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Kochanowsky R, Carothers K, Roxas BAP, Anwar F, Viswanathan VK, Vedantam G. Clostridioides difficile superoxide reductase mitigates oxygen sensitivity. J Bacteriol 2024:e0017524. [PMID: 38953644 DOI: 10.1128/jb.00175-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Clostridioides difficile causes a serious diarrheal disease and is a common healthcare-associated bacterial pathogen. Although it has a major impact on human health, the mechanistic details of C. difficile intestinal colonization remain undefined. C. difficile is highly sensitive to oxygen and requires anaerobic conditions for in vitro growth. However, the mammalian gut is not devoid of oxygen, and C. difficile tolerates moderate oxidative stress in vivo. The C. difficile genome encodes several antioxidant proteins, including a predicted superoxide reductase (SOR) that is upregulated upon exposure to antimicrobial peptides. The goal of this study was to establish SOR enzymatic activity and assess its role in protecting C. difficile against oxygen exposure. Insertional inactivation of sor rendered C. difficile more sensitive to superoxide, indicating that SOR contributes to antioxidant defense. Heterologous C. difficile sor expression in Escherichia coli conferred protection against superoxide-dependent growth inhibition, and the corresponding cell lysates showed superoxide scavenging activity. Finally, a C. difficile SOR mutant exhibited global proteome changes under oxygen stress when compared to the parent strain. Collectively, our data establish the enzymatic activity of C. difficile SOR, confirm its role in protection against oxidative stress, and demonstrate SOR's broader impacts on the C. difficile vegetative cell proteome.IMPORTANCEClostridioides difficile is an important pathogen strongly associated with healthcare settings and capable of causing severe diarrheal disease. While considered a strict anaerobe in vitro, C. difficile has been shown to tolerate low levels of oxygen in the mammalian host. Among other well-characterized antioxidant proteins, the C. difficile genome encodes a predicted superoxide reductase (SOR), an understudied component of antioxidant defense in pathogens. The significance of the research reported herein is the characterization of SOR's enzymatic activity, including confirmation of its role in protecting C. difficile against oxidative stress. This furthers our understanding of C. difficile pathogenesis and presents a potential new avenue for targeted therapies.
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Affiliation(s)
- Rebecca Kochanowsky
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Katelyn Carothers
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Bryan Angelo P Roxas
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - Farhan Anwar
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
| | - V K Viswanathan
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
- BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, USA
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, Arizona, USA
- BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, Arizona, USA
- Southern Arizona VA Healthcare System, Tucson, Arizona, USA
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Kolte B, Nübel U. Genetic determinants of resistance to antimicrobial therapeutics are rare in publicly available Clostridioides difficile genome sequences. J Antimicrob Chemother 2024; 79:1320-1328. [PMID: 38598696 PMCID: PMC11144481 DOI: 10.1093/jac/dkae101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
OBJECTIVES To determine the frequencies and clonal distributions of putative genetic determinants of resistance to antimicrobials applied for treatment of Clostridioides difficile infection (CDI), as documented in the genomic record. METHODS We scanned 26 557 C. difficile genome sequences publicly available from the EnteroBase platform for plasmids, point mutations and gene truncations previously reported to reduce susceptibility to vancomycin, fidaxomicin or metronidazole, respectively. We measured the antimicrobial susceptibility of 143 selected C. difficile isolates. RESULTS The frequency of mutations causing reduced susceptibility to vancomycin and metronidazole, respectively, increased strongly after 2000, peaking at up to 52% of all sequenced C. difficile genomes. However, both mutations declined sharply more recently, reflecting major changes in CDI epidemiology. We detected mutations associated with fidaxomicin resistance in several major genotypes, but found no evidence of international spread of resistant clones. The pCD-METRO plasmid, conferring metronidazole resistance, was detected in a single previously unreported C. difficile isolate, recovered from a hospital patient in Germany in 2008. The pX18-498 plasmid, putatively associated with decreased vancomycin susceptibility, was confined to related, recent isolates from the USA. Phenotype measurements confirmed that most of those genetic features were useful predictors of antibiotic susceptibility, even though ranges of MICs typically overlapped among isolates with and without specific mutations. CONCLUSIONS Genomic data suggested that resistance to therapeutic antimicrobial drugs is rare in C. difficile. Public antimicrobial resistance marker databases were not equipped to detect most of the genetic determinants relevant to antibiotic therapy of CDI.
