-processing for more informative bacterial GWAS. Microb Genom 2020; 6. [PMID: 32310745 PMCID: PMC7371116 DOI: 10.1099/mgen.0.000368] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
While variant identification pipelines are becoming increasingly standardized, less attention has been paid to the pre-processing of variants prior to their use in bacterial genome-wide association studies (bGWAS). Three nuances of variant pre-processing that impact downstream identification of genetic associations include the separation of variants at multiallelic sites, separation of variants in overlapping genes, and referencing of variants relative to ancestral alleles. Here we demonstrate the importance of these variant pre-processing steps on diverse bacterial genomic datasets and present prewas, an R package, that standardizes the pre-processing of multiallelic sites, overlapping genes, and reference alleles before bGWAS. This package facilitates improved reproducibility and interpretability of bGWAS results. prewas enables users to extract maximal information from bGWAS by implementing multi-line representation for multiallelic sites and variants in overlapping genes. prewas outputs a binary SNP matrix that can be used for SNP-based bGWAS and will prevent the masking of minor alleles during bGWAS analysis. The optional binary gene matrix output can be used for gene-based bGWAS, which will enable users to maximize the power and evolutionary interpretability of their bGWAS studies. prewas is available for download from GitHub.
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Affiliation(s)
- Katie Saund
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Zena Lapp
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA
| | - Stephanie N Thiede
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Ali Pirani
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Evan S Snitkin
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA.,Department of Internal Medicine/Division of Infectious Diseases, University of Michigan, Ann Arbor, Michigan, USA
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22
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Selle K, Fletcher JR, Tuson H, Schmitt DS, McMillan L, Vridhambal GS, Rivera AJ, Montgomery SA, Fortier LC, Barrangou R, Theriot CM, Ousterout DG. In Vivo Targeting of Clostridioides difficile Using Phage-Delivered CRISPR-Cas3 Antimicrobials. mBio 2020; 11:e00019-20. [PMID: 32156803 PMCID: PMC7064742 DOI: 10.1128/mbio.00019-20] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 01/23/2020] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile is an important nosocomial pathogen that causes approximately 500,000 cases of C. difficile infection (CDI) and 29,000 deaths annually in the United States. Antibiotic use is a major risk factor for CDI because broad-spectrum antimicrobials disrupt the indigenous gut microbiota, decreasing colonization resistance against C. difficile Vancomycin is the standard of care for the treatment of CDI, likely contributing to the high recurrence rates due to the continued disruption of the gut microbiota. Thus, there is an urgent need for the development of novel therapeutics that can prevent and treat CDI and precisely target the pathogen without disrupting the gut microbiota. Here, we show that the endogenous type I-B CRISPR-Cas system in C. difficile can be repurposed as an antimicrobial agent by the expression of a self-targeting CRISPR that redirects endogenous CRISPR-Cas3 activity against the bacterial chromosome. We demonstrate that a recombinant bacteriophage expressing bacterial genome-targeting CRISPR RNAs is significantly more effective than its wild-type parent bacteriophage at killing C. difficile both in vitro and in a mouse model of CDI. We also report that conversion of the phage from temperate to obligately lytic is feasible and contributes to the therapeutic suitability of intrinsic C. difficile phages, despite the specific challenges encountered in the disease phenotypes of phage-treated animals. Our findings suggest that phage-delivered programmable CRISPR therapeutics have the potential to leverage the specificity and apparent safety of phage therapies and improve their potency and reliability for eradicating specific bacterial species within complex communities, offering a novel mechanism to treat pathogenic and/or multidrug-resistant organisms.IMPORTANCEClostridioides difficile is a bacterial pathogen responsible for significant morbidity and mortality across the globe. Current therapies based on broad-spectrum antibiotics have some clinical success, but approximately 30% of patients have relapses, presumably due to the continued perturbation to the gut microbiota. Here, we show that phages can be engineered with type I CRISPR-Cas systems and modified to reduce lysogeny and to enable the specific and efficient targeting and killing of C. difficilein vitro and in vivo. Additional genetic engineering to disrupt phage modulation of toxin expression by lysogeny or other mechanisms would be required to advance a CRISPR-enhanced phage antimicrobial for C. difficile toward clinical application. These findings provide evidence into how phage can be combined with CRISPR-based targeting to develop novel therapies and modulate microbiomes associated with health and disease.
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Affiliation(s)
- Kurt Selle
- Locus Biosciences, Inc., Morrisville, North Carolina, USA
| | - Joshua R Fletcher
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Hannah Tuson
- Locus Biosciences, Inc., Morrisville, North Carolina, USA
| | | | - Lana McMillan
- Locus Biosciences, Inc., Morrisville, North Carolina, USA
| | | | - Alissa J Rivera
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Stephanie A Montgomery
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Canada
| | - Rodolphe Barrangou
- Locus Biosciences, Inc., Morrisville, North Carolina, USA
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, North Carolina, USA
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
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Abstract
Clostridium (reclassified as " Clostridioides ") difficile infection (CDI) is a healthcare-associated infection and significant source of potentially preventable morbidity, recurrence, and death, particularly among hospitalized older adults. Additional risk factors include antibiotic use and severe underlying illness. The increasing prevalence of community-associated CDI is gaining recognition as a novel source of morbidity in previously healthy patients. Even after recovery from initial infection, patients remain at risk for recurrence or reinfection with a new strain. Some pharmaco-epidemiologic studies have suggested an increased risk associated with proton pump inhibitors and protective effect from statins, but these findings have not been uniformly reproduced in all studies. Certain ribotypes of C. difficile , including the BI/NAP1/027, 106, and 018, are associated with increased antibiotic resistance and potential for higher morbidity and mortality. CDI remains a high-morbidity healthcare-associated infection, and better understanding of ribotypes and medication risk factors could help to target treatment, particularly for patients with high recurrence risk.
