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Rasmussen TS, Mao X, Forster S, Larsen SB, Von Münchow A, Tranæs KD, Brunse A, Larsen F, Mejia JLC, Adamberg S, Hansen AK, Adamberg K, Hansen CHF, Nielsen DS. Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments. MICROBIOME 2024; 12:119. [PMID: 38951925 PMCID: PMC11218093 DOI: 10.1186/s40168-024-01820-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 04/19/2024] [Indexed: 07/03/2024]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinder their wider clinical application in treating less acute diseases. METHODS To overcome these challenges, we developed methods to broaden FVT's clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: (1) chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), (2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and (3) pyronin-Y treatment to inhibit RNA virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in a C. difficile infection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline. RESULTS FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to FMT, FVT-PyT, and saline (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizing C. difficile cells and associated toxin A/B levels. There was a potential elimination of C. difficile colonization, with seven out of eight mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence of C. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels, and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy. CONCLUSIONS This proof-of-concept study shows that specific modifications of FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limiting C. difficile colonization in mice, with solvent/detergent treatment and chemostat propagation of donor phages emerging as promising approaches. Video Abstract.
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Affiliation(s)
- Torben Sølbeck Rasmussen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark.
| | - Xiaotian Mao
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Sarah Forster
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Sabina Birgitte Larsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Alexandra Von Münchow
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Kaare Dyekær Tranæs
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Anders Brunse
- Section of Comparative Pediatrics and Nutrition, Department of Veterinary and Animal Sciences, University of Copenhagen, Dyrlægevej 68, 1870, Frederiksberg, Denmark
| | - Frej Larsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Josue Leonardo Castro Mejia
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Axel Kornerup Hansen
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Akadeemia tee 15, 12618, Tallinn, Estonia
| | - Camilla Hartmann Friis Hansen
- Section of Experimental Animal Models, Department, of Veterinary and Animal Sciences, University of Copenhagen, Ridebanevej 9 1, 1871, Frederiksberg, Denmark
| | - Dennis Sandris Nielsen
- Section of Food Microbiology, Gut Health, and Fermentation, Department of Food Science, University of Copenhagen, Rolighedsvej 26 4, 1958, Frederiksberg, Denmark.
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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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Huang H, Li L, Wu M, Liu Z, Zhao Y, Peng J, Ren X, Chen S. Antibiotics and antibiotic-associated diarrhea: a real-world disproportionality study of the FDA adverse event reporting system from 2004 to 2022. BMC Pharmacol Toxicol 2023; 24:73. [PMID: 38049920 PMCID: PMC10694877 DOI: 10.1186/s40360-023-00710-w] [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: 05/04/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Our study aimed to assess the risk signals of antibiotic-associated diarrhea (AAD) caused by various antibiotics using real-world data and provide references for safe clinical applications. METHODS We analyzed data extracted from the FDA Adverse Event Reporting System (FAERS) database, covering the period from the first quarter of 2004 to the third quarter of 2022. We computed the reporting odds ratio (ROR) for each antibiotic or antibiotic class to compare the signal difference. Furthermore, we also examined the differences in the onset times and outcomes of AAD caused by various antibiotics. RESULTS A total of 5,397 reports met the inclusion requirements. Almost all antibiotics, except tobramycin and minocycline (ROR 0.98; 95%CI: 0.64-1.51 and 0.42; 95%CI: 0.16-1.11, respectively), showed a significant correlation with AAD. The analysis of the correlation between different classes of antibiotics and AAD revealed that lincomycins (ROR 29.19; 95%CI: 27.06-31.50), third-generation cephalosporins (ROR 15.96; 95%CI: 14.58-17.47), and first/second generation cephalosporins (ROR 15.29; 95%CI: 13.74-17.01) ranked the top three. The ROR values for antibiotics from the same class of antibiotics also varied greatly, with the ROR values for third-generation cephalosporins ranging from 9.97 to 58.59. There were also differences in ROR values between β-lactamase inhibitors and their corresponding β-lactamase drugs, such as amoxicillin-clavulanate (ROR = 13.31; 95%CI: 12.09-14.65) and amoxicillin (ROR = 6.50; 95%CI: 5.69-7.44). 91.35% of antibiotics have an onset time of less than four weeks. CONCLUSIONS There is a significant correlation between almost all antibiotics and AAD, particularly lincomycins and β-lactam antibiotics, as well as a different correlation within the same class. These findings offer valuable evidence for selecting antibiotics appropriately.
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Affiliation(s)
- Haining Huang
- Department of Clinical Pharmacy, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Lanfang Li
- Department of Clinical Pharmacy, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Mingli Wu
- Department of Clinical Pharmacy, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Zhen Liu
- Department of Clinical Pharmacy, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Yanyan Zhao
- Department of Clinical Pharmacy, Affiliated Hospital of Jining Medical University, Jining, Shandong, China
| | - Jing Peng
- Department of Clinical Pharmacy, Affiliated Hospital of Jining Medical University, Jining, Shandong, China.
| | - Xiaolei Ren
- Data Center, Affiliated Hospital of Jining Medical University, Jining, Shandong, China.
| | - Shuai Chen
- Department of Pathology, Affiliated Hospital of Jining Medical University, Jining, Shandong, China.
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Rubio-Mendoza D, Martínez-Meléndez A, Maldonado-Garza HJ, Córdova-Fletes C, Garza-González E. Review of the Impact of Biofilm Formation on Recurrent Clostridioides difficile Infection. Microorganisms 2023; 11:2525. [PMID: 37894183 PMCID: PMC10609348 DOI: 10.3390/microorganisms11102525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 09/25/2023] [Accepted: 09/29/2023] [Indexed: 10/29/2023] Open
Abstract
Clostridioides difficile infection (CDI) may recur in approximately 10-30% of patients, and the risk of recurrence increases with each successive recurrence, reaching up to 65%. C. difficile can form biofilm with approximately 20% of the bacterial genome expressed differently between biofilm and planktonic cells. Biofilm plays several roles that may favor recurrence; for example, it may act as a reservoir of spores, protect the vegetative cells from the activity of antibiotics, and favor the formation of persistent cells. Moreover, the expression of several virulence genes, including TcdA and TcdB toxins, has been associated with recurrence. Several systems and structures associated with adhesion and biofilm formation have been studied in C. difficile, including cell-wall proteins, quorum sensing (including LuxS and Agr), Cyclic di-GMP, type IV pili, and flagella. Most antibiotics recommended for the treatment of CDI do not have activity on spores and do not eliminate biofilm. Therapeutic failure in R-CDI has been associated with the inadequate concentration of drugs in the intestinal tract and the antibiotic resistance of a biofilm. This makes it challenging to eradicate C. difficile in the intestine, complicating antibacterial therapies and allowing non-eliminated spores to remain in the biofilm, increasing the risk of recurrence. In this review, we examine the role of biofilm on recurrence and the challenges of treating CDI when the bacteria form a biofilm.
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Affiliation(s)
- Daira Rubio-Mendoza
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (D.R.-M.); (H.J.M.-G.); (C.C.-F.)
| | - Adrián Martínez-Meléndez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza 66455, Mexico;
| | - Héctor Jesús Maldonado-Garza
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (D.R.-M.); (H.J.M.-G.); (C.C.-F.)
| | - Carlos Córdova-Fletes
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (D.R.-M.); (H.J.M.-G.); (C.C.-F.)
| | - Elvira Garza-González
- Facultad de Medicina, Universidad Autónoma de Nuevo León, Monterrey 64460, Mexico; (D.R.-M.); (H.J.M.-G.); (C.C.-F.)
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5
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Larsen IS, Chenaux M, Collins FWJ, Mandic A, Hansen LBS, Lauridsen CAS, Haller RF, Elvig-Jørgensen S, Horwell E, Christiansen J, Silva A, Vehreschild MJGT, Cutting SM, Roggenbuck-Wedemeyer M, Kristensen NN. Bacillus velezensis DSM 33864 reduces Clostridioides difficile colonization without disturbing commensal gut microbiota composition. Sci Rep 2023; 13:14941. [PMID: 37696924 PMCID: PMC10495459 DOI: 10.1038/s41598-023-42128-8] [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: 04/17/2023] [Accepted: 09/05/2023] [Indexed: 09/13/2023] Open
Abstract
Up to 25% of the US population harbor Clostridioides difficile in the gut. Following antibiotic disruption of the gut microbiota, C. difficile can act as an opportunistic pathogen and induce potentially lethal infections. Consequently, reducing the colonization of C. difficile in at-risk populations is warranted, prompting us to identify and characterize a probiotic candidate specifically targeting C. difficile colonization. We identified Bacillus velezensis DSM 33864 as a promising strain to reduce C. difficile levels in vitro. We further investigated the effects of B. velezensis DSM 33864 in an assay including human fecal medium and in healthy or clindamycin-treated mouse models of C. difficile colonization. The addition of B. velezensis DSM 33864 to human fecal samples was shown to reduce the colonization of C. difficile in vitro. This was supported in vivo where orally administered B. velezensis DSM 33864 spores reduced C. difficile levels in clindamycin-treated mice. The commensal microbiota composition or post-antibiotic reconstitution was not impacted by B. velezensis DSM 33864 in human fecal samples, short-, or long-term administration in mice. In conclusion, oral administration of B. velezensis DSM 33864 specifically reduced C. difficile colonization in vitro and in vivo without adversely impacting the commensal gut microbiota composition.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Ed Horwell
- Bioscience Innovation Centre, Sporegen Ltd., 2 Royal College Street, London, NW1 0NH, UK
| | | | | | - Maria J G T Vehreschild
- Department of Internal Medicine, Infectious Diseases, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Simon M Cutting
- Bioscience Innovation Centre, Sporegen Ltd., 2 Royal College Street, London, NW1 0NH, UK
- Department of Biological Sciences, Royal Holloway University of London, Egham, Surrey, UK
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Dicks LMT. Biofilm Formation of Clostridioides difficile, Toxin Production and Alternatives to Conventional Antibiotics in the Treatment of CDI. Microorganisms 2023; 11:2161. [PMID: 37764005 PMCID: PMC10534356 DOI: 10.3390/microorganisms11092161] [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: 06/29/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Clostridioides difficile is considered a nosocomial pathogen that flares up in patients exposed to antibiotic treatment. However, four out of ten patients diagnosed with C. difficile infection (CDI) acquired the infection from non-hospitalized individuals, many of whom have not been treated with antibiotics. Treatment of recurrent CDI (rCDI) with antibiotics, especially vancomycin (VAN) and metronidazole (MNZ), increases the risk of experiencing a relapse by as much as 70%. Fidaxomicin, on the other hand, proved more effective than VAN and MNZ by preventing the initial transcription of RNA toxin genes. Alternative forms of treatment include quorum quenching (QQ) that blocks toxin synthesis, binding of small anion molecules such as tolevamer to toxins, monoclonal antibodies, such as bezlotoxumab and actoxumab, bacteriophage therapy, probiotics, and fecal microbial transplants (FMTs). This review summarizes factors that affect the colonization of C. difficile and the pathogenicity of toxins TcdA and TcdB. The different approaches experimented with in the destruction of C. difficile and treatment of CDI are evaluated.