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Affiliation(s)
- Baban Kolte
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Microbial Genome Research, Inhoffenstr. 7B, 38124, Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
| | - Ulrich Nübel
- Leibniz Institute DSMZ—German Collection of Microorganisms and Cell Cultures, Microbial Genome Research, Inhoffenstr. 7B, 38124, Braunschweig, Germany
- Technical University Braunschweig, Institute of Microbiology, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany
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3
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Brouwer L, Carroll A, McNamara E. Genotypic and phenotypic antimicrobial resistance of Irish Clostridioides difficile isolates, 2022. Anaerobe 2024; 88:102857. [PMID: 38670525 DOI: 10.1016/j.anaerobe.2024.102857] [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: 02/01/2024] [Revised: 04/12/2024] [Accepted: 04/14/2024] [Indexed: 04/28/2024]
Abstract
OBJECTIVES Infection with Clostridioides difficile usually occurs after antibiotic treatment for other infections and can cause gastro-intestinal disorders of variable severity. C. difficile can be resistant to a wide spectrum of antimicrobials. Detection of antimicrobial resistance (AMR) is important to direct optimal treatment and surveillance of AMR patterns in the overall population. Correlation between genotypic markers and phenotypic AMR is not yet well defined. The aim for this study is to assess whether and to what extent genotypic determinants of AMR correlate with phenotypic resistance. METHODS C. difficile isolates (n = 99) were phenotypically characterized for resistance to eight antibiotics using Sensititre plates or E-tests. Their genomes were screened for genetic markers of resistance. Accuracy, sensitivity, specificity, positive and negative predictive values were calculated. RESULTS We found high rates of resistance (>50 %) to cefoxitin and clindamycin, intermediate rates of resistance (10 %-50 %) to moxifloxacin and tetracycline and low rates of resistance (<10 %) to imipenem, metronidazole, vancomycin, and rifampicin. For moxifloxacin, tetracycline, and clindamycin, we found a good correlation between genotypic and phenotypic AMR, with an overall accuracy of 98 % (95 % CI 93%-100 %), 78 % (95 % CI 68%-86 %) and 86 % (95 % CI 77%-92 %) respectively. For the other five antibiotics, accurate estimates on the correlation could not be made. CONCLUSION Our results suggest that for moxifloxacin, tetracycline and clindamycin, phenotypic resistance in C. difficile can be predicted by genetic indicators and used for public health purposes. However, for the other five antibiotics, the model is not accurate and further development is necessary.
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Affiliation(s)
- Lieke Brouwer
- Clostridioides Difficile National Reference Laboratory, Public Health Laboratory, Health Service Executive, Cherry Orchard Hospital, Dublin, Ireland; European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control, Stockholm, Sweden.
| | - Anne Carroll
- Clostridioides Difficile National Reference Laboratory, Public Health Laboratory, Health Service Executive, Cherry Orchard Hospital, Dublin, Ireland; European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Eleanor McNamara
- Clostridioides Difficile National Reference Laboratory, Public Health Laboratory, Health Service Executive, Cherry Orchard Hospital, Dublin, Ireland; European Public Health Microbiology Training Programme (EUPHEM), European Centre for Disease Prevention and Control, Stockholm, Sweden
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4
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Markantonis JE, Fallon JT, Madan R, Alam MZ. Clostridioides difficile Infection: Diagnosis and Treatment Challenges. Pathogens 2024; 13:118. [PMID: 38392856 PMCID: PMC10891949 DOI: 10.3390/pathogens13020118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/25/2024] Open
Abstract
Clostridioides difficile is the most important cause of healthcare-associated diarrhea in the United States. The high incidence and recurrence rates of C. difficile infection (CDI), associated with high morbidity and mortality, pose a public health challenge. Although antibiotics targeting C. difficile bacteria are the first treatment choice, antibiotics also disrupt the indigenous gut flora and, therefore, create an environment that is favorable for recurrent CDI. The challenge of treating CDI is further exacerbated by the rise of antibiotic-resistant strains of C. difficile, placing it among the top five most urgent antibiotic resistance threats in the USA. The evolution of antibiotic resistance in C. difficile involves the acquisition of new resistance mechanisms, which can be shared among various bacterial species and different C. difficile strains within clinical and community settings. This review provides a summary of commonly used diagnostic tests and antibiotic treatment strategies for CDI. In addition, it discusses antibiotic treatment and its resistance mechanisms. This review aims to enhance our current understanding and pinpoint knowledge gaps in antimicrobial resistance mechanisms in C. difficile, with an emphasis on CDI therapies.
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Affiliation(s)
- John E. Markantonis
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, NC 27834, USA; (J.E.M.); (J.T.F.)
| | - John T. Fallon
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, NC 27834, USA; (J.E.M.); (J.T.F.)
| | - Rajat Madan
- Division of Infectious Diseases, Department of Internal Medicine, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA;
- Veterans Affairs Medical Center, Cincinnati, OH 45220, USA
| | - Md Zahidul Alam
- Department of Pathology and Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, NC 27834, USA; (J.E.M.); (J.T.F.)
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5
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Li X, Wang Y, Cao R, Xiao F, Wang X, Ye L, Xiao Y, Li D, Zhang T. Antimicrobial Resistance of Clostridioides difficile in Children from a Tertiary Pediatric Hospital in Shanghai, China. Infect Drug Resist 2024; 17:329-339. [PMID: 38293314 PMCID: PMC10826549 DOI: 10.2147/idr.s441312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/13/2023] [Indexed: 02/01/2024] Open
Abstract
Background Our previous study reported a high rate of recurrence in children with Clostridioides difficile (C. difficile) infection (CDI) after conventional antibiotic therapy. Here, we aimed to explore whether metronidazole and vancomycin resistant C. difficile isolates are circulating in pediatric CDI. Methods Antimicrobial susceptibility testing (AST) using the agar dilution method according to the Clinical and Laboratory Standard Institute (CLSI) were performed on C. difficile isolates collected from children with CDI between 2019 and 2022 at the Shanghai Children's Hospital. Whole-genome sequencing (WGS) was performed on all C. difficile isolates, and the presence of antibiotic resistance genes (ARGs) were identified using Resfinder and the Comprehensive Antibiotic Resistance Database (CARD). The presence of plasmid pCD-METRO was detected using SRST2 (v0.2.0) against 8 pCD-METRO coding sequences. Results A total of 50 C. difficile isolates were collected from stools of CDI children. The overall resistance rate on all isolates was 30.00% for metronidazole, 6.00% for vancomycin, 0% for rifaximin, 2.00% for rifampin, 24.00% for meropenem, 100.00% for ceftriaxone and clindamycin, 86.00% for erythromycin, 30.0% for levofloxacin, and 50.0% for tetracycline. Multidrug-resistant (MDR) was presented in 44 isolates (88.00%). Sixteen reported potential ARGs relating with resistance to antibiotic classes of aminoglycoside (AAC(6')-Ie-APH(2")-Ia, aad(6), ANT(6)-Ib, APH(2")-If, APH(3')-IIIa), lincosamide-clindamycin-erythromycin (ErmB, ErmQ), fluoroquinolones (CdeA), glycopeptides (vanRG), nucleoside (SAT-4), tetracycline (tetM, tetA(P), tetB(P), tetO), and trimethoprim (dfrF) were identified. However, the pCD-METRO plasmid and vanA/B were not detected in any isolates. Conclusion C. difficile isolates from children with reduced susceptibility to metronidazole and vancomycin are emerging in pediatric CDI in China. The lack of pCD-METRO plasmid and vanA/B associated with reduced antibiotic susceptibility suggests there are additional mechanisms of resistance.