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Affiliation(s)
- Ana C. De Roo
- Center for Healthcare Outcomes and Policy, University of Michigan, Ann Arbor, Michigan
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
| | - Scott E. Regenbogen
- Center for Healthcare Outcomes and Policy, University of Michigan, Ann Arbor, Michigan
- Department of Surgery, University of Michigan, Ann Arbor, Michigan
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Shen A. Clostridioides difficile Spores: Bile Acid Sensors and Trojan Horses of Transmission. Clin Colon Rectal Surg 2020; 33:58-66. [PMID: 32104157 DOI: 10.1055/s-0040-1701230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The Gram-positive, spore-forming bacterium, Clostridioides difficile is the leading cause of healthcare-associated infections in the United States, although it also causes a significant number of community-acquired infections. C. difficile infections, which range in severity from mild diarrhea to toxic megacolon, cost more to treat than matched infections, with an annual treatment cost of approximately $6 billion for almost half-a-million infections. These high-treatment costs are due to the high rates of C. difficile disease recurrence (>20%) and necessity for special disinfection measures. These complications arise in part because C. difficile makes metabolically dormant spores, which are the major infectious particle of this obligate anaerobe. These seemingly inanimate life forms are inert to antibiotics, resistant to commonly used disinfectants, readily disseminated, and capable of surviving in the environment for a long period of time. However, upon sensing specific bile salts in the vertebrate gut, C. difficile spores transform back into the vegetative cells that are responsible for causing disease. This review discusses how spores are ideal vectors for disease transmission and how antibiotics modulate this process. We also describe the resistance properties of spores and how they create challenges eradicating spores, as well as promote their spread. Lastly, environmental reservoirs of C. difficile spores and strategies for destroying them particularly in health care environments will be discussed.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts
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25
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Fuzi M, Rodriguez Baño J, Toth A. Global Evolution of Pathogenic Bacteria With Extensive Use of Fluoroquinolone Agents. Front Microbiol 2020; 11:271. [PMID: 32158437 PMCID: PMC7052298 DOI: 10.3389/fmicb.2020.00271] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/06/2020] [Indexed: 12/11/2022] Open
Abstract
It is well-established that the spread of many multidrug-resistant (MDR) bacteria is predominantly clonal. Interestingly the international clones/sequence types (STs) of most pathogens emerged and disseminated during the last three decades. Strong experimental evidence from multiple laboratories indicate that diverse fitness cost associated with high-level resistance to fluoroquinolones contributed to the selection and promotion of the international clones/STs of hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA), extended-spectrum β-lactamase-(ESBL)-producing Klebsiella pneumoniae, ESBL-producing Escherichia coli and Clostridioides difficile. The overwhelming part of the literature investigating the epidemiology of the pathogens as a function of fluoroquinolone use remain in concordence with these findings. Moreover, recent in vitro data clearly show the potential of fluoroquinolone exposure to shape the clonal evolution of Salmonella Enteritidis. The success of the international clones/STs in all these species was linked to the strains' unique ability to evolve multiple energetically beneficial gyrase and topoisomerase IV mutations conferring high-level resistance to fluorquinolones and concomittantly permitting the acquisition of an extra resistance gene load without evoking appreciable fitness cost. Furthermore, by analyzing the clonality of multiple species, the review highlights, that in environments under high antibiotic exposure virulence factors play only a subsidiary role in the clonal dynamics of bacteria relative to multidrug-resistance coupled with favorable fitness (greater speed of replication). Though other groups of antibiotics should also be involved in selecting clones of bacterial pathogens the role of fluoroquinolones due to their peculiar fitness effect remains unique. It is suggested that probably no bacteria remain immune to the influence of fluoroquinolones in shaping their evolutionary dynamics. Consequently a more judicious use of fluoroquinolones, attuned to the proportion of international clone/ST isolates among local pathogens, would not only decrease resistance rates against this group of antibiotics but should also ameliorate the overall antibiotic resistance landscape.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis University, Budapest, Hungary
| | - Jesus Rodriguez Baño
- Unit of Infectious Diseases, Clinical Microbiology and Preventive Medicine, Department of Medicine, Hospital Universitario Virgen Macarena, University of Seville - Biomedicine Institute of Seville (IBiS), Seville, Spain
| | - Akos Toth
- Department of Bacteriology, Mycology and Parasitology, National Public Health Center, Budapest, Hungary
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Simecka JW, Fulda KG, Pulse M, Lee JH, Vitucci J, Nguyen P, Taylor P, Filipetto F, Espinoza AM, Sharma S. Primary care clinics can be a source of exposure to virulent Clostridium (now Clostridioides) difficile: An environmental screening study of hospitals and clinics in Dallas-Fort Worth region. PLoS One 2019; 14:e0220646. [PMID: 31415582 PMCID: PMC6695158 DOI: 10.1371/journal.pone.0220646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 07/19/2019] [Indexed: 01/05/2023] Open
Abstract
C. difficile is an endospore-forming pathogen, which is becoming a common cause of microbial health-care associated gastrointestinal disease in the United States. Both healthy and symptomatic patients can shed C. difficile spores into the environment, which can survive for long periods, being resistant to desiccation, heat, and disinfectants. In healthcare facilities, environmental contamination with C. difficile is a major concern as a potential source of exposure to this pathogen and risk of disease in susceptible patients. Although hospital-acquired infection is recognized, community-acquired infection is an increasingly recognized health problem. Primary care clinics may be a significant source of exposure to this pathogen; however, there are limited data about presence of environmental C. difficile within clinics. To address the potential for primary care clinics as a source of environmental exposure to virulent C. difficile, we measured the frequency of environmental contamination with spores in clinic examination rooms and hospital rooms in Dallas-Fort Worth (DFW) area of Texas. The ribotypes and presence of toxin genes from some environmental isolates were compared. Our results indicate primary care clinics have higher frequencies of contamination than hospitals. After notification of the presence of C. difficile spores in the clinics and an educational discussion to emphasize the importance of this infection and methods of infection prevention, environmental contamination in clinics was reduced on subsequent sampling to that found in hospitals. Thus, primary care clinics can be a source of exposure to virulent C. difficile, and recognition of this possibility can result in improved infection prevention, potentially reducing community-acquired C. difficile infections and subsequent disease.
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Affiliation(s)
- Jerry W. Simecka
- Department of Pharmaceutical Sciences and UNT Preclinical Services, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, United States of America
- * E-mail:
| | - Kimberly G. Fulda
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, United States of America
- The North Texas Primary Care Practice-Based Research Network (NorTex), University of North Texas Health Science Center, Fort Worth, TX, United States of America
| | - Mark Pulse
- Department of Pharmaceutical Sciences and UNT Preclinical Services, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, United States of America
| | - Joon-hak Lee
- Department of Biostatistics and Epidemiology, School of Public Health, University of North Texas Health Science Center, Fort Worth, TX, United States of America
| | - John Vitucci
- Department of Pharmaceutical Sciences and UNT Preclinical Services, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, United States of America
| | - Phung Nguyen
- Department of Pharmaceutical Sciences and UNT Preclinical Services, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, TX, United States of America
| | - Patricia Taylor
- The Dallas-Fort Worth Hospital Council Education and Research Foundation, Irving, TX, United States of America
| | - Frank Filipetto
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, United States of America
- The North Texas Primary Care Practice-Based Research Network (NorTex), University of North Texas Health Science Center, Fort Worth, TX, United States of America
| | - Anna M. Espinoza
- Texas College of Osteopathic Medicine, University of North Texas Health Science Center, Fort Worth, TX, United States of America
- The North Texas Primary Care Practice-Based Research Network (NorTex), University of North Texas Health Science Center, Fort Worth, TX, United States of America
| | - Sushma Sharma
- The Dallas-Fort Worth Hospital Council Education and Research Foundation, Irving, TX, United States of America
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27
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Rohlfing AE, Eckenroth BE, Forster ER, Kevorkian Y, Donnelly ML, Benito de la Puebla H, Doublié S, Shen A. The CspC pseudoprotease regulates germination of Clostridioides difficile spores in response to multiple environmental signals. PLoS Genet 2019; 15:e1008224. [PMID: 31276487 PMCID: PMC6636752 DOI: 10.1371/journal.pgen.1008224] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 07/17/2019] [Accepted: 05/31/2019] [Indexed: 12/18/2022] Open
Abstract
The gastrointestinal pathogen, Clostridioides difficile, initiates infection when its metabolically dormant spore form germinates in the mammalian gut. While most spore-forming bacteria use transmembrane germinant receptors to sense nutrient germinants, C. difficile is thought to use the soluble pseudoprotease, CspC, to detect bile acid germinants. To gain insight into CspC's unique mechanism of action, we solved its crystal structure. Guided by this structure, we identified CspC mutations that confer either hypo- or hyper-sensitivity to bile acid germinant. Surprisingly, hyper-sensitive CspC variants exhibited bile acid-independent germination as well as increased sensitivity to amino acid and/or calcium co-germinants. Since mutations in specific residues altered CspC's responsiveness to these different signals, CspC plays a critical role in regulating C. difficile spore germination in response to multiple environmental signals. Taken together, these studies implicate CspC as being intimately involved in the detection of distinct classes of co-germinants in addition to bile acids and thus raises the possibility that CspC functions as a signaling node rather than a ligand-binding receptor.