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Affiliation(s)
- Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
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7
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Williams P, Hill P, Bonev B, Chan WC. Quorum-sensing, intra- and inter-species competition in the staphylococci. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001381. [PMID: 37578829 PMCID: PMC10482373 DOI: 10.1099/mic.0.001381] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023]
Abstract
In Gram-positive bacteria such as Staphylococcus aureus and the coagulase-negative staphylococci (CoNS), the accessory gene regulator (agr) is a highly conserved but polymorphic quorum-sensing system involved in colonization, virulence and biofilm development. Signalling via agr depends on the interaction of an autoinducing peptide (AIP) with AgrC, a transmembrane sensor kinase that, once phosphorylated activates the response regulator AgrA. This in turn autoinduces AIP biosynthesis and drives target gene expression directly via AgrA or via the post-transcriptional regulator, RNAIII. In this review we describe the molecular mechanisms underlying the agr-mediated generation of, and response to, AIPs and the molecular basis of AIP-dependent activation and inhibition of AgrC. How the environment impacts on agr functionality is considered and the consequences of agr dysfunction for infection explored. We also discuss the concept of AIP-driven competitive interference between S. aureus and the CoNS and its anti-infective potential.
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Affiliation(s)
- Paul Williams
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Phil Hill
- School of Biosciences, Sutton Bonington Campus, University of Nottingham, Loughborough, LE12 5RD, UK
| | - Boyan Bonev
- Biodiscovery Institute and School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Weng C. Chan
- School of Pharmacy, Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK
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Polaske TJ, West KHJ, Zhao K, Widner DL, York JT, Blackwell HE. Chemical and biomolecular insights into the Staphylococcus aureus agr quorum sensing system: Current progress and ongoing challenges. Isr J Chem 2023; 63:e202200096. [PMID: 38765792 PMCID: PMC11101167 DOI: 10.1002/ijch.202200096] [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: 10/31/2022] [Indexed: 03/19/2023]
Abstract
Staphylococcus aureus is a ubiquitous bacterium that has become a major threat to human health due to its extensive toxin production and tremendous capacity for antibiotic resistance (e.g., MRSA "superbug" infections). Amid a worsening antibiotic resistance crisis, new strategies to combat this deadly microbe that remove the selective pressure of traditional approaches are in high demand. S. aureus utilizes an accessory gene regulator (agr) quorum sensing network to monitor its local cellular population and trigger a devastating communal attack, like an invading horde, once a threshold cell density has been reached. The role of the agr system in a range of disease types is still being unraveled. Herein, we discuss the present-day biochemical understanding of agr along with unresolved details, describe its connection to the progression of infection, and review how chemical strategies have been implemented to study and intercept this signaling pathway. This research is illuminating the potential of agr as an anti-virulence target in S. aureus and should inform the study of similar, yet less studied, agr systems in related bacterial pathogens.
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Affiliation(s)
- Thomas J. Polaske
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Korbin H. J. West
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Ke Zhao
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Danielle L. Widner
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Jordan T. York
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
| | - Helen E. Blackwell
- Department of Chemistry, University of Wisconsin–Madison, 1101 University Ave., Madison, WI 53706 USA
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9
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Chandra H, Sorg JA, Hassett DJ, Sun X. Regulatory transcription factors of Clostridioides difficile pathogenesis with a focus on toxin regulation. Crit Rev Microbiol 2023; 49:334-349. [PMID: 35389761 PMCID: PMC11209739 DOI: 10.1080/1040841x.2022.2054307] [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: 05/11/2021] [Revised: 02/26/2022] [Accepted: 03/14/2022] [Indexed: 11/03/2022]
Abstract
Clostridioides difficile (CD), a nosocomial gut pathogen, produces two major exotoxins, TcdA and TcdB, which disrupt the gut epithelial barrier and induce inflammatory/immune responses, leading to symptoms ranging from mild diarrhoea to pseudomembranous colitis and potentially to death. The expression of toxins is regulated by various transcription factors (TFs) which are induced in response to CD physiological life stages, nutritional availability, and host environment. This review summarises our current understanding on the regulation of toxin expression by TFs that interconnect with pathways of flagellar synthesis, quorum sensing, motility, biofilm formation, sporulation, and phase variation. The pleiotropic roles of some key TFs suggest that toxin production is tightly linked to other cellular processes of the CD physiology.
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Affiliation(s)
- Harish Chandra
- Department of Environmental Microbiology, School of Environmental and Earth Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow, India
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Joseph A. Sorg
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Daniel J Hassett
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, OH, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
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10
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Falà AK, Álvarez-Ordóñez A, Filloux A, Gahan CGM, Cotter PD. Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting. Front Microbiol 2022; 13:1002185. [PMID: 36504831 PMCID: PMC9733432 DOI: 10.3389/fmicb.2022.1002185] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 10/17/2022] [Indexed: 11/27/2022] Open
Abstract
Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.
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Affiliation(s)
- A. Kate Falà
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland
| | - Avelino Álvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Cormac G. M. Gahan
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,School of Pharmacy, University College Cork, Cork, Ireland
| | - Paul D. Cotter
- APC Microbiome Ireland, University College Cork, Cork, Ireland,Food Bioscience Department, Teagasc Food Research Centre, Fermoy, Ireland,*Correspondence: Paul D. Cotter,
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Anwar F, Roxas BAP, Shehab KW, Ampel N, Viswanathan VK, Vedantam G. Low-Toxin Clostridioides difficile RT027 Strains Exhibit Robust Virulence. Emerg Microbes Infect 2022; 11:1982-1993. [PMID: 35880487 PMCID: PMC9361768 DOI: 10.1080/22221751.2022.2105260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Clostridioides difficile is a leading cause of healthcare-associated infections worldwide. Currently, there is a lack of consensus for an optimal diagnostic method for C. difficile infection (CDI). Multi-step diagnostic algorithms use enzyme immunosorbent analysis (EIA)-based detection of C. difficile toxins TcdA/TcdB in stool, premised on the rationale that EIA toxin-negative (Tox−) patients have less severe disease and shorter diarrhoea duration. The aim of this study was to characterize toxigenic (i.e. tcdA/tcdB-positive) C. difficile strains isolated from diarrheic patient stool with an EIA Tox− (i.e. “discrepant”) CDI diagnostic test result. Recovered strains were DNA fingerprinted (ribotyped), subjected to multiple toxin, genome and proteome evaluations, and assessed for virulence. Overall, of 1243 C. difficile-positive patient stool specimens from Southern Arizona hospitals, 31% were discrepant. For RT027 (the most prevalent ribotype)-containing specimens, 34% were discrepant; the corresponding RT027 isolates were cytotoxic to cultured fibroblasts, but their total toxin levels were comparable to, or lower than, the historic low-toxin-producing C. difficile strain CD630. Nevertheless, these low-toxin RT027 strains (LT-027) exhibited similar lethality to a clade-matched high-toxin RT027 strain in Golden Syrian hamsters, and heightened colonization and persistence in mice. Genomics and proteomics analyses of LT-027 strains identified unique genes and altered protein abundances, respectively, relative to high-toxin RT027 strains. Collectively, our data highlight the robust virulence of LT-027 C. difficile, provide a strong argument for reconsidering the clinical significance of a Tox− EIA result, and underscore the potential limitations of current diagnostic protocols.
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Affiliation(s)
- Farhan Anwar
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Bryan Angelo P Roxas
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA
| | - Kareem W Shehab
- Department of Pediatrics, The University of Arizona College of Medicine, Tucson, AZ, USA
| | | | - V K Viswanathan
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA.,Department of Immunobiology, The University of Arizona College of Medicine, Tucson, AZ, USA.,BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, AZ, USA
| | - Gayatri Vedantam
- School of Animal and Comparative Biomedical Sciences, The University of Arizona, Tucson, AZ, USA.,Department of Immunobiology, The University of Arizona College of Medicine, Tucson, AZ, USA.,BIO5 Institute for Collaborative Research, The University of Arizona, Tucson, AZ, USA.,Southern Arizona VA Healthcare System, Tucson, AZ, USA
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12
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Wynendaele E, Debunne N, Janssens Y, De Spiegeleer A, Verbeke F, Tack L, Van Welden S, Goossens E, Knappe D, Hoffmann R, Van De Wiele C, Laukens D, Van Eenoo P, Vereecke L, Van Immerseel F, De Wever O, De Spiegeleer B. The quorum sensing peptide EntF* promotes colorectal cancer metastasis in mice: a new factor in the host-microbiome interaction. BMC Biol 2022; 20:151. [PMID: 35761265 PMCID: PMC9238271 DOI: 10.1186/s12915-022-01317-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/29/2022] [Indexed: 12/15/2022] Open
Abstract
Background Colorectal cancer, one of the most common malignancies worldwide, is associated with a high mortality rate, mainly caused by metastasis. Comparative metagenome-wide association analyses of healthy individuals and cancer patients suggest a role for the human intestinal microbiota in tumor progression. However, the microbial molecules involved in host-microbe communication are largely unknown, with current studies mainly focusing on short-chain fatty acids and amino acid metabolites as potential mediators. Quorum sensing peptides are not yet considered in this context since their presence in vivo and their ability to affect host cells have not been reported so far. Results Here, we show that EntF*, a metabolite of the quorum sensing peptide EntF produced by Enterococcus faecium, is naturally present in mice bloodstream. Moreover, by using an orthotopic mouse model, we show that EntF* promotes colorectal cancer metastasis in vivo, with metastatic lesions in liver and lung tissues. In vitro tests suggest that EntF* regulates E-cadherin expression and consequently the epithelial-mesenchymal transition, via the CXCR4 receptor. In addition, alanine-scanning analysis indicates that the first, second, sixth, and tenth amino acid of EntF* are critical for epithelial-mesenchymal transition and tumor metastasis. Conclusion Our work identifies a new class of molecules, quorum sensing peptides, as potential regulators of host-microbe interactions. We prove, for the first time, the presence of a selected quorum sensing peptide metabolite in a mouse model, and we demonstrate its effects on colorectal cancer metastasis. We believe that our work represents a starting point for future investigations on the role of microbiome in colorectal cancer metastasis and for the development of novel bio-therapeutics in other disease areas. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01317-z.
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Affiliation(s)
- Evelien Wynendaele
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Nathan Debunne
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Yorick Janssens
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Anton De Spiegeleer
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Frederick Verbeke
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Liesa Tack
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sophie Van Welden
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Evy Goossens
- Department of Pathology, Bacteriology and Poultry diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Daniel Knappe
- Center of Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
| | - Ralf Hoffmann
- Center of Biotechnology and Biomedicine, Faculty of Chemistry and Mineralogy, Universität Leipzig, Leipzig, Germany
| | - Christophe Van De Wiele
- Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Debby Laukens
- Department of Internal Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Peter Van Eenoo
- Department of Diagnostic Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Lars Vereecke
- Department of Rheumatology, Faculty of Medicine and Health Sciences, Ghent, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Poultry diseases, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium
| | - Olivier De Wever
- Department of Human Structure and Repair, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium.