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Affiliation(s)
- Xiaolu Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yizhong Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Gut Microbiota and Metabolic Research Center, Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Rong Cao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Fangfei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Xufei Wang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lin Ye
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yongmei Xiao
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Dan Li
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Ting Zhang
- Department of Gastroenterology, Hepatology and Nutrition, Shanghai Children’s Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Gut Microbiota and Metabolic Research Center, Institute of Pediatric Infection, Immunity and Critical Care Medicine, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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Oludiran A, Malik A, Zourou AC, Wu Y, Gross SP, Siryapon A, Poudel A, Alleyne K, Adams S, Courson DS, Cotten ML, Purcell EB. Host-defense piscidin peptides as antibiotic adjuvants against Clostridioides difficile. PLoS One 2024; 19:e0295627. [PMID: 38252641 PMCID: PMC10802969 DOI: 10.1371/journal.pone.0295627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/26/2023] [Indexed: 01/24/2024] Open
Abstract
The spore-forming intestinal pathogen Clostridioides difficile causes multidrug resistant infection with a high rate of recurrence after treatment. Piscidins 1 (p1) and 3 (p3), cationic host defense peptides with micromolar cytotoxicity against C. difficile, sensitize C. difficile to clinically relevant antibiotics tested at sublethal concentrations. Both peptides bind to Cu2+ using an amino terminal copper and nickel binding motif. Here, we investigate the two peptides in the apo and holo states as antibiotic adjuvants against an epidemic strain of C. difficile. We find that the presence of the peptides leads to lower doses of metronidazole, vancomycin, and fidaxomicin to kill C. difficile. The activity of metronidazole, which targets DNA, is enhanced by a factor of 32 when combined with p3, previously shown to bind and condense DNA. Conversely, the activity of vancomycin, which acts at bacterial cell walls, is enhanced 64-fold when combined with membrane-active p1-Cu2+. As shown through microscopy monitoring the permeabilization of membranes of C. difficile cells and vesicle mimics of their membranes, the adjuvant effect of p1 and p3 in the apo and holo states is consistent with a mechanism of action where the peptides enable greater antibiotic penetration through the cell membrane to increase their bioavailability. The variations in effects obtained with the different forms of the peptides reveal that while all piscidins generally sensitize C. difficile to antibiotics, co-treatments can be optimized in accordance with the underlying mechanism of action of the peptides and antibiotics. Overall, this study highlights the potential of antimicrobial peptides as antibiotic adjuvants to increase the lethality of currently approved antibiotic dosages, reducing the risk of incomplete treatments and ensuing drug resistance.
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Affiliation(s)
- Adenrele Oludiran
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
| | - Areej Malik
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
- Biomedical Sciences Program, Old Dominion University, Norfolk, Virginia, United States of America
| | - Andriana C. Zourou
- Department of Applied Science, William & Mary, Williamsburg, Virginia, United States of America
| | - Yonghan Wu
- Irvine Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
| | - Steven P. Gross
- Ivrine Department of Developmental and Cell Biology, University of California, Los Angeles, California, United States of America
| | - Albert Siryapon
- Irvine Department of Physics and Astronomy, University of California, Los Angeles, California, United States of America
| | - Asia Poudel
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
| | - Kwincy Alleyne
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
| | - Savion Adams
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
| | - David S. Courson
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
| | - Myriam L. Cotten
- Department of Applied Science, William & Mary, Williamsburg, Virginia, United States of America
| | - Erin B. Purcell
- Department of Chemistry and Biochemistry, Old Dominion University, Norfolk, Virginia, United States of America
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7
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Spigaglia P, Mastrantonio P, Barbanti F. Antibiotic Resistances of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:169-198. [PMID: 38175476 DOI: 10.1007/978-3-031-42108-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The rapid evolution of antibiotic resistance in Clostridioides difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are a matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances, and most of the epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways or biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Paola Mastrantonio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Fabrizio Barbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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Hastie JL, Carmichael HL, Werner BM, Dunbar KE, Carlson PE. Clostridioides difficile utilizes siderophores as an iron source and FhuDBGC contributes to ferrichrome uptake. J Bacteriol 2023; 205:e0032423. [PMID: 37971230 PMCID: PMC10729759 DOI: 10.1128/jb.00324-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE This study is the first example of C. difficile growing with siderophores as the sole iron source and describes the characterization of the ferric hydroxamate uptake ABC transporter (FhuDBGC). This transporter shows specificity to the siderophore ferrichrome. While not required for pathogenesis, this transporter highlights the redundancy in iron acquisition mechanisms that C. difficile uses to compete for iron during an infection.