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Affiliation(s)
- Amy E. Rohlfing
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Brian E. Eckenroth
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Emily R. Forster
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Yuzo Kevorkian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - M. Lauren Donnelly
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
- Sackler School of Graduate Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hector Benito de la Puebla
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, Vermont, United States of America
| | - Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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28
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To Lump or To Split: Does Strain Lineage for Clostridioides difficile Matter? J Clin Microbiol 2019; 57:JCM.00196-19. [PMID: 30867236 DOI: 10.1128/jcm.00196-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Since 2001, numerous descriptive ecological studies of Clostridioides difficile infections (CDI) have identified a single lineage (BI/NAP1/027) associated with the epidemics of CDI, increased severity of CDI, and increased likelihood of incident CDI to become recurrent. Establishing causality between the clinical severity and outcomes for CDI and the lineages of the infecting strains, however, has proved elusive, with many conflicting results in previous observational studies. In this issue of the Journal of Clinical Microbiology, J. R. Garneau, C. N. Abou Chakra, L.-C. Fortier, A.-C. Labbé, et al. (J Clin Microbiol 57:e01724-18, 2019, https://doi.org/10.1128/JCM.01724-18) performed multilocus variable-number tandem-repeat analysis (MLVA) on 450 isolates from epidemic strain CDI arising in 10 Canadian centers during a previously well-described epidemic to assess the hypothesis that subpopulations of this lineage are associated with adverse clinical outcomes. The authors' key finding, however, was that MLVA genotyping grouped infections closely with associated hospital centers; CDI severity was not associated with any particular sublineage by MLVA. While the study does not support any causal inferences about strain-specific virulence of CDI, it does highlight the power of MLVA, a genotyping tool that remains valuable in tracking the geospatial transmission dynamics of CDI.
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29
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Wehrhahn MC, Keighley C, Kurtovic J, Knight DR, Hong S, Hutton ML, Lyras D, Wang Q, Leong R, Borody T, Edye M, Riley TV. A series of three cases of severe Clostridium difficile infection in Australia associated with a binary toxin producing clade 2 ribotype 251 strain. Anaerobe 2018; 55:117-123. [PMID: 30500477 DOI: 10.1016/j.anaerobe.2018.11.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/13/2018] [Accepted: 11/26/2018] [Indexed: 02/08/2023]
Abstract
Three patients with severe Clostridium difficile infection (CDI) caused by an unusual strain of C. difficile, PCR ribotype (RT) 251, were identified in New South Wales, Australia. All cases presented with severe diarrhoea, two had multiple recurrences and one died following a colectomy. C. difficile RT251 strains were isolated by toxigenic culture. Genetic characterisation was performed using techniques including toxin gene profiling, PCR ribotyping, whole genome sequencing (WGS), in-silico multi-locus-sequence-typing (MLST) and core-genome single nucleotide variant (SNV) analyses. Antimicrobial susceptibility was determined using an agar incorporation method. In vitro toxin production was confirmed by Vero cell cytotoxicity assay and pathogenicity was assessed in a murine model of CDI. All RT251 isolates contained toxin A (tcdA), toxin B (tcdB) and binary toxin (cdtA and cdtB) genes. Core-genome analyses revealed the RT251 strains were clonal, with 0-5 SNVs between isolates. WGS and MLST clustered RT251 in the same evolutionary clade (clade 2) as RT027. Despite comparatively lower levels of in vitro toxin production, in the murine model RT251 infection resembled RT027 infection. Mice showed marked weight loss, severe disease within 48 h post-infection and death. All isolates were susceptible to metronidazole and vancomycin. Our observations suggest C. difficile RT251 causes severe disease and emphasise the importance of ongoing surveillance for new and emerging strains of C. difficile with enhanced virulence.
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Affiliation(s)
- Michael C Wehrhahn
- Microbiology Department, Douglass Hanly Moir Pathology, Macquarie Park, NSW, Australia.
| | - Caitlin Keighley
- Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead, NSW, Australia
| | - Jelica Kurtovic
- Gastrointestinal and Liver Unit, Prince of Wales Hospital, Randwick, NSW, Australia
| | - Daniel R Knight
- School of Veterinary & Life Sciences, Murdoch University, Murdoch, WA, Australia
| | - Stacey Hong
- School of Biomedical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
| | - Melanie L Hutton
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology Laboratory Services, Westmead, NSW, Australia
| | - Rupert Leong
- Macquarie GI, Macquarie University Hospital, NSW, Australia
| | - Tom Borody
- Centre for Digestive Diseases, Five Dock, NSW, Australia
| | - Michael Edye
- Blacktown Mount Druitt Clinical School, Western Sydney University, NSW, Australia
| | - Thomas V Riley
- School of Veterinary & Life Sciences, Murdoch University, Murdoch, WA, Australia; School of Biomedical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; School of Medical & Health Sciences, Edith Cowan University, Joondalup, WA, Australia
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30
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Lactobacillus plantarum 299v Reduces the Incidence of Clostridium difficile Infection in Nephrology and Transplantation Ward-Results of One Year Extended Study. Nutrients 2018; 10:nu10111574. [PMID: 30355985 PMCID: PMC6266863 DOI: 10.3390/nu10111574] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 12/15/2022] Open
Abstract
Background: Lactobacillus plantarum 299v (LP299v) is a probiotic strain which influences on the intestinal bacterial flora. This is why, it has been introduced into clinical practice for the prevention and treatment of diarrheal disorders and alleviation of their symptoms in patients during antibiotic therapy. However, the use of probiotics in the prophylaxis of Clostridium difficile infections (CDI) in these patients is problematic. The aim of this clinical, retrospective, single-centre study was to analyse the incidence of CDI among patients hospitalized in the nephrology and transplantation ward in the period before, during and after stopping of LP299v prophylaxis. Methods: Among 5341 patients hospitalized in the nephrology and transplantation ward over a three year period, 34 patients with CDI were diagnosed and included in this analysis. From December 2013 to December 2014 all patients under antibiotic and immunosuppressive therapies received LP299v as a prophylaxis of CDI. The observation period consisted of three twelve-months periods: before, during LP299v use and after stopping of such method of CDI prevention. Results: A significant (p = 0.0003) reduction of CDI incidence during LP299v use (0.11%) was observed compared to two other periods, that is, before and after LP299v use (1.03% and 0.77%, respectively). Conclusions: Routine use of LP299v as a CDI prophylaxis may prevent CDI during antibiotics therapy in patients treated with immunosuppressive agents in nephrology and transplantation ward.
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Coullon H, Rifflet A, Wheeler R, Janoir C, Boneca IG, Candela T. N-Deacetylases required for muramic-δ-lactam production are involved in Clostridium difficile sporulation, germination, and heat resistance. J Biol Chem 2018; 293:18040-18054. [PMID: 30266804 DOI: 10.1074/jbc.ra118.004273] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/24/2018] [Indexed: 01/08/2023] Open
Abstract
Spores are produced by many organisms as a survival mechanism activated in response to several environmental stresses. Bacterial spores are multilayered structures, one of which is a peptidoglycan layer called the cortex, containing muramic-δ-lactams that are synthesized by at least two bacterial enzymes, the muramoyl-l-alanine amidase CwlD and the N-deacetylase PdaA. This study focused on the spore cortex of Clostridium difficile, a Gram-positive, toxin-producing anaerobic bacterial pathogen that can colonize the human intestinal tract and is a leading cause of antibiotic-associated diarrhea. Using ultra-HPLC coupled with high-resolution MS, here we found that the spore cortex of the C. difficile 630Δerm strain differs from that of Bacillus subtilis Among these differences, the muramic-δ-lactams represented only 24% in C. difficile, compared with 50% in B. subtilis CD630_14300 and CD630_27190 were identified as genes encoding the C. difficile N-deacetylases PdaA1 and PdaA2, required for muramic-δ-lactam synthesis. In a pdaA1 mutant, only 0.4% of all muropeptides carried a muramic-δ-lactam modification, and muramic-δ-lactams were absent in the cortex of a pdaA1-pdaA2 double mutant. Of note, the pdaA1 mutant exhibited decreased sporulation, altered germination, decreased heat resistance, and delayed virulence in a hamster infection model. These results suggest a much greater role for muramic-δ-lactams in C. difficile than in other bacteria, including B. subtilis In summary, the spore cortex of C. difficile contains lower levels of muramic-δ-lactams than that of B. subtilis, and PdaA1 is the major N-deacetylase for muramic-δ-lactam biosynthesis in C. difficile, contributing to sporulation, heat resistance, and virulence.