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13
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Yamaki J, Chawla S, Tong S, Lozada KA, Yang S. Iron Effects on Clostridioides difficile Toxin Production and Antimicrobial Susceptibilities. Antibiotics (Basel) 2022; 11:537. [PMID: 35625180 PMCID: PMC9137654 DOI: 10.3390/antibiotics11050537] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 03/30/2022] [Accepted: 04/18/2022] [Indexed: 12/10/2022] Open
Abstract
Despite the benefits of red blood cell (RBC) transfusion therapy, it can render patients vulnerable to iron overload. The excess iron deposits in various body tissues cause severe complications and organ damage such as cardiotoxicity and mold infections. Clostridioides difficile infection (CDI) is the most common cause of nosocomial diarrhea among cancer patients and is associated with significant morbidity and mortality. Our study aims to determine the role of iron overload and the effects of iron chelators on CDI. Our results demonstrated that iron (Fe3+) stimulated the growth of C. difficile with increased colony formation units (CFU) in a dose-dependent manner. Exposure to excess iron also increased the gene expression levels of tcdA and tcdB. The production of C. difficile toxin A, necessary for the pathogenesis of C. difficile, was also elevated after iron treatment. In the presence of excess iron, C. difficile becomes less susceptible to metronidazole with significantly elevated minimum inhibitory concentration (MIC) but remains susceptible to vancomycin. Iron-stimulated colony formation and production of C. difficile toxins were effectively diminished by iron chelator deferoxamine co-treatment. Incorporating iron overload status as a potential factor in developing a risk prediction model of CDI and antibiotic treatment response may aid clinical practitioners in optimizing CDI management in oncology patients.
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Affiliation(s)
- Jason Yamaki
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (J.Y.); (S.C.)
| | - Swati Chawla
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (J.Y.); (S.C.)
| | - Shirley Tong
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (S.T.); (K.A.L.)
| | - Kate Alison Lozada
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (S.T.); (K.A.L.)
| | - Sun Yang
- Department of Pharmacy Practice, Chapman University School of Pharmacy, Irvine, CA 92618, USA; (J.Y.); (S.C.)
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14
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Mechanisms and Applications of Bacterial Sporulation and Germination in the Intestine. Int J Mol Sci 2022; 23:ijms23063405. [PMID: 35328823 PMCID: PMC8953710 DOI: 10.3390/ijms23063405] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/15/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Recent studies have suggested a major role for endospore forming bacteria within the gut microbiota, not only as pathogens but also as commensal and beneficial members contributing to gut homeostasis. In this review the sporulation processes, spore properties, and germination processes will be explained within the scope of the human gut. Within the gut, spore-forming bacteria are known to interact with the host’s immune system, both in vegetative cell and spore form. Together with the resistant nature of the spore, these characteristics offer potential for spores’ use as delivery vehicles for therapeutics. In the last part of the review, the therapeutic potential of spores as probiotics, vaccine vehicles, and drug delivery systems will be discussed.
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15
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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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16
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Regulation of Clostridioides difficile toxin production. Curr Opin Microbiol 2022; 65:95-100. [PMID: 34781095 PMCID: PMC8792210 DOI: 10.1016/j.mib.2021.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 02/03/2023]
Abstract
Clostridioides difficile produces toxins TcdA and TcdB during infection. Since the severity of the illness is directly correlated with the level of toxins produced, researchers have long been interested in the regulation mechanisms of toxin production. The advent of new genetics and mutagenesis technologies in C. difficile has allowed a slew of new investigations in the last decade, which considerably improved our understanding of this crucial regulatory network. The current body of work shows that the toxin regulatory network overlaps with the regulatory networks of sporulation, motility, and key metabolic pathways. This implies that toxin production is a complicated process initiated by bacteria in response to numerous host factors during infection. We summarize the existing knowledge about the toxin gene regulatory network here.
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17
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Ahmed UKB, Ballard JD. Autoinducing peptide-based quorum signaling systems in Clostridioides difficile. Curr Opin Microbiol 2022; 65:81-86. [PMID: 34773906 PMCID: PMC8792308 DOI: 10.1016/j.mib.2021.10.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 10/20/2021] [Accepted: 10/25/2021] [Indexed: 02/03/2023]
Abstract
The autoinducing peptide-based Agr system in Clostridioides difficile is involved in virulence factor expression, motility, and sporulation. This review highlights several of the recent discoveries regarding C. difficile Agr. Typical Agr systems rely on the combined activities of four proteins involved in peptide expression, peptide processing, peptide sensing, and transcriptional regulation. As emphasized in this review, at least two C. difficile Agr systems (Agr1 and Agr3) lack the set of proteins associated with this regulatory network. In line with this, recent finding indicate Agr1 can function in ways that may not depend on accumulation of extracellular peptide. Also, described are the similarities and differences in Agr systems within the pathogenic Clostridia.
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18
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A bioanalytical screening method for Enterococcus faecalis RNPP-type quorum sensing peptides in murine feces. Bioanalysis 2022; 14:151-167. [PMID: 35014887 DOI: 10.4155/bio-2021-0225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: Bacteria coordinate their behavior as a group via communication with their peers, known as 'quorum sensing'. Enterococcus faecalis employs quorum sensing via RNPP-peptides which were not yet reported to be present in mammalian biofluids. Results: Solid phase extraction of murine feces was performed, followed by ultra high performance liquid chromatography (UHPLC-MS/MS) in multiple reaction monitoring (MRM) mode (in total <90 min/sample) for the nine known RNPP peptides. Limits of detection ranged between 0.045 and 52 nM. Adequate identification criteria allowed detection of RNPP quorum sensing peptides in 2/20 wild-type murine feces samples (i.e., cAM373 and cOB1). Conclusion: A fit-for-purpose UHPLC-MS/MS method detected these RNPP peptides in wild-type murine feces samples.
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19
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Verbeke F, borght KVD, De Spiegeleer A, Debunne N, Janssens Y, Wynendaele E, De Spiegeleer B. A fit-for-purpose LC-MS/MS method for the analysis of selected Streptococcal quorum sensing peptides in human saliva. J Pharm Biomed Anal 2022; 213:114594. [DOI: 10.1016/j.jpba.2022.114594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/12/2022] [Accepted: 01/13/2022] [Indexed: 10/19/2022]
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20
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Abstract
In the struggle with antibiotic resistance, we are losing. There is now a serious threat of moving into a postantibiotic world. High levels of resistance, in terms of both frequency and strength, have evolved against all clinically approved antibiotics worldwide. The usable life span of new clinically approved antibiotics is typically less than a decade before resistance reaches frequencies so high as to require only guarded usage. However, microbes have produced antibiotics for millennia without resistance becoming an existential issue. If resistance is the inevitable consequence of antibiotic usage, as has been the human experience, why has it not become an issue for microbes as well, especially since resistance genes are as prevalent in nature as the genes responsible for antibiotic production? Here, we ask how antibiotics can exist given the almost ubiquitous presence of resistance genes in the very microbes that have produced and used antibiotics since before humans walked the planet. We find that the context of both production and usage of antibiotics by microbes may be key to understanding how resistance is managed over time, with antibiotic synthesis and resistance existing in a paired relationship, much like a cipher and key, that impacts microbial community assembly. Finally, we put forward the cohesive, ecologically based "secret society" hypothesis to explain the longevity of antibiotics in nature.
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Affiliation(s)
- Fabrizio Spagnolo
- Biology Department, Queens College of The City University of New York, Flushing, New York, USA
| | - Monica Trujillo
- Department of Biological Sciences and Geology, Queensborough Community College, The City University of New York, Bayside, New York, USA
| | - John J. Dennehy
- Biology Department, Queens College of The City University of New York, Flushing, New York, USA
- The Graduate Center of The City University of New York, New York, New York, USA
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21
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Buckley AM, Moura IB, Arai N, Spittal W, Clark E, Nishida Y, Harris HC, Bentley K, Davis G, Wang D, Mitra S, Higashiyama T, Wilcox MH. Trehalose-Induced Remodelling of the Human Microbiota Affects Clostridioides difficile Infection Outcome in an In Vitro Colonic Model: A Pilot Study. Front Cell Infect Microbiol 2021; 11:670935. [PMID: 34277467 PMCID: PMC8284250 DOI: 10.3389/fcimb.2021.670935] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 06/02/2021] [Indexed: 12/19/2022] Open
Abstract
Within the human intestinal tract, dietary, microbial- and host-derived compounds are used as signals by many pathogenic organisms, including Clostridioides difficile. Trehalose has been reported to enhance virulence of certain C. difficile ribotypes; however, such variants are widespread and not correlated with clinical outcomes for patients suffering from C. difficile infection (CDI). Here, we make preliminary observations on how trehalose supplementation affects the microbiota in an in vitro model and show that trehalose-induced changes can reduce the outgrowth of C. difficile, preventing simulated CDI. Three clinically reflective human gut models simulated the effects of sugar (trehalose or glucose) or saline ingestion on the microbiota. Models were instilled with sugar or saline and further exposed to C. difficile spores. The recovery of the microbiota following antibiotic treatment and CDI induction was monitored in each model. The human microbiota remodelled to utilise the bioavailable trehalose. Clindamycin induction caused simulated CDI in models supplemented with either glucose or saline; however, trehalose supplementation did not result in CDI, although limited spore germination did occur. The absence of CDI in trehalose model was associated with enhanced abundances of Finegoldia, Faecalibacterium and Oscillospira, and reduced abundances of Klebsiella and Clostridium spp., compared with the other models. Functional analysis of the microbiota in the trehalose model revealed differences in the metabolic pathways, such as amino acid metabolism, which could be attributed to prevention of CDI. Our data show that trehalose supplementation remodelled the microbiota, which prevented simulated CDI, potentially due to enhanced recovery of nutritionally competitive microbiota against C. difficile.
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Affiliation(s)
- Anthony M. Buckley
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Ines B. Moura
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Norie Arai
- R&D Division, Hayashibara Co. Ltd./NAGASE Group, Okayama, Japan
| | - William Spittal
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Emma Clark
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | | | - Hannah C. Harris
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Karen Bentley
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Georgina Davis
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | - Dapeng Wang
- LeedsOmics, University of Leeds, Leeds, United Kingdom
| | - Suparna Mitra
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
| | | | - Mark H. Wilcox
- Healthcare Associated Infection Research Group, Molecular Gastroenterology, Leeds Institute of Medical Research, University of Leeds, Leeds, United Kingdom
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22
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Molloy EM, Dell M, Hänsch VG, Dunbar KL, Feldmann R, Oberheide A, Seyfarth L, Kumpfmüller J, Horch T, Arndt H, Hertweck C. Enzyme‐Primed Native Chemical Ligation Produces Autoinducing Cyclopeptides in Clostridia. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Evelyn M. Molloy
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Veit G. Hänsch
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Kyle L. Dunbar
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Romy Feldmann
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Ansgar Oberheide
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Lydia Seyfarth
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Therese Horch
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
| | - Hans‐Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry Friedrich Schiller University Jena Humboldtstr. 10 07743 Jena Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry Leibniz Institute for Natural, Product Research and Infection Biology HKI Beutenbergstr. 11a 07745 Jena Germany
- Faculty of Biological Sciences Friedrich Schiller University Jena 07743 Jena Germany
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23
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Systematic Evaluation of Parameters Important for Production of Native Toxin A and Toxin B from Clostridioides difficile. Toxins (Basel) 2021; 13:toxins13040240. [PMID: 33801738 PMCID: PMC8066640 DOI: 10.3390/toxins13040240] [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: 02/19/2021] [Revised: 03/19/2021] [Accepted: 03/25/2021] [Indexed: 12/26/2022] Open
Abstract
In the attempt to improve the purification yield of native toxin A (TcdA) and toxin B (TcdB) from Clostridioides difficile (C. difficile), we systematically evaluated culture parameters for their influence on toxin production. In this study, we showed that culturing C. difficile in a tryptone-yeast extract medium buffered in PBS (pH 7.5) that contained 5 mM ZnCl2 and 10 mM glucose supported the highest TcdB production, measured by the sandwich ELISA. These culture conditions were scalable into 5 L and 15 L dialysis tube cultures, and we were able to reach a TcdB concentration of 29.5 µg/mL of culture. Furthermore, we established a purification protocol for TcdA and TcdB using FPLC column chromatography, reaching purities of >99% for both toxins with a yield around 25% relative to the starting material. Finally, by screening the melting temperatures of TcdA and TcdB in various buffer conditions using differential scanning fluorimetry, we found optimal conditions for improving the protein stability during storage. The results of this study present a complete protocol for obtaining high amounts of highly purified native TcdA and TcdB from C. difficile.