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Affiliation(s)
- Jessica L. Hastie
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Hannah L. Carmichael
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Bailey M. Werner
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Kristin E. Dunbar
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
| | - Paul E. Carlson
- Food and Drug Administration, Center for Biologics Evaluation and Research, Office of Vaccines Research and Review, Division of Bacterial Parasitic and Allergenic Products, Laboratory of Mucosal Pathogens and Cellular Immunology, Silver Spring, Maryland, USA
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9
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Olaitan AO, Dureja C, Youngblom MA, Topf MA, Shen WJ, Gonzales-Luna AJ, Deshpande A, Hevener KE, Freeman J, Wilcox MH, Palmer KL, Garey KW, Pepperell CS, Hurdle JG. Decoding a cryptic mechanism of metronidazole resistance among globally disseminated fluoroquinolone-resistant Clostridioides difficile. Nat Commun 2023; 14:4130. [PMID: 37438331 DOI: 10.1038/s41467-023-39429-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 06/13/2023] [Indexed: 07/14/2023] Open
Abstract
Severe outbreaks and deaths have been linked to the emergence and global spread of fluoroquinolone-resistant Clostridioides difficile over the past two decades. At the same time, metronidazole, a nitro-containing antibiotic, has shown decreasing clinical efficacy in treating C. difficile infection (CDI). Most metronidazole-resistant C. difficile exhibit an unusual resistance phenotype that can only be detected in susceptibility tests using molecularly intact heme. Here, we describe the mechanism underlying this trait. We find that most metronidazole-resistant C. difficile strains carry a T-to-G mutation (which we term PnimBG) in the promoter of gene nimB, resulting in constitutive transcription. Silencing or deleting nimB eliminates metronidazole resistance. NimB is related to Nim proteins that are known to confer resistance to nitroimidazoles. We show that NimB is a heme-dependent flavin enzyme that degrades nitroimidazoles to amines lacking antimicrobial activity. Furthermore, occurrence of the PnimBG mutation is associated with a Thr82Ile substitution in DNA gyrase that confers fluoroquinolone resistance in epidemic strains. Our findings suggest that the pandemic of fluoroquinolone-resistant C. difficile occurring over the past few decades has also been characterized by widespread resistance to metronidazole.
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Affiliation(s)
- Abiola O Olaitan
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Madison A Youngblom
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Madeline A Topf
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Wan-Jou Shen
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Aditi Deshpande
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA
| | - Kirk E Hevener
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, TN, USA
| | - Jane Freeman
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Mark H Wilcox
- Department of Microbiology, Leeds Teaching Hospitals Trust, Leeds, UK
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Kelli L Palmer
- Department of Biological Sciences, University of Texas at Dallas, Richardson, TX, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, TX, USA
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA.
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, TX, USA.
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10
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Lv Z, Yin S, Jiang K, Wang W, Luan Y, Wu S, Shi J, Li Z, Ma X, Wang Z, Yan H. The whole-cell proteome shows the characteristics of macrolides-resistant Bordetella pertussis in China linked to the biofilm formation. Arch Microbiol 2023; 205:219. [PMID: 37148370 PMCID: PMC10164027 DOI: 10.1007/s00203-023-03566-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/08/2023]
Abstract
The macrolides-resistant Bordetella pertussis (MR-Bp) isolates in China evolved from the ptxP1/fhaB3 allele and rapidly became predominant, suggestive of an adaptive transmission ability. This was different from the global prevalent ptxP3 strains, in which MR-Bp was rarely reported. The study aimed to determine the underlying mechanism responsible for fitness and resistance in these two strains. We identify proteomic differences between ptxP1/fhaB3 and ptxP3/fhaB1 strains using tandem mass tag (TMT)-based proteomics. We then performed in-depth bioinformatic analysis to determine differentially expressed genes (DEGs), followed by gene ontology (GO), and protein-protein interaction (PPI) network analysis. Further parallel reaction monitoring (PRM) analysis confirmed the expression of four target proteins. Finally, the crystal violet method was used to determine biofilm-forming ability. The results showed that the main significantly different proteins between the two represent isolates were related to biofilm formation. Furthermore, we have confirmed that ptxP1/fhaB3 showed hyperbiofilm formation in comparison with ptxP3/fhaB1. It is suggested that the resistance and adaptability of ptxP1/fhaB3 strains may be related to the formation of biofilm through proteomics. In a word, we determined the significantly different proteins between the ptxP1/fhaB3 and ptxP3/fhaB1 strains through whole-cell proteome, which were related to biofilm formation.
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Affiliation(s)
- Zhe Lv
- Department of Epidemiology and Health Statistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China
| | - Sha Yin
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases; Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, No. 69, Xijuyuan Lane, Xi'an, 710003, China
| | - Kaichong Jiang
- National Regional Children's Medical Center (Northwest), Key Laboratory of Precision Medicine to Pediatric Diseases of Shaanxi Province, Xi'an Key Laboratory of Children's Health and Diseases, Shaanxi Institute for Pediatric Diseases; Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, No. 69, Xijuyuan Lane, Xi'an, 710003, China
| | - Wei Wang
- Department of Clinical Laboratory, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, No. 69, Xijuyuan Lane, Xi'an, 710003, China
| | - Yang Luan
- Xi'an Center for Disease Control and Prevention, 599 Xiying Road, Xi'an, 710054, China
| | - Shuang Wu
- Department of Clinical Laboratory, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, No. 69, Xijuyuan Lane, Xi'an, 710003, China
| | - Jianfei Shi
- Department of Clinical Laboratory, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, No. 69, Xijuyuan Lane, Xi'an, 710003, China
| | - Zhe Li
- Department of Diphtheria, Tetanus and Pertussis Vaccine and Toxins, National Institute for Food and Drug Control, Beijing, China
| | - Xiao Ma
- Department of Diphtheria, Tetanus and Pertussis Vaccine and Toxins, National Institute for Food and Drug Control, Beijing, China
| | - Zengguo Wang
- Department of Clinical Laboratory, Xi'an Children's Hospital, Affiliated Children's Hospital of Xi'an Jiaotong University, No. 69, Xijuyuan Lane, Xi'an, 710003, China.
| | - Hong Yan
- Department of Epidemiology and Health Statistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, 710061, China.