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Affiliation(s)
- Héloise Coullon
- From the EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, 92290 Châtenay-Malabry
| | - Aline Rifflet
- the Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, 75724 Paris, and; INSERM, Équipe Avenir, 75015 Paris, France
| | - Richard Wheeler
- the Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, 75724 Paris, and; INSERM, Équipe Avenir, 75015 Paris, France
| | - Claire Janoir
- From the EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, 92290 Châtenay-Malabry
| | - Ivo Gomperts Boneca
- the Institut Pasteur, Unité Biologie et Génétique de la Paroi Bactérienne, 75724 Paris, and; INSERM, Équipe Avenir, 75015 Paris, France
| | - Thomas Candela
- From the EA4043 Unité Bactéries Pathogènes et Santé (UBaPS), Université Paris-Sud, Université Paris-Saclay, 92290 Châtenay-Malabry,.
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32
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Watanabe H, Koizumi Y, Matsumoto A, Asai N, Yamagishi Y, Mikamo H. Association between Clostridioides difficile ribotypes, restriction endonuclease analysis types, and toxin gene expression. Anaerobe 2018; 54:140-143. [PMID: 30201540 DOI: 10.1016/j.anaerobe.2018.09.002] [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: 06/03/2018] [Revised: 08/16/2018] [Accepted: 09/03/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES Clostridioides difficile strains cause severe infection. Previous studies suggested that the virulence of C. difficile is dependent on ribotype; however, this hypothesis is still controversial. We aim to investigate the relationship between ribotypes, restriction endonuclease analysis (REA) types, and toxin gene expression in C. difficile strains. METHODS We utilized 53 clinical C. difficile strains. All strains were assigned a molecular strain type using PCR ribotyping and REA typing and classified into 17 ribotypes and six REA types. The expression of toxin genes (tcdA, tcdB, and cdtB) in C. difficile strains were quantified by real-time PCR using each specific primer set, and expression was normalized to that of the housekeeping gene rpoA. RESULTS All 53 strains expressed tcdB and four strains expressed cdtB. Five strains did not express tcdA. Most ribotype and REA type strains expressed tcdA and tcdB similar to the BAA-1870 strain. In cdtB-positive strains, the cdtB expression levels were similar to those in the BAA-1870 strain. tcdA and tcdB expression levels were similar in the cdtB-positive and cdtB-negative strains. CONCLUSION Toxin gene expression was not associated with the ribotype. Production of binary toxin C. difficile transferase was not related to tcdA and tcdB expression levels.
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Affiliation(s)
- Hiroki Watanabe
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan
| | - Yusuke Koizumi
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan
| | - Asami Matsumoto
- Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan
| | - Nobuhiro Asai
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan
| | - Yuka Yamagishi
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan; Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan
| | - Hiroshige Mikamo
- Department of Clinical Infectious Diseases, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan; Department of Infection Control and Prevention, Aichi Medical University Hospital, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan; Department of Clinical Infectious Diseases, Aichi Medical University Graduate School of Medicine, 1-1, Yazako-karimata, Nagakute, Aichi 480-1195, Japan.
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Horvat S, Rupnik M. Interactions Between Clostridioides difficile and Fecal Microbiota in in Vitro Batch Model: Growth, Sporulation, and Microbiota Changes. Front Microbiol 2018; 9:1633. [PMID: 30087660 PMCID: PMC6066498 DOI: 10.3389/fmicb.2018.01633] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 06/29/2018] [Indexed: 12/14/2022] Open
Abstract
Disturbance in gut microbiota is crucial for the development of Clostridioides difficile infection (CDI). Different mechanisms through which gut microbiota influences C. difficile colonization are known. However, C. difficile could also affect gut microbiota balance as previously demonstrated by cultivation of fecal microbiota in C. difficile conditioned medium. In current study, the interactions of C. difficile cells with gut microbiota were addressed. Three different strains (ribotypes 027, 014/020, and 010) were co-cultivated with two types of fecal microbiota (healthy and dysbiotic) using in vitro batch model. While all strains showed higher sporulation frequency in the presence of dysbiotic fecal microbiota, the growth was strain dependent. C. difficile either proliferated to comparable levels in the presence of dysbiotic and healthy fecal microbiota or grew better in co-culture with dysbiotic microbiota. In co-cultures with any C. difficile strain fecal microbiota showed decreased richness and diversity. Dysbiotic fecal microbiota was more affected after co-culture with C. difficile than healthy microbiota. Altogether, 62 OTUs were significantly changed in co-cultures of dysbiotic microbiota/C. difficile and 45 OTUs in co-cultures of healthy microbiota/C. difficile. However, the majority of significantly changed OTUs in both types of microbiota belonged to the phylum Firmicutes with Lachnospiraceae and Ruminococcaceae origin.
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Affiliation(s)
- Sabina Horvat
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Maja Rupnik
- Department of Microbiology, Faculty of Medicine, University of Maribor, Maribor, Slovenia.,Centre for Medical Microbiology, National Laboratory for Health, Environment and Food, Maribor, Slovenia
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Gu H, Shi K, Liao Z, Qi H, Chen S, Wang H, Li S, Ma Y, Wang J. Time-resolved transcriptome analysis of Clostridium difficile R20291 response to cysteine. Microbiol Res 2018; 215:114-125. [PMID: 30172297 DOI: 10.1016/j.micres.2018.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/21/2018] [Accepted: 07/07/2018] [Indexed: 01/05/2023]
Abstract
The incidence of Clostridium difficile infection has been steadily rising over the past decade. The increase in the rate of incidence is associated with the specific NAP1/BI/027 strains which are "hypervirulent" and have led to several large outbreaks since their emergence. However, the relation between these outbreaks and virulence regulation mechanisms remains unclear. It has been reported that the major virulence factor TcdA and TcdB in C. difficile could be repressed by cysteine. Here, we investigated the functional and virulence-associated regulation of C. difficile R20291 response to cysteine by using a time-resolved genome-wide transcriptome analysis. Dramatic changes of gene expression in C. difficile revealed functional processes related to transport, metabolism, and regulators in the presence of cysteine during different phases of growth. Flagellar and ribosomal genes were significantly down-regulated in long-term response to cysteine. Many NAP1/BI/027- specific genes were also modulated by cysteine. In addition, cdsB inactivation in C. difficile R20291 could remove the repression of toxin synthesis but could not remove the repression of butyrate production in the presence of cysteine. This suggests that toxin synthesis and butyrate production might have different regulatory controls in response to cysteine. Altogether, our research provides important insights into the regulatory mechanisms of C. difficile response to cysteine.
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Affiliation(s)
- Huawei Gu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Kan Shi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Zhengping Liao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Haonan Qi
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shuyi Chen
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Haiying Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Shan Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, China.