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Molloy EM, Dell M, Hänsch VG, Dunbar KL, Feldmann R, Oberheide A, Seyfarth L, Kumpfmüller J, Horch T, Arndt HD, Hertweck C. Enzyme-Primed Native Chemical Ligation Produces Autoinducing Cyclopeptides in Clostridia. Angew Chem Int Ed Engl 2021; 60:10670-10679. [PMID: 33625794 PMCID: PMC8251862 DOI: 10.1002/anie.202016378] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 12/14/2022]
Abstract
Clostridia coordinate many important processes such as toxin production, infection, and survival by density‐dependent communication (quorum sensing) using autoinducing peptides (AIPs). Although clostridial AIPs have been proposed to be (thio)lactone‐containing peptides, their true structures remain elusive. Here, we report the genome‐guided discovery of an AIP that controls endospore formation in Ruminiclostridium cellulolyticum. Through a combination of chemical synthesis and chemical complementation assays with a mutant strain, we reveal that the genuine chemical mediator is a homodetic cyclopeptide (cAIP). Kinetic analyses indicate that the mature cAIP is produced via a cryptic thiolactone intermediate that undergoes a rapid S→N acyl shift, in a manner similar to intramolecular native chemical ligation (NCL). Finally, by implementing a chemical probe in a targeted screen, we show that this novel enzyme‐primed, intramolecular NCL is a widespread feature of clostridial AIP biosynthesis.
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Affiliation(s)
- Evelyn M Molloy
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Maria Dell
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Veit G Hänsch
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Kyle L Dunbar
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Romy Feldmann
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Ansgar Oberheide
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Lydia Seyfarth
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Jana Kumpfmüller
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Therese Horch
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany
| | - Hans-Dieter Arndt
- Institute for Organic Chemistry and Macromolecular Chemistry, Friedrich Schiller University Jena, Humboldtstr. 10, 07743, Jena, Germany
| | - Christian Hertweck
- Dept. of Biomolecular Chemistry, Leibniz Institute for Natural, Product Research and Infection Biology, HKI, Beutenbergstr. 11a, 07745, Jena, Germany.,Faculty of Biological Sciences, Friedrich Schiller University Jena, 07743, Jena, Germany
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Modulation of quorum sensing-associated virulence in bacteria: carbohydrate as a key factor. Arch Microbiol 2021; 203:1881-1890. [PMID: 33641039 DOI: 10.1007/s00203-021-02235-4] [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] [Received: 09/01/2020] [Revised: 12/11/2020] [Accepted: 02/11/2021] [Indexed: 01/21/2023]
Abstract
Quorum sensing (QS) is a method of inter-cellular communication that permits bacteria to dispense information about cell density and to synchronize the gene expression accordingly. Gram-positive and Gram-negative bacteria utilize distinct quorum sensing mechanisms for effective pathogenesis. Virulence factor production by pathogenic bacteria is one of the important traits that is under the control of QS. A growing body of evidence has indicated the role of the nutritional environment notably by carbohydrates in dictating the QS-associated virulence gene regulation. The modulation of QS by carbohydrates mitigates the survival and establishment of the pathogen within its host which in turn leads to an increase in morbidity and mortality. This mini-review throws light on the predilection of pathogenic bacteria to rapidly regulate its QS-linked virulence gene expression based on the changing nutrient levels that assist them in prospering within diverse niches.
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Potential role of probiotics in reducing Clostridioides difficile virulence: Interference with quorum sensing systems. Microb Pathog 2021; 153:104798. [PMID: 33609647 DOI: 10.1016/j.micpath.2021.104798] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/05/2021] [Accepted: 02/08/2021] [Indexed: 12/23/2022]
Abstract
Opportunistic pathogenic bacteria may cause disease after the normally protective microbiome is disrupted (typically by antibiotic exposure). Clostridioides difficile is one such pathogen having a severe impact on healthcare facilities and increasing costs of medical care. The search for new therapeutic strategies that are not reliant on additional antibiotic exposures are currently being explored. One such strategy is to disrupt the production of C. difficile virulence factors by interfering with quorum sensing (QS) systems. QS has been well studied in other bacteria, but our understanding in C. difficile is not so well understood. Some probiotic strains or combinations of strains have been shown to be effective in the treatment or primary prevention of C. difficile infections and may possess multiple mechanisms of action. One mechanism of probiotics might be the inhibition of QS, but their role has not been clearly defined yet. A literature search was conducted using standard databases (PubMed, Google Scholar) from database inception to August 2020. The objective of this paper is to update our understanding of how QS leads to toxin production by C. difficile, which is important in pathogenesis, and how QS inhibitors or probiotics may disrupt this pathway. We found two main QS systems for C. difficile (Agr and Lux systems) that are involved in C. difficile pathogenesis by regulating toxin production, motility and adherence. Probiotics and other QS inhibitors targeting QS systems may represent important new directions of therapy and prevention of CDI.
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27
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Combined and Distinct Roles of Agr Proteins in Clostridioides difficile 630 Sporulation, Motility, and Toxin Production. mBio 2020; 11:mBio.03190-20. [PMID: 33443122 PMCID: PMC8534292 DOI: 10.1128/mbio.03190-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The Clostridioides difficile accessory gene regulator 1 (agr1) locus consists of two genes, agrB1 and agrD1, that presumably constitute an autoinducing peptide (AIP) system. Typically, AIP systems function through the AgrB-mediated processing of AgrD to generate a processed form of the AIP that provides a concentration-dependent extracellular signal. Here, we show that the C. difficile 630 Agr1 system has multiple functions, not all of which depend on AgrB1. CRISPR-Cas9n deletion of agrB1, agrD1, or the entire locus resulted in changes in transcription of sporulation-related factors and an overall loss in spore formation. Sporulation was recovered in the mutants by providing supernatant from stationary-phase cultures of the parental strain. In contrast, C. difficile motility was reduced only when both AgrB1 and AgrD1 were disrupted. Finally, in the absence of AgrB1, the AgrD1 peptide accumulated within the cytoplasm and this correlated with increased expression of tcdR (15-fold), as well as tcdA (20-fold) and tcdB (5-fold), which encode the two major C. difficile toxins. The combined deletion of agrB1/agrD1 or deletion of only agrD1 did not significantly alter expression of tcdR or tcdB but did show a minor effect on tcdA expression. Overall, these data indicate that the Agr1-based system in C. difficile 630 carries out multiple functions, some of which are associated with prototypical AIP signaling and others of which involve previously undescribed mechanisms of action.IMPORTANCE C. difficile is a spore-forming, toxigenic, anaerobic bacterium that causes severe gastrointestinal illness. Understanding the ways in which C. difficile senses growth conditions to regulate toxin expression and sporulation is essential to advancing our understanding of this pathogen. The Agr1 system in C. difficile has been thought to function by generating an extracellular autoinducing peptide that accumulates and exogenously activates two-component signaling. The absence of the peptide or protease should, in theory, result in similar phenotypes. However, in contrast to longstanding assumptions about Agr, we found that mutants of individual agr1 genes exhibit distinct phenotypes in C. difficile These findings suggest that the Agr1 system may have other regulatory mechanisms independent of the typical Agr quorum sensing system. These data not only challenge models for Agr's mechanism of action in C. difficile but also may expand our conceptions of how this system works in other Gram-positive pathogens.
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28
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Javed I, Cui X, Wang X, Mortimer M, Andrikopoulos N, Li Y, Davis TP, Zhao Y, Ke PC, Chen C. Implications of the Human Gut-Brain and Gut-Cancer Axes for Future Nanomedicine. ACS NANO 2020; 14:14391-14416. [PMID: 33138351 DOI: 10.1021/acsnano.0c07258] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Recent clinical and pathological evidence have implicated the gut microbiota as a nexus for modulating the homeostasis of the human body, impacting conditions from cancer and dementia to obesity and social behavior. The connections between microbiota and human diseases offer numerous opportunities in medicine, most of which have limited or no therapeutic solutions available. In light of this paradigm-setting trend in science, this review aims to provide a comprehensive and timely summary of the mechanistic pathways governing the gut microbiota and their implications for nanomedicines targeting cancer and neurodegenerative diseases. Specifically, we discuss in parallel the beneficial and pathogenic relationship of the gut microbiota along the gut-brain and gut-cancer axes, elaborate on the impact of dysbiosis and the gastrointestinal corona on the efficacy of nanomedicines, and highlight a molecular mimicry that manipulates the universal cross-β backbone of bacterial amyloid to accelerate neurological disorders. This review further offers a forward-looking section on the rational design of cancer and dementia nanomedicines exploiting the gut-brain and gut-cancer axes.
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Affiliation(s)
- Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Xuejing Cui
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Xiaoyu Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Monika Mortimer
- Institute of Environmental and Health Sciences, College of Quality and Safety Engineering, China Jiliang University, Hangzhou, Zhejiang 310018, China
| | - Nikolaos Andrikopoulos
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria 3052, Australia
| | - Yuhuan Li
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai 200032, China
| | - Thomas P Davis
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria 3052, Australia
| | - Yuliang Zhao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, Victoria 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai 200032, China
| | - Chunying Chen
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety and CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology of China, Beijing 100190, China
- GBA Research Innovation Institute for Nanotechnology, Guangdong 510700, China
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29
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Colonization of the Murine Oropharynx by Streptococcus pyogenes Is Governed by the Rgg2/3 Quorum Sensing System. Infect Immun 2020; 88:IAI.00464-20. [PMID: 32747598 DOI: 10.1128/iai.00464-20] [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: 07/27/2020] [Accepted: 07/27/2020] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pyogenes is a human-restricted pathogen most often found in the human nasopharynx. Multiple bacterial factors are known to contribute to persistent colonization of this niche, and many are important in mucosal immunity and vaccine development. In this work, mice were infected intranasally with transcriptional regulator mutants of the Rgg2/3 quorum sensing (QS) system-a peptide-based signaling system conserved in sequenced isolates of S. pyogenes Deletion of the QS system's transcriptional activator (Δrgg2) dramatically diminished the percentage of colonized mice, while deletion of the transcriptional repressor (Δrgg3) increased the percentage of colonized mice compared to that of the wild type (WT). Stimulation of the QS system using synthetic pheromones prior to inoculation did not significantly increase the percentage of animals colonized, indicating that QS-dependent colonization is responsive to the intrinsic conditions within the host upper respiratory tract. Bacterial RNA extracted directly from oropharyngeal swabs and evaluated by quantitative reverse transcription-PCR (qRT-PCR) subsequently confirmed QS upregulation within 1 h of inoculation. In the nasal-associated lymphoid tissue (NALT), a muted inflammatory response to the Δrgg2 bacteria suggests that their rapid elimination failed to elicit the previously characterized response to intranasal inoculation of GAS. This work identifies a new transcriptional regulatory system governing the ability of S. pyogenes to colonize the nasopharynx and provides knowledge that could help lead to decolonization therapeutics.