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11
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Garey KW, Rose W, Gunter K, Serio AW, Wilcox MH. Omadacycline and Clostridioides difficile: A Systematic Review of Preclinical and Clinical Evidence. Ann Pharmacother 2023; 57:184-192. [PMID: 35656828 PMCID: PMC9874691 DOI: 10.1177/10600280221089007] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVE The objective of this systematic review is to summarize in vitro, preclinical, and human data related to omadacycline and Clostridioides difficile infection (CDI). DATA SOURCES PubMed and Google Scholar were searched for "omadacycline" AND ("Clostridium difficile" OR "C difficile" OR "Clostridioides difficile") for any studies published before February 15, 2022. The US Food and Drug Administration (FDA) Adverse Events Reporting System (AERS) was searched for omadacycline (for reports including "C. difficile" or "CDI" or "gastrointestinal infection"). The publications list publicly available at Paratek Pharmaceuticals, Inc. Web site was reviewed. STUDY SELECTION AND DATA EXTRACTION Publications presenting primary data on omadacycline and C. difficile published in English were included. DATA SYNTHESIS Preclinical and clinical evidence was extracted from 14 studies. No case reports in indexed literature and no reports on FDA AERS were found. Omadacycline has potent in vitro activity against many C. difficile clinical strains and diverse ribotypes. In phase 3 studies, there were no reports of CDI in patients who received omadacycline for either community-acquired bacterial pneumonia or acute bacterial skin and skin structure infection. RELEVANCE TO PATIENT CARE AND CLINICAL PRACTICE Omadacycline should be considered a low-risk antibiotic regarding its propensity to cause CDI. CONCLUSIONS Reducing the burden of CDI on patients and the health care system should be a priority. Patients with appropriate indications who are at heightened risk of CDI may be suitable candidates for omadacycline therapy. In these patients, omadacycline may be preferable to antibiotics with a high CDI risk.
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Affiliation(s)
- Kevin W. Garey
- University of Houston College of
Pharmacy, Houston, TX, USA
| | - Warren Rose
- School of Pharmacy, University of
Wisconsin–Madison, Madison, WI, USA
| | - Kyle Gunter
- Paratek Pharmaceuticals, Inc., King of
Prussia, PA, USA,Kyle Gunter, Director of Medical Science,
Paratek Pharmaceuticals, Inc., 1000 First Avenue, Suite 200, King of Prussia, PA
19406, USA.
| | | | - Mark H. Wilcox
- University of Leeds & Leeds
Teaching Hospitals, Leeds, UK
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12
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Make It Less difficile: Understanding Genetic Evolution and Global Spread of Clostridioides difficile. Genes (Basel) 2022; 13:genes13122200. [PMID: 36553467 PMCID: PMC9778335 DOI: 10.3390/genes13122200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection can lead to fulminant colitis associated with shock, hypotension, megacolon, and, in severe cases, death. It is therefore of the utmost urgency to fully characterize this pathogen and better understand its spread, in order to reduce infection rates and improve therapy success. This review aims to provide a state-of-the-art overview of the genetic variation of C. difficile, with particular regard to pathogenic genes and the correlation with clinical issues of its infection. We also summarize the current typing techniques and, based on them, the global distribution of the most common ribotypes. Finally, we discuss genomic surveillance actions and new genetic engineering strategies as future perspectives to make it less difficile.
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13
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Doan THD, Bernet-Camard MF, Hoÿs S, Janoir C, Péchiné S. Impact of Subinhibitory Concentrations of Metronidazole on Morphology, Motility, Biofilm Formation and Colonization of Clostridioides difficile. Antibiotics (Basel) 2022; 11:624. [PMID: 35625268 PMCID: PMC9137534 DOI: 10.3390/antibiotics11050624] [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: 03/25/2022] [Revised: 04/22/2022] [Accepted: 04/27/2022] [Indexed: 12/04/2022] Open
Abstract
Clostridioides difficile infection (CDI) is the primary cause of health-care-associated infectious diarrhea. Treatment requires mostly specific antibiotics such as metronidazole (MTZ), vancomycin or fidaxomicin. However, approximately 20% of treated patients experience recurrences. Treatment with MTZ is complicated by reduced susceptibility to this molecule, which could result in high failure and recurrence rates. However, the mechanism remains unclear. In this study, we investigated the impact of subinhibitory concentrations of MTZ on morphology, motility, biofilm formation, bacterial adherence to the intestinal Caco-2/TC7 differentiated monolayers, and colonization in monoxenic and conventional mouse models of two C. difficile strains (VPI 10463 and CD17-146), showing different susceptibility profiles to MTZ. Our results revealed that in addition to the inhibition of motility and the downregulation of flagellar genes for both strains, sub-inhibitory concentrations of MTZ induced various in vitro phenotypes for the strain CD17-146 exhibiting a reduced susceptibility to this antibiotic: elongated morphology, enhanced biofilm production and increased adherence to Caco-2/TC7 cells. Weak doses of MTZ induced higher level of colonization in the conventional mouse model and a trend to thicker 3-D structures entrapping bacteria in monoxenic mouse model. Thus, sub-inhibitory concentrations of MTZ can have a wide range of physiological effects on bacteria, which may contribute to their persistence after treatment.