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An Observational Cohort Study of Clostridium difficile Ribotype 027 and Recurrent Infection. mSphere 2018; 3:3/3/e00033-18. [PMID: 29794054 PMCID: PMC5967198 DOI: 10.1128/msphere.00033-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 05/02/2018] [Indexed: 12/18/2022] Open
Abstract
CDI is a major public health issue, with over 400,000 cases per year in the United States alone. Recurrent CDI is common, occurring in approximately one in five individuals after a primary episode. Although interventions exist that could reduce the risk of recurrence, deployment in all patients is limited by cost, invasiveness, and/or an undetermined long-term safety profile. Thus, clinicians need risk stratification tools to properly allocate treatments. Because prior research on clinical predictors has failed to yield a reliable, reproducible, and effective predictive model to assist treatment decisions, accurate biomarkers of recurrence would be of great value. This study tested whether PCR ribotype independently predicted rCDI, and the data build upon prior research in showing that ribotype 027 is associated with rCDI. Recurrent Clostridium difficile infection (rCDI) frequently complicates recovery from CDI. Accurately predicting rCDI would allow judicious allocation of limited resources, but published models have met with limited success. Thus, biomarkers predictive of recurrence have been sought. This study tested whether PCR ribotype independently predicted rCDI. Stool samples from nonpregnant inpatients ≥18 years of age with diarrhea were included from October 2010 to January 2013 after the patients tested positive for C. difficile in the clinical microbiology laboratory. Per guidelines, the rCDI was defined as a positive test for C. difficile at >2 weeks but ≤8 weeks from the index episode. For each sample, a single colony of C. difficile was isolated by anaerobic culture, confirmed to be toxigenic by PCR, and ribotyped. Simple logistic regression and multiple logistic regression were used to model the primary outcome of rCDI, incorporating a wide range of clinical parameters. In total, 927 patients with 968 index episodes of CDI were included, with 110 (11.4%) developing rCDI. Age and use of proton pump inhibitors or concurrent antibiotics did not increase the risk of rCDI. Low serum bilirubin levels and ribotype 027 were associated with increased risk of rCDI on unadjusted analysis, with health care-associated CDI being inversely associated. In the final multivariable model, ribotype 027 was the strongest independent predictor of rCDI (odds ratio, 2.17; 95% confidence interval, 1.33 to 3.56; P = 0.002). Ribotype 027 is an independent predictor of rCDI. IMPORTANCE CDI is a major public health issue, with over 400,000 cases per year in the United States alone. Recurrent CDI is common, occurring in approximately one in five individuals after a primary episode. Although interventions exist that could reduce the risk of recurrence, deployment in all patients is limited by cost, invasiveness, and/or an undetermined long-term safety profile. Thus, clinicians need risk stratification tools to properly allocate treatments. Because prior research on clinical predictors has failed to yield a reliable, reproducible, and effective predictive model to assist treatment decisions, accurate biomarkers of recurrence would be of great value. This study tested whether PCR ribotype independently predicted rCDI, and the data build upon prior research in showing that ribotype 027 is associated with rCDI.
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Abstract
Each year in the United States, billions of dollars are spent combating almost half a million Clostridium difficile infections (CDIs) and trying to reduce the ∼29,000 patient deaths in which C. difficile has an attributed role. In Europe, disease prevalence varies by country and level of surveillance, though yearly costs are estimated at €3 billion. One factor contributing to the significant health care burden of C. difficile is the relatively high frequency of recurrent CDIs. Recurrent CDI, i.e., a second episode of symptomatic CDI occurring within 8 weeks of successful initial CDI treatment, occurs in ∼25% of patients, with 35 to 65% of these patients experiencing multiple episodes of recurrent disease. Using microbial communities to treat recurrent CDI, either as whole fecal transplants or as defined consortia of bacterial isolates, has shown great success (in the case of fecal transplants) or potential promise (in the case of defined consortia of isolates). This review will briefly summarize the epidemiology and physiology of C. difficile infection, describe our current understanding of how fecal microbiota transplants treat recurrent CDI, and outline potential ways that knowledge can be used to rationally design and test alternative microbe-based therapeutics.
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Chilton C, Pickering D, Freeman J. Microbiologic factors affecting Clostridium difficile recurrence. Clin Microbiol Infect 2018; 24:476-482. [DOI: 10.1016/j.cmi.2017.11.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 12/17/2022]
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Blanco N, Walk S, Malani AN, Rickard A, Benn M, Eisenberg M, Zhang M, Foxman B. Clostridium difficile shows no trade-off between toxin and spore production within the human host. J Med Microbiol 2018. [PMID: 29533173 DOI: 10.1099/jmm.0.000719] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
PURPOSE This study aimed to describe the correlation between Clostridium difficile spore and toxin levels within the human host. In addition, we assessed whether overgrowth of Candida albicans modified this association. METHODOLOGY We measured toxin, spore and Candida albicans levels among 200 successively collected stool samples that tested positive for C. difficile, and PCR ribotyped these C. difficile isolates. Analysis of variance and linear regression were used to test the association between spore and toxin levels. Kruskal-Wallis tests and t-tests were used to compare the association between spore or toxin levels and host, specimen, or pathogen characteristics. RESULTS C. difficile toxin and spore levels were positively associated (P<0.001); this association did not vary significantly with C. albicans overgrowth [≥5 logs of C. albicans colony-forming units (c.f.u.) g-1]. However, ribotypes 027 and 078-126 were significantly associated with higher levels of toxin and spores, and C. albicans overgrowth. CONCLUSION The strong positive association observed between in vivo levels of C. difficile toxin and spores suggests that patients with more severe C. difficile infections may have increased spore production, enhancing C. difficile transmission. Although, on average, spore levels were higher in toxin-positive samples than in toxin-negative/PCR-positive samples, spores were found in almost all toxin-negative samples. The ubiquity of spore production among toxin-negative and formed stool samples emphasizes the importance of following infection prevention and control measures for all C. difficile-positive patients during their entire hospital stay.
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Affiliation(s)
- Natalia Blanco
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Seth Walk
- Department of Microbiology and Immunology, College of Letters & Science, Montana State, Bozeman, Montana, USA
| | - Anurag N Malani
- Department of Infection Prevention and Control, Department of Internal Medicine, Division of Infectious Diseases, St Joseph Mercy Health System, Ann Arbor, Michigan, USA
| | - Alexander Rickard
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Michele Benn
- Department of Pathology, Microbiology Laboratory, St Joseph Mercy Health System, Ann Arbor, Michigan, USA
| | - Marisa Eisenberg
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Min Zhang
- Department of Infection Prevention and Control, Department of Internal Medicine, Division of Infectious Diseases, St Joseph Mercy Health System, Ann Arbor, Michigan, USA.,Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
| | - Betsy Foxman
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, Michigan, USA
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Sachsenheimer FE, Yang I, Zimmermann O, Wrede C, Müller LV, Gunka K, Groß U, Suerbaum S. Genomic and phenotypic diversity of Clostridium difficile during long-term sequential recurrences of infection. Int J Med Microbiol 2018; 308:364-377. [PMID: 29490877 DOI: 10.1016/j.ijmm.2018.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/22/2018] [Accepted: 02/18/2018] [Indexed: 01/26/2023] Open
Abstract
Infection with the emerging pathogen Clostridioides (Clostridium) difficile might lead to colonization of the gastrointestinal tract of humans and mammals eventually resulting in antibiotic-associated diarrhea, which can be mild to possibly life-threatening. Recurrences after antibiotic treatment have been described in 15-30% of the cases and are either caused by the original (relapse) or by new strains (reinfection). In this study, we describe a patient with ongoing recurrent C. difficile infections over 13 months. During this time, ten C. difficile strains of six different ribotypes could be isolated that were further characterized by phenotypic and genomic analyses including motility and sporulation assays, growth fitness and antibiotic susceptibility as well as whole-genome sequencing. PCR ribotyping of the isolates confirmed that the recurrences were a mixture of relapses and reinfections. One recurrence was due to a mixed infection with three different strains of two different ribotypes. Furthermore, genomes were sequenced and multi-locus sequence typing (MLST) was carried out, which identified the strains as members of sequence types (STs) 10, 11, 14 and 76. Comparison of the genomes of isolates of the same ST originating from recurrent CDI (relapses) indicated little within-patient microevolution and some concurrent within-patient diversity of closely related strains. Isolates of ribotype 126 that are binary toxin positive differed from other ribotypes in various phenotypic aspects including motility, sporulation behavior and cell morphology. Ribotype 126 is genetically related to ribotype 078 that has been associated with increased virulence. Isolates of the ribotype 126 exhibited elongated cells and a chaining phenotype, which was confirmed by membrane staining and scanning electron microscopy. Furthermore, this strain exhibits a sinking behavior in liquid medium in stationary growth phase. Taken together, our observation has proven multiple CDI recurrences that were based on a mixture of relapses and reinfections.