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30
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Budi N, Safdar N, Rose WE. Treatment issues in recurrent Clostridioides difficile infections and the possible role of germinants. FEMS MICROBES 2020; 1:xtaa001. [PMID: 37333958 PMCID: PMC10117431 DOI: 10.1093/femsmc/xtaa001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 09/14/2020] [Indexed: 07/30/2023] Open
Abstract
Clostridioides difficile is the number one cause of hospital-acquired infections in the United States and one of the CDC's urgent-level pathogen threats. The inflammation caused by pathogenic C. difficile results in diarrhea and pseudomembranous colitis. Patients who undergo clinically successful treatment for this disease commonly experience recurrent infections. Current treatment options can eradicate the vegetative cell form of the bacteria but do not impact the spore form, which is impervious to antibiotics and resists conventional environmental cleaning procedures. Antibiotics used in treating C. difficile infections (CDI) often do not eradicate the pathogen and can prevent regeneration of the microbiome, leaving them vulnerable to recurrent CDI and future infections upon subsequent non-CDI-directed antibiotic therapy. Addressing the management of C. difficile spores in the gastrointestinal (GI) tract is important to make further progress in CDI treatment. Currently, no treatment options focus on reducing GI spores throughout CDI antibiotic therapy. This review focuses on colonization of the GI tract, current treatment options and potential treatment directions emphasizing germinant with antibiotic combinations to prevent recurrent disease.
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Affiliation(s)
- Noah Budi
- Corresponding author: School of Pharmacy, University of Wisconsin-Madison, Room 4123, 777 Highland Avenue, Madison, WI 53705, USA. Tel: +1-920-419-7704; E-mail:
| | - Nasia Safdar
- Division of Infectious Diseases, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA, 53726
| | - Warren E Rose
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, USA, 53705
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31
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Abstract
Bacteria are highly interactive and possess an extraordinary repertoire of intercellular communication and social behaviors, including quorum sensing (QS). QS has been studied in detail at the molecular level, so mechanistic details are well understood in many species and are often involved in virulence. The use of different animal host models has demonstrated QS-dependent control of virulence determinants and virulence in several human pathogenic bacteria. QS also controls virulence in several plant pathogenic species. Despite the role QS plays in virulence during animal and plant laboratory-engineered infections, QS mutants are frequently isolated from natural infections, demonstrating that the function of QS during infection and its role in pathogenesis remain poorly understood and are fruitful areas for future research. We discuss the role of QS during infection in various organisms and highlight approaches to better understand QS during human infection. This is an important consideration in an era of growing antimicrobial resistance, when we are looking for new ways to target bacterial infections.
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Affiliation(s)
- Sheyda Azimi
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; , .,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Alexander D Klementiev
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; , .,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; , .,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, USA.,Emory-Children's Cystic Fibrosis Center, Atlanta, Georgia 30329, USA
| | - Stephen P Diggle
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA; , .,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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32
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Debunne N, De Spiegeleer A, Depuydt D, Janssens Y, Descamps A, Wynendaele E, De Spiegeleer B. Influence of Blood Collection Methods and Long-Term Plasma Storage on Quorum-Sensing Peptide Stability. ACS OMEGA 2020; 5:16120-16127. [PMID: 32656434 PMCID: PMC7346264 DOI: 10.1021/acsomega.0c01723] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 06/08/2020] [Indexed: 05/08/2023]
Abstract
Finding adequate biomarkers for rapid and accurate disease detection, prognosis, and therapy is increasingly important. Quorum-sensing peptides are herein a new emerging group, produced by bacteria, fungi, protozoa, and viruses, with blood being the most straightforward sample type to detect/quantitate them. However, detailed information about suitable blood sample collection methods and storage conditions for measuring these quorum-sensing peptides hampers further clinical research and development. Here, we first tested the time-dependent stability of a set of chemically diverse quorum-sensing peptides, spiked in blood at different temperatures (4, 21, and 37 °C) in four different ethylenediamine tetraacetic acid (EDTA)-containing plasma tubes (with different protein-stabilizing additives) over a period of up to 7.5 h. Next, we determined the storage stability of these quorum-sensing peptides in plasma at different temperatures (4, -35, and -80 °C). UPLC/MS-MS was used to selectively detect and quantify the spiked quorum-sensing peptides. The results of this study indicate that a cost-effective tube, designed for traditional proteomics and stored at 4 °C, is the preferred collection condition when quorum-sensing peptides need to be detected/quantified in human plasma. When the tubes are handled at room temperature (21 °C), a more specialized tube is required. Long-term storage of plasma samples, even under low-temperature conditions (-80 °C), indicates rapid degradation of certain quorum-sensing peptides.
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Affiliation(s)
- Nathan Debunne
- Drug
Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical
Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Anton De Spiegeleer
- Drug
Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical
Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
- Department
of Geriatrics, Faculty of Medicine and Health Sciences, Ghent University Hospital, C. Heymanslaan 10, Ghent B-9000, Belgium
- VIB
Inflammation Research Center, Unit for Molecular Immunology and Inflammation, Ghent University, Technologiepark 71, B-9000 Ghent, Belgium
| | - Dorian Depuydt
- Drug
Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical
Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Yorick Janssens
- Drug
Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical
Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Amélie Descamps
- Drug
Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical
Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Evelien Wynendaele
- Drug
Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical
Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
| | - Bart De Spiegeleer
- Drug
Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical
Sciences, Ghent University, Ottergemsesteenweg 460, B-9000 Ghent, Belgium
- . Tel.: +32 9 264 81 00. Fax: +32 9 264 81 93
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Liu D, Zeng L, Yan Z, Jia J, Gao J, Wei Y. The mechanisms and safety of probiotics against toxigenic clostridium difficile. Expert Rev Anti Infect Ther 2020; 18:967-975. [PMID: 32520637 DOI: 10.1080/14787210.2020.1778464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Toxigenic Clostridium difficile (C. difficile) is the main cause of antibiotic-associated diarrhea and can induce pseudomembranous colitis and infrequent toxic megacolon, which are potentially fatal. The standard antibiotic therapy for C. difficile infection (CDI) is limited by antibiotics' broad spectrum and further disruptive effects on indigenous microbiota. Probiotics may offer a prospective and alternative strategy for the prevention and treatment of CDI. AREAS COVERED In this article, the mechanisms implying the probiotic effect against C. difficile and the safety profile highlighting the patient groups with inappropriate application of probiotics were reviewed from 2015 to 2020. EXPERT OPINION Although many strains with ability against C. difficile have been reported, the usage of probiotics for CDI prevention and/or treatment is scarce since the number of clinical trials is not sufficient to prove probiotics' efficacy and safety in CDI treatment, especially for premature infant and immunocompromised patient. Especially, there are few well-defined clinical studies supporting safety of probiotics for CDI. A few strains from Lactobacillus and Saccharomyces genus have been studied more extensively than other probiotic strains through clinical trials for CDI. Thus, more clinical intervention studies regarding the benefit and the comprehensive safety assessments of probiotics for CDI are needed.
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Affiliation(s)
- Dianbin Liu
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
| | - Lingbing Zeng
- Department of clinical microbiology, The First Affiliated Hospital of Nanchang University , Nanchang, Jiangxi Province, China
| | - Zhihan Yan
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
| | - Junqi Jia
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
| | - Jing Gao
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
| | - Yanxia Wei
- School of Stomatology/Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University , Xuzhou, Jiangsu Province, China
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34
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Okada Y, Okugawa S, Ikeda M, Kobayashi T, Saito R, Higurashi Y, Moriya K. Genetic diversity and epidemiology of accessory gene regulator loci in Clostridioides difficile. Access Microbiol 2020; 2:acmi000134. [PMID: 32974597 PMCID: PMC7497831 DOI: 10.1099/acmi.0.000134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/25/2020] [Indexed: 02/04/2023] Open
Abstract
Quorum sensing is known to regulate bacterial virulence, and the accessory gene regulator (agr) loci is one of the genetic loci responsible for its regulation. Recent reports examining Clostridioides difficile show that two agr loci, agr1 and agr2, regulate toxin production, but the diversity of agr loci and their epidemiology is unknown. In our study, in silico analysis was performed to research genetic diversity of agr, and C. difficile isolates from clinical samples underwent multilocus sequence typing (MLST) and PCR analysis of agr loci. To reveal the distribution of agr among different strains, phylogenetic analysis was also performed. In our in silico analysis, two different subtypes, named agr2R and agr2M, were found in agr2, which were previously reported. PCR analysis of 133 C . difficile isolates showed that 131 strains had agr1, 61 strains had agr2R, and 26 strains had agr2M; agr2R was mainly found in clade 1 or clade 2 organisms, whereas agr2M was only found in clade 4. With rare exception, agr1-negative sequence types (STs) belonged to clade C-Ⅰ and C-Ⅲ, and one clade 4 strain had agr2R. Our study revealed subtypes of agr2 not previously recognized, and the distribution of several agr loci in C. difficile . These findings provide a foundation for further functional and clinical research of the agr loci.
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Affiliation(s)
- Yuta Okada
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Shu Okugawa
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Mahoko Ikeda
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Tatsuya Kobayashi
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yoshimi Higurashi
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
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35
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Kester JC, Brubaker DK, Velazquez J, Wright C, Lauffenburger DA, Griffith LG. Clostridioides difficile-Associated Antibiotics Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms. Antimicrob Agents Chemother 2020; 64:e01404-19. [PMID: 31988098 PMCID: PMC7179307 DOI: 10.1128/aac.01404-19] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 01/04/2020] [Indexed: 12/16/2022] Open
Abstract
A clinically relevant risk factor for Clostridioides difficile-associated disease (CDAD) is recent antibiotic treatment. Although broad-spectrum antibiotics have been shown to disrupt the structure of the gut microbiota, some antibiotics appear to increase CDAD risk without being highly active against intestinal anaerobes, suggesting direct nonantimicrobial effects. We examined cell biological effects of antibiotic exposure that may be involved in bacterial pathogenesis using an in vitro germfree human colon epithelial culture model. We found a marked loss of mucosal barrier and immune function with exposure to the CDAD-associated antibiotics clindamycin and ciprofloxacin, distinct from the results of pretreatment with an antibiotic unassociated with CDAD, tigecycline, which did not reduce innate immune or mucosal barrier functions. Importantly, pretreatment with CDAD-associated antibiotics sensitized mucosal barriers to C. difficile toxin activity in primary cell-derived enteroid monolayers. These data implicate commensal-independent gut mucosal barrier changes in the increased risk of CDAD with specific antibiotics and warrant further studies in in vivo systems. We anticipate this work to suggest potential avenues of research for host-directed treatment and preventive therapies for CDAD.