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Affiliation(s)
| | - Marie-Françoise Bernet-Camard
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (M.-F.B.-C.); (S.H.); (C.J.)
| | - Sandra Hoÿs
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (M.-F.B.-C.); (S.H.); (C.J.)
| | - Claire Janoir
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (M.-F.B.-C.); (S.H.); (C.J.)
| | - Séverine Péchiné
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350 Jouy-en-Josas, France; (M.-F.B.-C.); (S.H.); (C.J.)
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14
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Dureja C, Olaitan AO, Hurdle JG. Mechanisms and impact of antimicrobial resistance in Clostridioides difficile. Curr Opin Microbiol 2022; 66:63-72. [PMID: 35077947 PMCID: PMC9064893 DOI: 10.1016/j.mib.2022.01.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 12/10/2021] [Accepted: 01/07/2022] [Indexed: 11/03/2022]
Abstract
The evolution of antimicrobial resistance in Clostridioides difficile has markedly shaped its epidemiology and detrimentally impacted patient care. C. difficile exhibits resistance to multiple classes of antimicrobials, due to accumulation of horizontally acquired resistance genes and de novo mutations to drug targets. Particularly worrying is that declines in clinical success of firstline CDI antimicrobials coincide with the spread of strains that are more resistant to these drugs. Yet, there is still much to learn regarding the prevalence of genetic elements in clinical isolates, their molecular mechanisms, and the extent to which this information can be translated to develop molecular diagnostics that improve antimicrobial prescribing and antimicrobial stewardship approaches for CDI. Thus, this perspective discusses current understanding and knowledge gaps of antimicrobial resistance mechanisms in C. difficile, emphasizing on CDI therapies.
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Affiliation(s)
- Chetna Dureja
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, 2121 West Holcombe Blvd, Houston, TX 77030, USA
| | - Abiola O Olaitan
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, 2121 West Holcombe Blvd, Houston, TX 77030, USA
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Department of Translational Medical Sciences, Texas A&M Health Science Center, 2121 West Holcombe Blvd, Houston, TX 77030, USA.
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15
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Xu T, Zhou F, Wang L, Wu S, Huang H. Metronidazole-Resistant Clostridioides difficile: Genomic and Transcriptomic Traits Acquired under In vitro Metronidazole Induction. Int J Antimicrob Agents 2022; 59:106570. [DOI: 10.1016/j.ijantimicag.2022.106570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/02/2022] [Accepted: 03/06/2022] [Indexed: 11/05/2022]
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16
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Gomez SY, Patel J, Lopez CA. What's metal got to do with it? Transition metals in Clostridioides difficile infection. Curr Opin Microbiol 2021; 65:116-122. [PMID: 34839238 DOI: 10.1016/j.mib.2021.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/27/2022]
Abstract
The enteric pathogen Clostridioides difficile overcomes barriers to colonization imposed by the microbiota and host immune response to induce disease. To navigate the dynamic gut environment, C. difficile must respond to dietary and host-mediated fluctuations in transition metal availability. Transition metals are required trace nutrients that foster inter-microbial competition when limited, inhibit bacterial growth through host sequestration, or induce toxicity in excess. This review highlights recent evidence that transition metals influence multiple stages of C. difficile colonization and that C. difficile initiates a coordinated response to maintain metal-dependent homeostasis. Further exploration of the mechanisms of C. difficile metal sensing and nutrient competition with the microbiota will be necessary for the therapeutic manipulation of the gut environment during C. difficile infection.
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Affiliation(s)
- Suzanna Y Gomez
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, United States
| | - Jay Patel
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, United States
| | - Christopher A Lopez
- Department of Biological Sciences, California State University Sacramento, Sacramento, CA, United States.
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17
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Ebselen Not Only Inhibits Clostridioides difficile Toxins but Displays Redox-Associated Cellular Killing. Microbiol Spectr 2021; 9:e0044821. [PMID: 34468187 PMCID: PMC8557875 DOI: 10.1128/spectrum.00448-21] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Ebselen, a reactive organoselenium compound, was shown to inhibit toxins TcdA and TcdB by covalently binding to their cysteine protease domains. It was suggested that ebselen lacked antimicrobial activity against Clostridioides difficile. However, this perception conflicts with C. difficile having essential cysteine-containing enzymes that could be potential targets and the reported antimicrobial activity of ebselen against other species. Hence, we reevaluated the anti-C. difficile properties of ebselen. Susceptibility testing revealed that its activity was either slightly reduced by pyruvate found in Wilkins-Chalgren agar or obliterated by blood in brucella agar. In brain heart infusion (BHI) agar, ebselen inhibited most C. difficile strains (MICs of 2 to 8 μg/ml), except for ribotype 078 that was intrinsically resistant (MIC = 32 to 128 μg/ml). Against C. difficile R20291, at concentrations below its minimal bactericidal concentration (MBC), 16 μg/ml, ebselen inhibited production of toxins and spores. Transcriptome analysis revealed that ebselen altered redox-associated processes and cysteine metabolism and enhanced expression of Stickland proline metabolism, likely to regenerate NAD+ from NADH. In cellular assays, ebselen induced uptake of cysteine, depleted nonprotein thiols, and disrupted the NAD+/NADH ratio. Taken together, killing of C. difficile cells by ebselen occurs by a multitarget action that includes disrupting intracellular redox, which is consistent with ebselen being a reactive molecule. However, the physiological relevance of these antimicrobial actions in treating acute C. difficile infection (CDI) is likely to be undermined by host factors, such as blood, which protect C. difficile from killing by ebselen. IMPORTANCE We show that ebselen kills pathogenic C. difficile by disrupting its redox homeostasis, changing the normal concentrations of NAD+ and NADH, which are critical for various metabolic functions in cells. However, this antimicrobial action is hampered by host components, namely, blood. Future discovery of ebselen analogues, or mechanistically similar compounds, that remain active in blood could be drug leads for CDI or probes to study C. difficile redox biology in vivo.