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Affiliation(s)
- F E Sachsenheimer
- Institute of Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, Göttingen, Germany.
| | - I Yang
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany; Lower Saxony Centre for Biomedical Engineering, Implant Research and Development, Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Stadtfelddamm 34, Hannover, Germany
| | - O Zimmermann
- Institute of Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, Göttingen, Germany
| | - C Wrede
- Institute of Functional and Applied Anatomy, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany
| | - L V Müller
- National Consulting Laboratory for Clostridium difficile, Germany
| | - K Gunka
- Institute of Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, Göttingen, Germany
| | - U Groß
- Institute of Medical Microbiology, University Medical Center Göttingen, Kreuzbergring 57, Göttingen, Germany
| | - S Suerbaum
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Carl-Neuberg-Str. 1, Hannover, Germany; Max von Pettenkofer Institute, Ludwig-Maximilians-Universität München, Pettenkoferstr. 9a, 80336 Munich, Germany; DZIF German Center for Infection Research, Hannover-Braunschweig and Munich Partner Sites, Germany
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40
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Blanco N, Foxman B, Malani AN, Zhang M, Walk S, Rickard AH, Eisenberg MC. An in silico evaluation of treatment regimens for recurrent Clostridium difficile infection. PLoS One 2017; 12:e0182815. [PMID: 28800598 PMCID: PMC5553947 DOI: 10.1371/journal.pone.0182815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 07/25/2017] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Clostridium difficile infection (CDI) is a significant nosocomial infection worldwide, that recurs in as many as 35% of infections. Risk of CDI recurrence varies by ribotype, which also vary in sporulation and germination rates. Whether sporulation/germination mediate risk of recurrence and effectiveness of treatment of recurring CDI remains unclear. We aim to assess the role of sporulation/germination patterns on risk of recurrence, and the relative effectiveness of the recommended tapered/pulsing regimens using an in silico model. METHODS We created a compartmental in-host mathematical model of CDI, composed of vegetative cells, toxins, and spores, to explore whether sporulation and germination have an impact on recurrence rates. We also simulated the effectiveness of three tapered/pulsed vancomycin regimens by ribotype. RESULTS Simulations underscored the importance of sporulation/germination patterns in determining pathogenicity and transmission. All recommended regimens for recurring CDI tested were effective in reducing risk of an additional recurrence. Most modified regimens were still effective even after reducing the duration or dosage of vancomycin. However, the effectiveness of treatment varied by ribotype. CONCLUSION Current CDI vancomycin regimen for treating recurrent cases should be studied further to better balance associated risks and benefits.
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Affiliation(s)
- Natalia Blanco
- Department of Epidemiology, School of Public Health, University of Michigan. Ann Arbor, Michigan, United States of America
| | - Betsy Foxman
- Department of Epidemiology, School of Public Health, University of Michigan. Ann Arbor, Michigan, United States of America
| | - Anurag N. Malani
- Department of Infection Prevention & Control, Department of Internal Medicine, Division of Infectious Diseases, St. Joseph Mercy Health System, Ann Arbor, Michigan, United States of America
| | - Min Zhang
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Seth Walk
- Department of Microbiology and Immunology, College of Letters & Science, Montana State, Bozeman, Montana, United States of America
| | - Alexander H. Rickard
- Department of Epidemiology, School of Public Health, University of Michigan. Ann Arbor, Michigan, United States of America
| | - Marisa C. Eisenberg
- Department of Epidemiology, School of Public Health, University of Michigan. Ann Arbor, Michigan, United States of America
- * E-mail:
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Clinical and laboratory features of the most common Clostridium difficile ribotypes isolated in Belgium. J Hosp Infect 2017; 95:394-399. [DOI: 10.1016/j.jhin.2016.12.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/11/2016] [Indexed: 11/19/2022]
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Abstract
Clostridium difficile infections (CDIs) have emerged as one of the principal threats to the health of hospitalized and immunocompromised patients. The importance of C difficile colonization is increasingly recognized not only as a source for false-positive clinical testing but also as a source of new infections within hospitals and other health care environments. In the last five years, several new treatment strategies that capitalize on the increasing understanding of the altered microbiome and host defenses in patients with CDI have completed clinical trials, including fecal microbiota transplantation. This article highlights the changing epidemiology, laboratory diagnostics, pathogenesis, and treatment of CDI.
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Abstract
Clostridium difficile is a Gram-positive spore-forming obligate anaerobe that is a leading cause of antibiotic-associated diarrhea worldwide. In order for C. difficile to initiate infection, its aerotolerant spore form must germinate in the gut of mammalian hosts. While almost all spore-forming organisms use transmembrane germinant receptors to trigger germination, C. difficile uses the pseudoprotease CspC to sense bile salt germinants. CspC activates the related subtilisin-like protease CspB, which then proteolytically activates the cortex hydrolase SleC. Activated SleC degrades the protective spore cortex layer, a step that is essential for germination to proceed. Since CspC incorporation into spores also depends on CspA, a related pseudoprotease domain, Csp family proteins play a critical role in germination. However, how Csps are incorporated into spores remains unknown. In this study, we demonstrate that incorporation of the CspC, CspB, and CspA germination regulators into spores depends on CD0311 (renamed GerG), a previously uncharacterized hypothetical protein. The reduced levels of Csps in gerG spores correlate with reduced responsiveness to bile salt germinants and increased germination heterogeneity in single-spore germination assays. Interestingly, asparagine-rich repeat sequences in GerG’s central region facilitate spontaneous gel formation in vitro even though they are dispensable for GerG-mediated control of germination. Since GerG is found exclusively in C. difficile, our results suggest that exploiting GerG function could represent a promising avenue for developing C. difficile-specific anti-infective therapies. The spore-forming bacterium Clostridium difficile is a leading cause of health care-associated infections. While a subset of antibiotics can treat C. difficile infections (CDIs), the primary determinant of CDI disease susceptibility is prior antibiotic exposure, since it reduces the colonization resistance conferred by a diverse microflora. Thus, therapies that minimize perturbations to the gut microbiome should be more effective at reducing CDIs and their recurrence, the main source of disease complications. Given that spore germination is essential for C. difficile to initiate infection and that C. difficile uses a unique pathway to initiate germination, methods that inhibit distinct elements of germination could selectively prevent C. difficile disease recurrence. Here, we identify GerG as a C. difficile-specific protein that controls the incorporation of germinant signaling proteins into spores. Since gerG mutant spores exhibit germination defects and are less responsive to germinant, GerG may represent a promising target for developing therapeutics against CDI.