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Affiliation(s)
- Jemila C Kester
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Douglas K Brubaker
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jason Velazquez
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Charles Wright
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Douglas A Lauffenburger
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Linda G Griffith
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Virulence Factors of Clostridioides ( Clostridium) difficile Linked to Recurrent Infections. CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY 2019; 2019:7127850. [PMID: 31933709 PMCID: PMC6942709 DOI: 10.1155/2019/7127850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 12/02/2019] [Accepted: 12/07/2019] [Indexed: 12/18/2022]
Abstract
From 20 to 30% of Clostridioides (Clostridium) difficile infection (CDI), patients might develop recurrence of the infection (RCDI) and, after the first recurrence, the risk of further episodes increases up to 60%. Several bacterial virulence factors have been associated with RCDI, including the elevated production of toxins A and B, the presence of a binary toxin CDT, and mutations in the negative regulator of toxin expression, tcdC. Additional factors have shown to regulate toxin production and virulence in C. difficile in RCDI, including the accessory-gene regulator agr, which acts as a positive switch for toxin transcription. Furthermore, adhesion and motility-associated factors, such as Cwp84, SlpA, and flagella, have shown to increase the adhesion efficiency to host epithelia, cell internalization, and the formation of biofilm. Finally, biofilm confers to C. difficile protection from antibiotics and acts as a reservoir for spores that allow the persistence of the infection in the host. In this review, we describe the key virulence factors of C. difficile that have been associated with recurrent infections.
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Increased Clinical Specificity with Ultrasensitive Detection of Clostridioides difficile Toxins: Reduction of Overdiagnosis Compared to Nucleic Acid Amplification Tests. J Clin Microbiol 2019; 57:JCM.00945-19. [PMID: 31434726 DOI: 10.1128/jcm.00945-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 08/13/2019] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile infection (CDI) is one of the most common health care-associated infections, resulting in significant morbidity, mortality, and economic burden. Diagnosis of CDI relies on the assessment of clinical presentation and laboratory tests. We evaluated the clinical performance of ultrasensitive single-molecule counting technology for detection of C. difficile toxins A and B. Stool specimens from 298 patients with suspected CDI were tested with the nucleic acid amplification test (NAAT; BD MAX Cdiff assay or Xpert C. difficile assay) and Singulex Clarity C. diff toxins A/B assay. Specimens with discordant results were tested with the cell cytotoxicity neutralization assay (CCNA), and the results were correlated with disease severity and outcome. There were 64 NAAT-positive and 234 NAAT-negative samples. Of the 32 NAAT+/Clarity- and 4 NAAT-/Clarity+ samples, there were 26 CCNA- and 4 CCNA- samples, respectively. CDI relapse was more common in NAAT+/toxin+ patients than in NAAT+/toxin- and NAAT-/toxin- patients. The clinical specificity of Clarity and NAAT was 97.4% and 89.0%, respectively, and overdiagnosis was more than three times more common in NAAT+/toxin- than in NAAT+/toxin+ patients. The Clarity assay was superior to NAATs for the diagnosis of CDI, by reducing overdiagnosis and thereby increasing clinical specificity, and the presence of toxins was associated with negative patient outcomes.
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Integrated Meta-omics Reveals a Fungus-Associated Bacteriome and Distinct Functional Pathways in Clostridioides difficile Infection. mSphere 2019; 4:4/4/e00454-19. [PMID: 31462412 PMCID: PMC6714892 DOI: 10.1128/msphere.00454-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Our data suggest a potential role for fungi in the most common nosocomial bacterial infection in the United States, introducing the concept of a transkingdom interaction between bacteria and fungi in this disease. We also provide the first direct measure of microbial community function in Clostridioides difficile infection using patient-derived tissue samples, revealing antibiotic-independent mechanisms by which C. difficile infection may resist a return to a healthy gut microbiome. There has been no prior application of matched metagenomics and metatranscriptomics in Clostridioides difficile infection (CDI) evaluating the role of fungi in CDI or identifying community functions that contribute to the development of this disease. We collected diarrheal stools from 49 inpatients (18 of whom tested positive for CDI) under stringent inclusion criteria. We utilized a tiered sequencing approach to identify enriched bacterial and fungal taxa, using 16S and internal transcribed spacer (ITS) rRNA gene amplicon sequencing, with matched metagenomics and metatranscriptomics performed on a subset of the population. Distinct bacterial and fungal compositions distinguished CDI-positive and -negative patients, with the greatest differentiation between the cohorts observed based on bacterial metatranscriptomics. Bipartite network analyses demonstrated that Aspergillus and Penicillium taxa shared a strong positive relationship in CDI patients and together formed negative cooccurring relationships with several bacterial taxa, including the Oscillospira, Comamonadaceae, Microbacteriaceae, and Cytophagaceae. Metatranscriptomics revealed enriched pathways in CDI patients associated with biofilm production primarily driven by Escherichia coli and Pseudomonas, quorum-sensing proteins, and two-component systems related to functions such as osmotic regulation, linoleic acid metabolism, and flagellar assembly. Differential expression of functional pathways unveiled a mechanism by which the causal dysbiosis of CDI may self-perpetuate, potentially contributing to treatment failures. We propose that CDI has a distinct fungus-associated bacteriome, and this first description of metatranscriptomics in human subjects with CDI demonstrates that inflammation, osmotic changes, and biofilm production are key elements of CDI pathophysiology. IMPORTANCE Our data suggest a potential role for fungi in the most common nosocomial bacterial infection in the United States, introducing the concept of a transkingdom interaction between bacteria and fungi in this disease. We also provide the first direct measure of microbial community function in Clostridioides difficile infection using patient-derived tissue samples, revealing antibiotic-independent mechanisms by which C. difficile infection may resist a return to a healthy gut microbiome.
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Tijerina-Rodríguez L, Villarreal-Treviño L, Baines SD, Morfín-Otero R, Camacho-Ortíz A, Flores-Treviño S, Maldonado-Garza H, Rodríguez-Noriega E, Garza-González E. High sporulation and overexpression of virulence factors in biofilms and reduced susceptibility to vancomycin and linezolid in recurrent Clostridium [Clostridioides] difficile infection isolates. PLoS One 2019; 14:e0220671. [PMID: 31365590 PMCID: PMC6668830 DOI: 10.1371/journal.pone.0220671] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 07/20/2019] [Indexed: 12/23/2022] Open
Abstract
Clostridium [Clostridioides] difficile infection (CDI) is one of the leading causes of diarrhea associated with medical care worldwide, and up to 60% of patients with CDI can develop a recurrent infection (R-CDI). A multi-species microbiota biofilm model of C. difficile was designed to evaluate the differences in the production of biofilms, sporulation, susceptibility to drugs, expression of sporulating (sigH, spo0A), quorum sensing (agrD1, and luxS), and adhesion-associated (slpA and cwp84) pathway genes between selected C. difficile isolates from R-CDI and non-recurrent patients (NR-CDI). We obtained 102 C. difficile isolates from 254 patients with confirmed CDI (66 from NR-CDI and 36 from R-CDI). Most of the isolates were biofilm producers, and most of the strains were ribotype 027 (81.374%, 83/102). Most C. difficile isolates were producers of biofilm (100/102), and most were strongly adherent. Sporulation was higher in the R-CDI than in the NR-CDI isolates (p = 0.015). The isolates from R-CDI patients more frequently demonstrated reduced susceptibility to vancomycin than isolates of NR-CDI patients (27.78% [10/36] and 9.09% [6/66], respectively, p = 0.013). The minimum inhibitory concentrations for vancomycin and linezolid against biofilms (BMIC) were up to 100 times and 20 times higher, respectively, than the corresponding planktonic MICs. Expression of sigH, spo0A, cwp84, and agrD1 was higher in R-CDI than in NR-CDI isolates. Most of the C. difficile isolates were producers of biofilms with no correlation with the ribotype. Sporulation was greater in R-CDI than in NR-CDI isolates in the biofilm model of C. difficile. The R-CDI isolates more frequently demonstrated reduced susceptibility to vancomycin and linezolid than the NR-CDI isolates in both planktonic cells and biofilm isolates. A higher expression of sporulating pathway (sigH, spo0A), quorum sensing (agrD1), and adhesion-associated (cwp84) genes was found in R-CDI than in NR-CDI isolates. All of these factors can have effect on the recurrence of the infection.
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Affiliation(s)
- Laura Tijerina-Rodríguez
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Licet Villarreal-Treviño
- Departamento de Microbiología e Inmunología, Facultad de Ciencias Biológicas, Universidad Autónoma de Nuevo León, San Nicolás de los Garza, Mexico
| | - Simon D. Baines
- Department of Biological and Environmental Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Rayo Morfín-Otero
- Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara, Mexico
| | - Adrián Camacho-Ortíz
- Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Samantha Flores-Treviño
- Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Héctor Maldonado-Garza
- Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey, Mexico
| | - Eduardo Rodríguez-Noriega
- Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Hospital Civil de Guadalajara “Fray Antonio Alcalde”, Guadalajara, Mexico
| | - Elvira Garza-González
- Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Monterrey, Mexico
- * E-mail:
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40
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Giau VV, Lee H, An SSA, Hulme J. Recent advances in the treatment of C. difficile using biotherapeutic agents. Infect Drug Resist 2019; 12:1597-1615. [PMID: 31354309 PMCID: PMC6579870 DOI: 10.2147/idr.s207572] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022] Open
Abstract
Clostridium difficile (C. difficile) is rapidly becoming one of the most prevalent health care–associated bacterial infections in the developed world. The emergence of new, more virulent strains has led to greater morbidity and resistance to standard therapies. The bacterium is readily transmitted between people where it can asymptomatically colonize the gut environment, and clinical manifestations ranging from frequent watery diarrhea to toxic megacolon can arise depending on the age of the individual or their state of gut dysbiosis. Several inexpensive approaches are shown to be effective against virulent C. difficile in research settings such as probiotics, fecal microbiota transfer and immunotherapies. This review aims to highlight the current advantages and limitations of the aforementioned approaches with an emphasis on recent studies.