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18
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O’Grady K, Knight DR, Riley TV. Antimicrobial resistance in Clostridioides difficile. Eur J Clin Microbiol Infect Dis 2021; 40:2459-2478. [DOI: 10.1007/s10096-021-04311-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023]
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19
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The Integrity of Heme Is Essential for Reproducible Detection of Metronidazole-Resistant Clostridioides difficile by Agar Dilution Susceptibility Tests. J Clin Microbiol 2021; 59:e0058521. [PMID: 34132582 DOI: 10.1128/jcm.00585-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Metronidazole resistance in clinical Clostridioides difficile is often described as unstable, since resistant strains reportedly appear susceptible following freezer storage or brief passage. This has presented a conundrum for adopting susceptibility testing to accurately evaluate the connection between metronidazole resistance and decreased clinical efficacy of metronidazole in patients with C. difficile infections (CDIs). We discovered that supplementation of microbiological media with the metalloporphyrin heme is crucial for detection of metronidazole-resistant C. difficile using the agar dilution susceptibility testing method. Known metronidazole-resistant strains appeared susceptible to metronidazole in media lacking heme. Similarly, these resistant strains exhibited increased susceptibility to metronidazole when tested on heme-containing agars that were exposed to room light for more than 1 day, likely due to heme photodecomposition. In parallel experiments, resistance was reproducibly detected when heme-containing agars were either prepared and used on the same day or protected from light and then used on subsequent days. Notably, heme did not influence the susceptibilities of drug-susceptible strains that were of the same ribotype as the resistant strains. These findings firmly show that the consistent detection of metronidazole-resistant C. difficile is dependent upon heme and its protection from light. Studies are warranted to determine the extent to which this heme-associated metronidazole-resistant phenotype affects the clinical efficacy of metronidazole in CDI and the underlying genetic and biochemical mechanisms.
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20
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Wickramage I, Spigaglia P, Sun X. Mechanisms of antibiotic resistance of Clostridioides difficile. J Antimicrob Chemother 2021; 76:3077-3090. [PMID: 34297842 DOI: 10.1093/jac/dkab231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile (CD) is one of the top five urgent antibiotic resistance threats in USA. There is a worldwide increase in MDR of CD, with emergence of novel strains which are often more virulent and MDR. Antibiotic resistance in CD is constantly evolving with acquisition of novel resistance mechanisms, which can be transferred between different species of bacteria and among different CD strains present in the clinical setting, community, and environment. Therefore, understanding the antibiotic resistance mechanisms of CD is important to guide optimal antibiotic stewardship policies and to identify novel therapeutic targets to combat CD as well as other bacteria. Epidemiology of CD is driven by the evolution of antibiotic resistance. Prevalence of different CD strains and their characteristic resistomes show distinct global geographical patterns. Understanding epidemiologically driven and strain-specific characteristics of antibiotic resistance is important for effective epidemiological surveillance of antibiotic resistance and to curb the inter-strain and -species spread of the CD resistome. CD has developed resistance to antibiotics with diverse mechanisms such as drug alteration, modification of the antibiotic target site and extrusion of drugs via efflux pumps. In this review, we summarized the most recent advancements in the understanding of mechanisms of antibiotic resistance in CD and analysed the antibiotic resistance factors present in genomes of a few representative well known, epidemic and MDR CD strains found predominantly in different regions of the world.
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Affiliation(s)
- Ishani Wickramage
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Down Blvd, Tampa, FL 33612, USA
| | - Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Down Blvd, Tampa, FL 33612, USA
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21
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Gonzales-Luna AJ, Olaitan AO, Shen WJ, Deshpande A, Carlson TJ, Dotson KM, Lancaster C, Begum K, Alam MJ, Hurdle JG, Garey KW. Reduced Susceptibility to Metronidazole Is Associated With Initial Clinical Failure in Clostridioides difficile Infection. Open Forum Infect Dis 2021; 8:ofab365. [PMID: 34381844 PMCID: PMC8351808 DOI: 10.1093/ofid/ofab365] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Background Clinical studies have demonstrated inferior cure rates when metronidazole (MTZ) is used to treat Clostridioides difficile infection (CDI). We hypothesized that a newly identified, heme-inducible form of reduced MTZ susceptibility in C. difficile leads to higher odds of initial clinical failure in patients with CDI treated with MTZ. Methods This multicenter cohort study included adults diagnosed with CDI between 2017 and 2018. C. difficile isolated from stool samples underwent agar dilution MTZ susceptibility testing with incorporation of fresh heme. Blinded investigators reviewed medical records for initial clinical failure and other relevant clinical variables. Classification and regression tree (CART) analysis was used to identify the MTZ minimum inhibitory concentration (MIC) breakpoint that was predictive of initial clinical failure. Results were confirmed using univariate and multivariable logistic regression analyses to account for potential confounders. Results Of the 356 patients included, 72% received MTZ-based therapy and 27% experienced initial clinical failure. CART analysis identified an MTZ MIC ≥1 µg/mL above which patients had a higher rate of initial clinical failure. MTZ MICs ranged from 0.25 to 8 µg/mL (MIC50/90 = 0.25/2 µg/mL), and approximately 18% of isolates had MTZ MICs ≥1 µg/mL. In multivariable analysis, an MTZ MIC ≥1 µg/mL was an independent predictor of initial clinical failure in patients receiving an MTZ-based treatment regimen (odds ratio, 2.27 [95% confidence interval, 1.18–4.34]). Conclusions Using a reproducible method to determine C. difficile MICs to MTZ, a breakpoint of ≥1 µg/mL identified patients at higher risk of initial clinical failure.