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Head BM, Alfa M, Sitar DS, Rubinstein E, Meyers AFA. In vitro evaluation of the effect of linezolid and levofloxacin on Bacillus anthracis toxin production, spore formation and cell growth. J Antimicrob Chemother 2016; 72:417-420. [PMID: 27798209 DOI: 10.1093/jac/dkw427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 08/30/2016] [Accepted: 09/12/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Owing to its ability to form spores and toxins, Bacillus anthracis is considered a bioterror agent. Although current therapeutic strategies can be effective, treatment does not prevent sporulation and toxin production. OBJECTIVES To quantify the combined effect of a protein synthesis inhibitor and a bactericidal agent on B. anthracis toxin production, sporulation and cell growth. METHODS Susceptibility and synergy titrations were conducted on B. anthracis Sterne and 03-0191 strains using linezolid and levofloxacin. The effect of antibiotic exposure on cell viability was evaluated using a continuous medium replacement model. In vitro static models were used to study the effect of linezolid and levofloxacin on sporulation and toxin production. Spores were quantified using the heat shock method. Toxin was quantified via commercial ELISA. RESULTS Synergy titrations indicated that the combination was synergistic or indifferent; however, in all models antagonism was observed. In the spore model, linezolid resulted in the lowest sporulation rates, while combination therapy resulted in the highest. In the toxin model, linezolid prevented toxin production altogether. CONCLUSIONS This study advances our understanding of the effects of combination therapy on B. anthracis infection. Used alone, linezolid therapy abolishes toxin production and reduces sporulation. These results suggest that studies using a step-wise approach using linezolid initially to stop sporulation and toxin production followed by levofloxacin to rapidly kill vegetative B. anthracis can be recommended.
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Affiliation(s)
- Breanne M Head
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Michelle Alfa
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,St Boniface Research Centre, Winnipeg, Canada
| | - Daniel S Sitar
- Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, Canada
| | - Ethan Rubinstein
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada
| | - Adrienne F A Meyers
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, Canada.,National Laboratory for HIV Immunology, JC Wilt Infectious Disease Research Centre, Public Health Agency of Canada, Winnipeg, Canada.,Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
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Tschudin-Sutter S, Braissant O, Erb S, Stranden A, Bonkat G, Frei R, Widmer AF. Growth Patterns of Clostridium difficile - Correlations with Strains, Binary Toxin and Disease Severity: A Prospective Cohort Study. PLoS One 2016; 11:e0161711. [PMID: 27598309 PMCID: PMC5012633 DOI: 10.1371/journal.pone.0161711] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 08/10/2016] [Indexed: 12/11/2022] Open
Abstract
A broad spectrum of symptoms has been associated with C. difficile infection (CDI). Several studies indicate that toxin-production correlates with growth rates of C. difficile. This study aimed to correlate growth rates of C. difficile with disease severity and strain characteristics. From 01/2003 to 10/2011, strains from a prospective cohort of all inpatients with CDI at the University Hospital Basel, Switzerland were analyzed regarding binary toxin, presence of the tcdC deletion and ribotype. Isothermal microcalorimetry was performed to determine growth rates, quantified by the Gompertz function. Ordered logistic regression models were used to correlate disease severity with strain features and clinical characteristics. Among 199 patients, 31 (16%) were infected with binary toxin-producing strains, of which the tcdC gene-deletion nt117 was detected in 9 (4%). Disease severity was classified as mild in 130 patients (65.3%), as severe in 59 patients (29.7%) and as severe/complicated in 10 patients (5.0%). Growth rates were inversely associated with disease severity in univariable (OR 0.514, 95%CI 0.29–0.91, p = 0.023) and multivariable analyses (OR 0.51, 95%CI 0.26–0.97, p = 0.040). While none of the strain characteristics such as presence of the tcdC gene deletion or binary toxin predicted CDI severity, growth rates were inversely correlated with disease severity. Further investigations are needed to analyze growth-regulators and respective correlations with the level of toxin production in C. difficile, which may be important determinants of disease severity.
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Affiliation(s)
- Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- * E-mail:
| | - Olivier Braissant
- Laboratory of Biomechanics and Biocalorimetry, University of Basel, Basel, Switzerland
| | - Stefan Erb
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Anne Stranden
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
| | - Gernot Bonkat
- Department of Urology, University Hospital Basel, Basel, Switzerland
| | - Reno Frei
- Division of Clinical Microbiology, University Hospital Basel, Basel, Switzerland
| | - Andreas F. Widmer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
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Chilton CH, Crowther GS, Ashwin H, Longshaw CM, Wilcox MH. Association of Fidaxomicin with C. difficile Spores: Effects of Persistence on Subsequent Spore Recovery, Outgrowth and Toxin Production. PLoS One 2016; 11:e0161200. [PMID: 27556739 PMCID: PMC4996525 DOI: 10.1371/journal.pone.0161200] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 08/01/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND We have previously shown that fidaxomicin instillation prevents spore recovery in an in-vitro gut model, whereas vancomycin does not. The reasons for this are unclear. Here, we have investigated persistence of fidaxomicin and vancomycin on C. difficile spores, and examined post-antibiotic exposure spore recovery, outgrowth and toxin production. METHODS Prevalent UK C. difficile ribotypes (n = 10) were incubated with 200mg/L fidaxomicin, vancomycin or a non-antimicrobial containing control for 1 h in faecal filtrate or Phosphate Buffered Saline. Spores were washed three times with faecal filtrate or phosphate buffered saline, and residual spore-associated antimicrobial activity was determined by bioassay. For three ribotypes (027, 078, 015), antimicrobial-exposed, faecal filtrate-washed spores and controls were inoculated into broth. Viable vegetative and spore counts were enumerated on CCEYL agar. Percentage phase bright spores, phase dark spores and vegetative cells were enumerated by phase contrast microscopy at 0, 3, 6, 24 and 48 h post-inoculation. Toxin levels (24 and 48h) were determined by cell cytotoxicity assay. RESULTS Fidaxomicin, but not vancomycin persisted on spores of all ribotypes following washing in saline (mean = 10.1mg/L; range = 4.0-14mg/L) and faecal filtrate (mean = 17.4mg/L; 8.4-22.1mg/L). Outgrowth and proliferation rates of vancomycin-exposed spores were similar to controls, whereas fidaxomicin-exposed spores showed no vegetative cell growth after 24 and 48 h. At 48h, toxin levels averaged 3.7 and 3.3 relative units (RU) in control and vancomycin-exposed samples, respectively, but were undetectable in fidaxomicin-exposed samples. CONCLUSION Fidaxomicin persists on C. difficile spores, whereas vancomycin does not. This persistence prevents subsequent growth and toxin production in vitro. This may have implications on spore viability, thereby impacting CDI recurrence and transmission rates.