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Affiliation(s)
- Vo Van Giau
- Department of BioNano Technology, Gachon University, Seongnam-si 461-701, Republic of Korea
| | - Hyon Lee
- Department of Neurology, Gachon University Gil Medical Center, Incheon, South Korea
| | - Seong Soo A An
- Department of BioNano Technology, Gachon University, Seongnam-si 461-701, Republic of Korea
| | - John Hulme
- Department of BioNano Technology, Gachon University, Seongnam-si 461-701, Republic of Korea
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Edwards AN, Anjuwon-Foster BR, McBride SM. RstA Is a Major Regulator of Clostridioides difficile Toxin Production and Motility. mBio 2019; 10:e01991-18. [PMID: 30862746 PMCID: PMC6414698 DOI: 10.1128/mbio.01991-18] [Citation(s) in RCA: 25] [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] [Received: 09/10/2018] [Accepted: 01/25/2019] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile infection (CDI) is a toxin-mediated diarrheal disease. Several factors have been identified that influence the production of the two major C. difficile toxins, TcdA and TcdB, but prior published evidence suggested that additional unknown factors were involved in toxin regulation. Previously, we identified a C. difficile regulator, RstA, that promotes sporulation and represses motility and toxin production. We observed that the predicted DNA-binding domain of RstA was required for RstA-dependent repression of toxin genes, motility genes, and rstA transcription. In this study, we further investigated the regulation of toxin and motility gene expression by RstA. DNA pulldown assays confirmed that RstA directly binds the rstA promoter via the predicted DNA-binding domain. Through mutational analysis of the rstA promoter, we identified several nucleotides that are important for RstA-dependent transcriptional regulation. Further, we observed that RstA directly binds and regulates the promoters of the toxin genes tcdA and tcdB, as well as the promoters for the sigD and tcdR genes, which encode regulators of toxin gene expression. Complementation analyses with the Clostridium perfringens RstA ortholog and a multispecies chimeric RstA protein revealed that the C. difficile C-terminal domain is required for RstA DNA-binding activity, suggesting that species-specific signaling controls RstA function. Our data demonstrate that RstA is a transcriptional repressor that autoregulates its own expression and directly inhibits transcription of the two toxin genes and two positive toxin regulators, thereby acting at multiple regulatory points to control toxin production.IMPORTANCEClostridioides difficile is an anaerobic, gastrointestinal pathogen of humans and other mammals. C. difficile produces two major toxins, TcdA and TcdB, which cause the symptoms of the disease, and forms dormant endospores to survive the aerobic environment outside the host. A recently discovered regulatory factor, RstA, inhibits toxin production and positively influences spore formation. Herein, we determine that RstA directly binds its own promoter DNA to repress its own gene transcription. In addition, our data demonstrate that RstA directly represses toxin gene expression and gene expression of two toxin gene activators, TcdR and SigD, creating a complex regulatory network to tightly control toxin production. This study provides a novel regulatory link between C. difficile sporulation and toxin production. Further, our data suggest that C. difficile toxin production is regulated through a direct, species-specific sensing mechanism.
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Affiliation(s)
- Adrianne N Edwards
- Department of Microbiology and Immunology, Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Brandon R Anjuwon-Foster
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Shonna M McBride
- Department of Microbiology and Immunology, Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, Georgia, USA
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Darkoh C, Plants-Paris K, Bishoff D, DuPont HL. Clostridium difficile Modulates the Gut Microbiota by Inducing the Production of Indole, an Interkingdom Signaling and Antimicrobial Molecule. mSystems 2019; 4:e00346-18. [PMID: 30944877 PMCID: PMC6426650 DOI: 10.1128/msystems.00346-18] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 02/27/2019] [Indexed: 02/07/2023] Open
Abstract
Clostridium (Clostridioides) difficile infection (CDI) is associated with dysbiosis. C. difficile has a characteristic propensity to persist and recur 1 to 4 weeks after treatment, but the mechanism is unknown. We hypothesized that C. difficile may persist by manipulating the intestinal microenvironment, thereby hampering gut microbiota reconstitution following antibiotic-mediated dysbiosis. By screening stools from CDI patients for unique markers, a metabolite identified to be indole by mass spectrometry and Fourier transform infrared spectroscopy was identified. The average fecal indole concentration detected in CDI patients (n = 216; mean, 1,684.0 ± 84.4 µM) was significantly higher than in stools of patients with non-C. difficile diarrhea (n = 204; mean, 762.8 ± 53.8 µM). Certain intestinal bacteria, but not C. difficile, produce indole, a potent antimicrobial antioxidant. Remarkably, C. difficile induced other indole-producing gut microbes to produce increasing amounts of indole. Furthermore, a C. difficile accessory gene regulator 1 quorum sensing system mutant cannot induce indole, but complementation of the mutant strain with the wild-type gene restored its ability to induce indole production. Indole tolerance assays indicated that the amount of indole required to inhibit growth of most gut-protective bacteria was within the range detected in the CDI stools. We think that a high indole level limits the growth of beneficial indole-sensitive bacteria in the colon and alters colonization resistance and this might allow C. difficile to proliferate and persist. Together, these results reveal a unique mechanism of C. difficile persistence and provide insight into complex interactions and chemical warfare among the gut microbiota. IMPORTANCE Clostridium difficile infection is the leading cause of hospital-acquired and antibiotic-associated diarrhea worldwide. C. difficile flourishes in the colon after the diversity of the beneficial and protective gut microbiota have been altered by antibiotic therapy. C. difficile tends to persist, as does dysbiosis, encouraging recurrence a few days to weeks after treatment, and this further complicates treatment options. Here, we show that C. difficile might persist by manipulating the indigenous microbiota to produce indole, a bioactive molecule that inhibits the growth and reconstitution of the protective gut microbiota during infection. This discovery may explain a unique strategy C. difficile uses to control other bacteria in the colon and provide insight into the complex interactions and chemical warfare among the gut microbiota.
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Affiliation(s)
- Charles Darkoh
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center For Infectious Diseases, Houston, Texas, USA
- Microbiology and Infectious Diseases Program, UTHealth Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Kimberly Plants-Paris
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center For Infectious Diseases, Houston, Texas, USA
| | - Dayna Bishoff
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center For Infectious Diseases, Houston, Texas, USA
| | - Herbert L. DuPont
- University of Texas Health Science Center, School of Public Health, Department of Epidemiology, Human Genetics, and Environmental Sciences, Center For Infectious Diseases, Houston, Texas, USA
- Microbiology and Infectious Diseases Program, UTHealth Graduate School of Biomedical Sciences, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
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Daou N, Wang Y, Levdikov VM, Nandakumar M, Livny J, Bouillaut L, Blagova E, Zhang K, Belitsky BR, Rhee K, Wilkinson AJ, Sun X, Sonenshein AL. Impact of CodY protein on metabolism, sporulation and virulence in Clostridioides difficile ribotype 027. PLoS One 2019; 14:e0206896. [PMID: 30699117 PMCID: PMC6353076 DOI: 10.1371/journal.pone.0206896] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 09/25/2018] [Indexed: 12/16/2022] Open
Abstract
Toxin synthesis and endospore formation are two of the most critical factors that determine the outcome of infection by Clostridioides difficile. The two major toxins, TcdA and TcdB, are the principal factors causing damage to the host. Spores are the infectious form of C. difficile, permit survival of the bacterium during antibiotic treatment and are the predominant cell form that leads to recurrent infection. Toxin production and sporulation have their own specific mechanisms of regulation, but they share negative regulation by the global regulatory protein CodY. Determining the extent of such regulation and its detailed mechanism is important for understanding the linkage between two apparently independent biological phenomena and raises the possibility of creating new ways of limiting infection. The work described here shows that a codY null mutant of a hypervirulent (ribotype 027) strain is even more virulent than its parent in a mouse model of infection and that the mutant expresses most sporulation genes prematurely during exponential growth phase. Moreover, examining the expression patterns of mutants producing CodY proteins with different levels of residual activity revealed that expression of the toxin genes is dependent on total CodY inactivation, whereas most sporulation genes are turned on when CodY activity is only partially diminished. These results suggest that, in wild-type cells undergoing nutrient limitation, sporulation genes can be turned on before the toxin genes.
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Affiliation(s)
- Nadine Daou
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Yuanguo Wang
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Vladimir M. Levdikov
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Madhumitha Nandakumar
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, United States of America
| | - Jonathan Livny
- Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Laurent Bouillaut
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Elena Blagova
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Keshan Zhang
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, MA, United States of America
| | - Boris R. Belitsky
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
| | - Kyu Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY, United States of America
| | - Anthony J. Wilkinson
- Structural Biology Laboratory, Department of Chemistry, University of York, York, United Kingdom
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States of America
| | - Abraham L. Sonenshein
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, United States of America
- * E-mail:
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Hebdon SD, Menon SK, Richter-Addo GB, Karr EA, West AH. Regulatory Targets of the Response Regulator RR_1586 from Clostridioides difficile Identified Using a Bacterial One-Hybrid Screen. J Bacteriol 2018; 200:e00351-18. [PMID: 30201779 PMCID: PMC6222199 DOI: 10.1128/jb.00351-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Accepted: 09/05/2018] [Indexed: 12/31/2022] Open
Abstract
The Clostridioides difficile R20291 genome encodes 57 response regulator proteins that, as part of two-component signaling pathways, regulate adaptation to environmental conditions. Genomic and transcriptomic studies in C. difficile have been limited, due to technical challenges, to the analysis of either high-throughput screens or high-priority targets, such as primary regulators of toxins or spore biology. We present the use of several technically accessible and generally applicable techniques to elucidate the putative regulatory targets of a response regulator, RR_1586, involved in sporulation of the hypervirulent C. difficile strain R20291. A DNA-binding specificity motif for RR_1586 was determined using a bacterial one-hybrid assay originally developed for Drosophila transcription factors. Comparative bioinformatics approaches identified and in vitro experiments confirmed RR_1586 binding sites upstream of putative target genes, including those that encode phosphate ion transporters, spermidine/putrescine biosynthesis and transport pathways, ABC type transport systems, known regulators of sporulation, and genes encoding spore structural proteins. Representative examples of these regulatory interactions have been tested and confirmed in Escherichia coli-based reporter assays. Finally, evidence of possible regulatory mechanisms is also presented. A working model includes self-regulation by RR_1586 and phosphorylation-dependent and -independent DNA binding at low- and high-fidelity binding sites, respectively. Broad application of this and similar approaches is anticipated to be an important catalyst for the study of gene regulation by two-component systems from pathogenic or technically challenging bacteria.IMPORTANCEClostridioides difficile spores survive under harsh conditions and can germinate into actively dividing cells capable of causing disease. An understanding of the regulatory networks controlling sporulation and germination in C. difficile could be exploited for therapeutic advantage. However, such studies are hindered by the challenges of working with an anaerobic pathogen recalcitrant to genetic manipulation. Although two-component response regulators can be identified from genetic sequences, identification of their downstream regulatory networks requires further development. This work integrates experimental and bioinformatic approaches, which provide practical advantages over traditional transcriptomic analyses, to identify the putative regulon of the C. difficile response regulator RR_1586 by first screening for protein-DNA interactions in E. coli and then predicting regulatory outputs in C. difficile.
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Affiliation(s)
- Skyler D Hebdon
- Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Smita K Menon
- Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - George B Richter-Addo
- Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
| | - Elizabeth A Karr
- Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman, Oklahoma, USA
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Ann H West
- Price Family Foundation Institute of Structural Biology, University of Oklahoma, Norman, Oklahoma, USA
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma, USA
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Ramírez-Vargas G, López-Ureña D, Badilla A, Orozco-Aguilar J, Murillo T, Rojas P, Riedel T, Overmann J, González G, Chaves-Olarte E, Quesada-Gómez C, Rodríguez C. Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements. Sci Rep 2018; 8:13951. [PMID: 30224751 PMCID: PMC6141592 DOI: 10.1038/s41598-018-32390-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/04/2018] [Indexed: 01/05/2023] Open
Abstract
The population structure of Clostridium difficile currently comprises eight major genomic clades. For the highly divergent C-I clade, only two toxigenic strains have been reported, which lack the tcdA and tcdC genes and carry a complete locus for the binary toxin (CDT) next to an atypical TcdB monotoxin pathogenicity locus (PaLoc). As part of a routine surveillance of C. difficile in stool samples from diarrheic human patients, we discovered three isolates that consistently gave negative results in a PCR-based screening for tcdC. Through phenotypic assays, whole-genome sequencing, experiments in cell cultures, and infection biomodels we show that these three isolates (i) escape common laboratory diagnostic procedures, (ii) represent new ribotypes, PFGE-types, and sequence types within the Clade C-I, (iii) carry chromosomal or plasmidal TcdBs that induce classical or variant cytopathic effects (CPE), and (iv) cause different levels of cytotoxicity and hamster mortality rates. These results show that new strains of C. difficile can be detected by more refined techniques and raise questions on the origin, evolution, and distribution of the toxin loci of C. difficile and the mechanisms by which this emerging pathogen causes disease.