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Affiliation(s)
- Anne J Gonzales-Luna
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Abiola O Olaitan
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Wan-Jou Shen
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Aditi Deshpande
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Travis J Carlson
- Department of Clinical Sciences, High Point University Fred Wilson School of Pharmacy, High Point, North Carolina, USA
| | | | - Chris Lancaster
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Khurshida Begum
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - M Jahangir Alam
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
| | - Julian G Hurdle
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M Health Science Center, Houston, Texas, USA
| | - Kevin W Garey
- Department of Pharmacy Practice and Translational Research, University of Houston College of Pharmacy, Houston, Texas, USA
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22
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Boekhoud IM, Sidorov I, Nooij S, Harmanus C, Bos-Sanders IMJG, Viprey V, Spittal W, Clark E, Davies K, Freeman J, Kuijper EJ, Smits WK. Haem is crucial for medium-dependent metronidazole resistance in clinical isolates of Clostridioides difficile. J Antimicrob Chemother 2021; 76:1731-1740. [PMID: 33876817 PMCID: PMC8212768 DOI: 10.1093/jac/dkab097] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
Background Until recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Objectives To identify factors that contribute to plasmid-independent metronidazole resistance of C. difficile. Methods Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile using a combination of antimicrobial susceptibility testing on different solid agar media and WGS of selected isolates. Results We find that nearly all isolates demonstrate a haem-dependent increase in the MIC of metronidazole, which in some cases leads to isolates qualifying as resistant (MIC >2 mg/L). Moreover, we find an SNP in the haem-responsive gene hsmA, which defines a metronidazole-resistant lineage of PCR ribotype 010/MLST ST15 isolates that also includes pCD-METRO-containing strains. Conclusions Our data demonstrate that haem is crucial for medium-dependent metronidazole resistance in C. difficile.
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Affiliation(s)
- Ilse M Boekhoud
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Igor Sidorov
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Céline Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Virginie Viprey
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - William Spittal
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Emma Clark
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK
| | - Kerrie Davies
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Jane Freeman
- Healthcare Associated Infection Research Group, School of Medicine, University of Leeds, Leeds, UK.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland.,National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.,European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
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Doan THD, Yen-Nicolaÿ S, Bernet-Camard MF, Martin-Verstraete I, Péchiné S. Impact of subinhibitory concentrations of metronidazole on proteome of Clostridioides difficile strains with different levels of susceptibility. PLoS One 2020; 15:e0241903. [PMID: 33166349 PMCID: PMC7652271 DOI: 10.1371/journal.pone.0241903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022] Open
Abstract
Clostridioides difficile is responsible for various intestinal symptoms from mild diarrhea to severe pseudomembranous colitis and is the primary cause of antibiotic-associated diarrhea in adults. Metronidazole was the first-line treatment for mild to moderate C. difficile infections for 30 years. However, clinical failure and recurrence rates of metronidazole is superior to oral vancomycin and metronidazole is now recommended only as an alternative to vancomycin or fidaxomicin, for an initial non-severe infection. The mechanisms of treatment failure and infection recurrence remain unclear. Given the poor fecal concentrations of metronidazole, the bacteria may be exposed to subinhibitory concentrations of metronidazole and develop adaptation strategy, which is likely to be the origin of an increase in treatment failures. In this study, a proteomic approach was used to analyze changes in the proteome of two strains with different levels of susceptibility to metronidazole in the presence of subinhibitory concentrations of this antibiotic. The two strains were grown to stationary phase: CD17-146, a clinical C. difficile isolate with reduced susceptibility to metronidazole, and VPI 10463, a metronidazole susceptible strain. Our study revealed that, whatever the strain, subinhibitory concentrations of metronidazole modified the amount of proteins involved in protein biosynthesis, glycolysis, and protection against stress induced by metronidazole, as well as in DNA repair. Several proteins involved in stress response are known to be synthesized under the control of Sigma factor B, which suggests a close link between Sigma factor B and metronidazole. Interestingly, impact of metronidazole on protein production for VPI 10463 strain differed from CD17-146 strain, for which the amount of two proteins involved in biofilm formation of CD17-146 were modified by metronidazole.
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Affiliation(s)
- Tri-Hanh-Dung Doan
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Stéphanie Yen-Nicolaÿ
- Université Paris-Saclay, UMS « Ingénierie et Plateformes au Service de l'Innovation Thérapeutique », Proteomic Facility, Châtenay-Malabry, France
| | | | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France
- Institut Universitaire de France, Paris, France
| | - Séverine Péchiné
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
- * E-mail:
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