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Affiliation(s)
- Caroline H. Chilton
- Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
- * E-mail:
| | - Grace S. Crowther
- Faculty of Science and Engineering, Manchester Metropolitan University, Manchester, United Kingdom
| | - Helen Ashwin
- Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
| | | | - Mark H. Wilcox
- Leeds Institute for Biomedical and Clinical Sciences, University of Leeds, Leeds, United Kingdom
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, The General Infirmary, Old Medical School, Leeds, United Kingdom
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Hegarty JP, Krzeminski J, Sharma AK, Guzman-Villanueva D, Weissig V, Stewart DB. Bolaamphiphile-based nanocomplex delivery of phosphorothioate gapmer antisense oligonucleotides as a treatment for Clostridium difficile. Int J Nanomedicine 2016; 11:3607-19. [PMID: 27536102 PMCID: PMC4975145 DOI: 10.2147/ijn.s109600] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Despite being a conceptually appealing alternative to conventional antibiotics, a major challenge toward the successful implementation of antisense treatments for bacterial infections is the development of efficient oligonucleotide delivery systems. Cationic vesicles (bolasomes) composed of dequalinium chloride ("DQAsomes") have been used to deliver plasmid DNA across the cardiolipin-rich inner membrane of mitochondria. As cardiolipin is also a component of many bacterial membranes, we investigated the application of cationic bolasomes to bacteria as an oligonucleotide delivery system. Antisense sequences designed in silico to target the expression of essential genes of the bacterial pathogen, Clostridium difficile, were synthesized as 2'-O-methyl phosphorothioate gapmer antisense oligonucleotides (ASO). These antisense gapmers were quantitatively assessed for their ability to block mRNA translation using luciferase reporter and C. difficile protein expression plasmid constructs in a coupled transcription-translation system. Cationic bolaamphiphile compounds (dequalinium derivatives) of varying alkyl chain length were synthesized and bolasomes were prepared via probe sonication of an aqueous suspension. Bolasomes were characterized by particle size distribution, zeta potential, and binding capacities for anionic oligonucleotide. Bolasomes and antisense gapmers were combined to form antisense nanocomplexes. Anaerobic C. difficile log phase cultures were treated with serial doses of gapmer nanocomplexes or equivalent amounts of empty bolasomes for 24 hours. Antisense gapmers for four gene targets achieved nanomolar minimum inhibitory concentrations for C. difficile, with the lowest values observed for oligonucleotides targeting polymerase genes rpoB and dnaE. No inhibition of bacterial growth was observed from treatments at matched dosages of scrambled gapmer nanocomplexes or plain, oligonucleotide-free bolasomes compared to untreated control cultures. We describe the novel application of cationic bolasomes to deliver ASOs into bacteria. We also report the first successful in vitro antisense treatment to inhibit the growth of C. difficile.
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Affiliation(s)
- John P Hegarty
- Deparment of Surgery, Pennsylvania State University College of Medicine Hershey, PA, USA
| | - Jacek Krzeminski
- Department of Pharmacology, Penn State Hershey Cancer Institute, Hershey, PA, USA
| | - Arun K Sharma
- Department of Pharmacology, Penn State Hershey Cancer Institute, Hershey, PA, USA
| | - Diana Guzman-Villanueva
- Department of Pharmaceutical Sciences, College of Pharmacy, Nanomedicine Center of Excellence in Translational Research, Midwestern University, Glendale, AZ, USA
| | - Volkmar Weissig
- Department of Pharmaceutical Sciences, College of Pharmacy, Nanomedicine Center of Excellence in Translational Research, Midwestern University, Glendale, AZ, USA
| | - David B Stewart
- Deparment of Surgery, Pennsylvania State University College of Medicine Hershey, PA, USA
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48
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Fuzi M. Dissimilar Fitness Associated with Resistance to Fluoroquinolones Influences Clonal Dynamics of Various Multiresistant Bacteria. Front Microbiol 2016; 7:1017. [PMID: 27458434 PMCID: PMC4935693 DOI: 10.3389/fmicb.2016.01017] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 06/15/2016] [Indexed: 01/24/2023] Open
Abstract
Fitness cost associated with resistance to fluoroquinolones was recently shown to vary across clones of methicillin-resistant Staphylococcus aureus and extended-spectrum β-lactamase-producing Klebsiella pneumoniae. The resulting dissimilar fitness should have influenced the clonal dynamics and thereby the rates of resistance for these pathogens. Moreover, a similar mechanism was recently proposed for the emergence of the H30 and H30R lineages of ESBL-producing E. coli and the major international clone (ribotype 027) of Clostridium difficile. Furthermore, several additional international clones of various multiresistant bacteria are suspect to have been selected by an analogous process. An ability to develop favorable mutations in the gyrase and topoisomerase IV genes seems to be a prerequisite for pathogens to retain fitness while showing high-level resistance to fluoroquinolones. Since, the consumption of other "non-fluoroquinolone" groups of antibiotics have also contributed to the rise in resistance rates a more judicious use of antibiotics in general and of fluoroquinolones in particular could ameliorate the international resistance situation.
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Affiliation(s)
- Miklos Fuzi
- Institute of Medical Microbiology, Semmelweis UniversityBudapest, Hungary
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49
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Thabit AK, Nicolau DP. An exploratory study to evaluate Clostridium difficile polymerase chain reaction ribotypes and infection outcomes. Infect Drug Resist 2016; 9:143-8. [PMID: 27390531 PMCID: PMC4930231 DOI: 10.2147/idr.s108325] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Clostridium difficile infection ranges from mild to severe prolonged diarrhea with systemic symptoms. Previous studies have assessed the correlation of some disease severity parameters to C. difficile ribotypes. However, certain clinical parameters of interest have not yet been evaluated. AIM We conducted an exploratory study to evaluate the correlation of C. difficile ribotypes to parameters not assessed previously, notably days to diarrhea resolution (in terms of days to formed stools and days to less than three stools per day), length of hospital stay, 30-day recurrence rates, and 30-day readmission rates. Additional severity parameters evaluated include leukocytosis, serum creatinine, fever, and nausea/vomiting. METHODS Polymerase chain reaction ribotyping was performed on C. difficile isolates from baseline stool samples of 29 patients. A retrospective chart review was conducted to assess the parameters of interest. RESULTS The most common ribotypes were 027 (38%), 014/020 (21%), and 106/174 (21%). Numerically, 027 ribotype patients required more days to less than three stools per day versus 014/020 and 106/174 ribotype patients (P=0.2). The three ribotypes were similar regarding time to formed stools, duration of hospitalization, and 30-day readmission rate (P=0.2, 0.6, and 0.8, respectively). Recurrence within 30 days occurred in two patients with 027 and two patients with 014/020 (P=0.6). Leukocytosis and fever were more prominent with 027 than with 014/020 and 106/174 (P=0.04 for both parameters), although the degree of nausea/vomiting did not differ between the three groups (P=0.3). A serum creatinine level ≥1.5 times the premorbid level was seen in only three patients, each infected with a different ribotype. CONCLUSION Although these data provide a baseline assessment of outcomes to aid in the design of future studies, the diversity of C. difficile ribotypes within the population must be considered, and additional work with other ribotypes may further explain the association with these outcomes.
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Affiliation(s)
- Abrar K Thabit
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, USA; Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | - David P Nicolau
- Center for Anti-Infective Research and Development, Hartford Hospital, Hartford, CT, USA; Division of Infectious Diseases, Hartford Hospital, Hartford, CT, USA
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Sporulation properties and antimicrobial susceptibility in endemic and rare Clostridium difficile PCR ribotypes. Anaerobe 2016; 39:183-8. [PMID: 27095618 DOI: 10.1016/j.anaerobe.2016.04.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/31/2016] [Accepted: 04/13/2016] [Indexed: 11/21/2022]
Abstract
Increased sporulation and antibiotic resistance have been proposed to be associated with certain Clostridium difficile epidemic strains such as PCR ribotype 027. In this study we examined these properties in another widespread PCR ribotype, 014/020, in comparison to prevalent PCR ribotype 002 and a group of rarely represented PCR ribotypes. Highest sporulation was observed in 014/020 strains at 24 h, while after 72 h PCR ribotype 002 and rare PCR ribotypes formed higher total number of spores. PCR ribotype 014/020 strains exhibited slightly higher resistance to tested antimicrobials, followed by group of rare PCR ribotypes and less common PCR ribotype 002. Neither sporulation properties nor antibiotic resistance clearly differed in endemic and rare strains.
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