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Affiliation(s)
- Gabriel Ramírez-Vargas
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Diana López-Ureña
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Adriana Badilla
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Josué Orozco-Aguilar
- Laboratory for Biological Assays (LEBi), University of Costa Rica, San José, Costa Rica
| | - Tatiana Murillo
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Priscilla Rojas
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner-site Hannover-Braunschweig, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner-site Hannover-Braunschweig, Braunschweig, Germany
| | - Gabriel González
- Research Center for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Esteban Chaves-Olarte
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Carlos Quesada-Gómez
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica.
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46
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Fortier LC. Bacteriophages Contribute to Shaping Clostridioides (Clostridium) difficile Species. Front Microbiol 2018; 9:2033. [PMID: 30233520 PMCID: PMC6127314 DOI: 10.3389/fmicb.2018.02033] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 08/13/2018] [Indexed: 12/13/2022] Open
Abstract
Bacteriophages (phages) are bacterial viruses that parasitize bacteria. They are highly prevalent in nature, with an estimated 1031 viral particles in the whole biosphere, and they outnumber bacteria by at least 10-fold. Hence, phages represent important drivers of bacterial evolution, although our knowledge of the role played by phages in the mammalian gut is still embryonic. Several pathogens owe their virulence to the integrated phages (prophages) they harbor, which encode diverse virulence factors such as toxins. Clostridioides (Clostridium) difficile is an important opportunistic pathogen and several phages infecting this species have been described over the last decade. However, their exact contribution to the biology and virulence of this pathogen remains elusive. Current data have shown that C. difficile phages can alter virulence-associated phenotypes, in particular toxin production, by interfering with bacterial regulatory circuits through crosstalk with phage proteins for example. One phage has also been found to encode a complete binary toxin locus. Multiple regulatory genes have also been identified in phage genomes, suggesting that their impact on the host can be complex and often subtle. In this minireview, the current state of knowledge, major findings, and pending questions regarding C. difficile phages will be presented. In addition, with the apparent role played by phages in the success of fecal microbiota transplantation and the perspective of phage therapy for treatment of recurrent C. difficile infection, it has become even more crucial to understand what C. difficile phages do in the gut, how they impact their host, and how they influence the epidemiology and evolution of this clinically important pathogen.
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Affiliation(s)
- Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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47
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Mechanisms of Bacterial Tolerance and Persistence in the Gastrointestinal and Respiratory Environments. Clin Microbiol Rev 2018; 31:31/4/e00023-18. [PMID: 30068737 DOI: 10.1128/cmr.00023-18] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Pathogens that infect the gastrointestinal and respiratory tracts are subjected to intense pressure due to the environmental conditions of the surroundings. This pressure has led to the development of mechanisms of bacterial tolerance or persistence which enable microorganisms to survive in these locations. In this review, we analyze the general stress response (RpoS mediated), reactive oxygen species (ROS) tolerance, energy metabolism, drug efflux pumps, SOS response, quorum sensing (QS) bacterial communication, (p)ppGpp signaling, and toxin-antitoxin (TA) systems of pathogens, such as Escherichia coli, Salmonella spp., Vibrio spp., Helicobacter spp., Campylobacter jejuni, Enterococcus spp., Shigella spp., Yersinia spp., and Clostridium difficile, all of which inhabit the gastrointestinal tract. The following respiratory tract pathogens are also considered: Staphylococcus aureus, Pseudomonas aeruginosa, Acinetobacter baumannii, Burkholderia cenocepacia, and Mycobacterium tuberculosis Knowledge of the molecular mechanisms regulating the bacterial tolerance and persistence phenotypes is essential in the fight against multiresistant pathogens, as it will enable the identification of new targets for developing innovative anti-infective treatments.
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48
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Thanissery R, Zeng D, Doyle RG, Theriot CM. A Small Molecule-Screening Pipeline to Evaluate the Therapeutic Potential of 2-Aminoimidazole Molecules Against Clostridium difficile. Front Microbiol 2018; 9:1206. [PMID: 29928268 PMCID: PMC5997789 DOI: 10.3389/fmicb.2018.01206] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Accepted: 05/17/2018] [Indexed: 12/19/2022] Open
Abstract
Antibiotics are considered to be the first line of treatment for mild to moderately severe Clostridium difficile infection (CDI) in humans. However, antibiotics are also risk factors for CDI as they decrease colonization resistance against C. difficile by altering the gut microbiota and metabolome. Finding compounds that selectively inhibit different stages of the C. difficile life cycle, while sparing the indigenous gut microbiota is important for the development of alternatives to standard antibiotic treatment. 2-aminoimidazole (2-AI) molecules are known to disrupt bacterial protection mechanisms in antibiotic resistant bacteria such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Staphylococcus aureus, but are yet to be evaluated against C. difficile. A comprehensive small molecule-screening pipeline was developed to investigate how novel small molecules affect different stages of the C. difficile life cycle (growth, toxin, and sporulation) in vitro, and a library of commensal bacteria that are associated with colonization resistance against C. difficile. The initial screening tested the efficacy of eleven 2-AI molecules (compound 1 through 11) against C. difficile R20291 compared to a vancomycin (2 μg/ml) control. Molecules were selected for their ability to inhibit C. difficile growth, toxin activity, and sporulation. Further testing included growth inhibition of other C. difficile strains (CD196, M68, CF5, 630, BI9, M120) belonging to distinct PCR ribotypes, and a commensal panel (Bacteroides fragilis, B. thetaiotaomicron, C. scindens, C. hylemonae, Lactobacillus acidophilus, L. gasseri, Escherichia coli, B. longum subsp. infantis). Three molecules compound 1 and 2, and 3 were microbicidal, whereas compounds 4, 7, 9, and 11 inhibited toxin activity without affecting the growth of C. difficile strains and the commensal microbiota. The antimicrobial and anti-toxin effects of 2-AI molecules need to be further characterized for mode of action and validated in a mouse model of CDI.
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Affiliation(s)
- Rajani Thanissery
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
| | - Daina Zeng
- Agile Sciences, Inc., Raleigh, NC, United States
| | - Raul G Doyle
- Agile Sciences, Inc., Raleigh, NC, United States
| | - Casey M Theriot
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC, United States
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49
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Wei Y, Yang F, Wu Q, Gao J, Liu W, Liu C, Guo X, Suwal S, Kou Y, Zhang B, Wang Y, Zheng K, Tang R. Protective Effects of Bifidobacterial Strains Against Toxigenic Clostridium difficile. Front Microbiol 2018; 9:888. [PMID: 29867801 PMCID: PMC5952185 DOI: 10.3389/fmicb.2018.00888] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 04/18/2018] [Indexed: 12/11/2022] Open
Abstract
Probiotics might offer an attractive alternative to prevent and control Clostridium difficile (C. difficile) infection (CDI). Limited information is available on the ability of commercially used bifidobacterial strains to inhibit C. difficile. This study examined the anti-clostridial effects of Bifidobacterium longum JDM301, a widely used commercial probiotic strain in China, in vitro and in vivo. In vitro evaluation revealed a significant reduction in C. difficile counts when JDM301 was co-cultured with C. difficile, which was correlated with the significant decrease in clostridial toxin titres (TcdA and TcdB). Furthermore, the cell-free culture supernatants (CFS) of JDM301 inhibited C. difficile growth and degraded TcdA and TcdB. Notably, the results showed that acid pH promoted the degradation of TcdA by CFS from JDM301. Furthermore, comparative studies among 10 B. longum strains were performed, which showed that the inhibitory effect of CFS from JDM301 was similar with the other 8 B. longum strains and higher than strain BLY1. However, when it was neutralized, the significant different was lost. When present together, it was suggested that the acid pH induced by probiotics not only played important roles in the growth inhibition against C. difficile resulting in the reduction of toxins titres, but also directly promoted the degradation of clostridial toxin. In vivo studies proved that JDM301 partially relieved damage to tissues caused by C. difficile and also decreased the number of C. difficile and toxin levels. In summary, our results demonstrated that the commercial strain, JDM301 could be considered a probiotic able to exert anti-toxin capability and most of the CFS from Bifidobacterium were able to inhibit the growth of C. difficile, depending on acid pH. These results highlighted a potential that JDM301 could be helpful in preventing CDI and that most of the bifidobacterial strains could (at least partially) exert protective effects by reducing toxin titres through growth inhibition against toxigenic C. difficile.
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Affiliation(s)
- Yanxia Wei
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Fan Yang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Qiong Wu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Jing Gao
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Wenli Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Chang Liu
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiaokui Guo
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Sharmila Suwal
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Yanbo Kou
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Bo Zhang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Yugang Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Kuiyang Zheng
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
| | - Renxian Tang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogenic Biology and Immunology, Laboratory of Infection and Immunity, Xuzhou Medical University, Xuzhou, China
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50
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Gao B, Bian X, Chi L, Tu P, Ru H, Lu K. Editor's Highlight: OrganophosphateDiazinon Altered Quorum Sensing, Cell Motility, Stress Response, and Carbohydrate Metabolism of Gut Microbiome. Toxicol Sci 2018; 157:354-364. [PMID: 28369659 DOI: 10.1093/toxsci/kfx053] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome plays a key role in energy production, immune system development, and host resistance against invading pathogens, etc. Disruption of gut bacterial homeostasis is associated with a number of human diseases. Several environmental chemicals have been reported to induce alterations of the gut microbiome. Diazinon, one of important organophosphate insecticides, has been widely used in agriculture. Diazinon and its metabolites are readily detected in different environmental settings and human urine. The toxicity of organophosphates has been a long-standing public health concern. We recently demonstrated that organophosphate insecticide diazinon perturbed the gut microbiome composition of mice. However, the functional impact of exposure on the gut microbiome has not been adequately assessed yet. In particular, the molecular mechanism responsible for exposure-induced microbial profile and community structure changes has not been identified. Therefore, in this study, we used metatranscriptomics to examine the effects of diazinon exposure on the gut metatranscriptome in C57BL/6 mice. Herein, we demonstrated for the first time that organophosphate diazinon modulated quorum sensing, which may serve as a key mechanism to regulate bacterial population, composition, and more importantly, their functional genes. In addition, we also found that diazinon exposure activated diverse stress response pathways and profoundly impaired energy metabolism of gut bacteria. These findings provide new understandings of the functional interplay between the gut microbiome and environmental chemicals, such as organophosphates.
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Affiliation(s)
- Bei Gao
- Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602.,Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Xiaoming Bian
- Department of Environmental Health Science, University of Georgia, Athens, Georgia 30602.,Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Liang Chi
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Pengcheng Tu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Hongyu Ru
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, North Carolina 27607
| | - Kun Lu
- Department of Environmental Sciences and Engineering, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
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