1
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Chen YYM, Yang YC, Shieh HR, Lin YJ, Ke WJ, Chiu CH. Functional Analysis of the Major Pilin Proteins of Type IV Pili in Streptococcus sanguinis CGMH010. Int J Mol Sci 2024; 25:5402. [PMID: 38791440 PMCID: PMC11121087 DOI: 10.3390/ijms25105402] [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: 03/29/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 05/26/2024] Open
Abstract
The pil gene cluster for Type IV pilus (Tfp) biosynthesis is commonly present and highly conserved in Streptococcus sanguinis. Nevertheless, Tfp-mediated twitching motility is less common among strains, and the factors determining twitching activity are not fully understood. Here, we analyzed the functions of three major pilin proteins (PilA1, PilA2, and PilA3) in the assembly and activity of Tfp in motile S. sanguinis CGMH010. Using various recombinant pilA deletion strains, we found that Tfp composed of different PilA proteins varied morphologically and functionally. Among the three PilA proteins, PilA1 was most critical in the assembly of twitching-active Tfp, and recombinant strains expressing motility generated more structured biofilms under constant shearing forces compared to the non-motile recombinant strains. Although PilA1 and PilA3 shared 94% identity, PilA3 could not compensate for the loss of PilA1, suggesting that the nature of PilA proteins plays an essential role in twitching activity. The single deletion of individual pilA genes had little effect on the invasion of host endothelia by S. sanguinis CGMH010. In contrast, the deletion of all three pilA genes or pilT, encoding the retraction ATPase, abolished Tfp-mediated invasion. Tfp- and PilT-dependent invasion were also detected in the non-motile S. sanguinis SK36, and thus, the retraction of Tfp, but not active twitching, was found to be essential for invasion.
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Affiliation(s)
- Yi-Ywan M. Chen
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-R.S.); (Y.-J.L.); (W.-J.K.)
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou 333, Taiwan;
| | - Yuan-Chen Yang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan;
| | - Hui-Ru Shieh
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-R.S.); (Y.-J.L.); (W.-J.K.)
| | - Yu-Juan Lin
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-R.S.); (Y.-J.L.); (W.-J.K.)
| | - Wan-Ju Ke
- Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Taoyuan 333, Taiwan; (H.-R.S.); (Y.-J.L.); (W.-J.K.)
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou 333, Taiwan;
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2
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Zhong S, Yang J, Huang H. The role of single and mixed biofilms in Clostridioides difficile infection and strategies for prevention and inhibition. Crit Rev Microbiol 2024; 50:285-299. [PMID: 36939635 DOI: 10.1080/1040841x.2023.2189950] [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: 10/27/2022] [Accepted: 03/06/2023] [Indexed: 03/21/2023]
Abstract
Clostridioides difficile infection (CDI) is a serious disease with a high recurrence rate. The single and mixed biofilms formed by C. difficile in the gut contribute to the formation of recurrent CDI (rCDI). In parallel, other gut microbes influence the formation and development of C. difficile biofilms, also known as symbiotic biofilms. Interactions between members within the symbiotic biofilm are associated with the worsening or alleviation of CDI. These interactions include effects on C. difficile adhesion and chemotaxis, modulation of LuxS/AI-2 quorum sensing (QS) system activity, promotion of cross-feeding by microbial metabolites, and regulation of intestinal bile acid and pyruvate levels. In the process of C. difficile biofilms control, inhibition of C. difficile initial biofilm formation and killing of C. difficile vegetative cells and spores are the main targets of action. The role of symbiotic biofilms in CDI suggested that targeting interventions of C. difficile-promoting gut microbes could indirectly inhibit the formation of C. difficile mixed biofilms and improved the ultimate therapeutic effect. In summary, this review outlines the mechanisms of C. difficile biofilm formation and summarises the treatment strategies for such single and mixed biofilms, aiming to provide new ideas for the prevention and treatment of CDI.
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Affiliation(s)
- Saiwei Zhong
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, China
| | - Jingpeng Yang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, China
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3
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Gong JJ, Huang IH, Su MSW, Xie SX, Liu WY, Huang CR, Hung YP, Wu SR, Tsai PJ, Ko WC, Chen JW. Phage transcriptional regulator X (PtrX)-mediated augmentation of toxin production and virulence in Clostridioides difficile strain R20291. Microbiol Res 2024; 280:127576. [PMID: 38183754 DOI: 10.1016/j.micres.2023.127576] [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: 10/03/2023] [Revised: 11/24/2023] [Accepted: 12/13/2023] [Indexed: 01/08/2024]
Abstract
Clostridioides difficile is a Gram-positive, anaerobic, and spore-forming bacterial member of the human gut microbiome. The primary virulence factors of C. difficile are toxin A and toxin B. These toxins damage the cell cytoskeleton and cause various diseases, from diarrhea to severe pseudomembranous colitis. Evidence suggests that bacteriophages can regulate the expression of the pathogenicity locus (PaLoc) genes of C. difficile. We previously demonstrated that the genome of the C. difficile RT027 strain NCKUH-21 contains a prophage-like DNA sequence, which was found to be markedly similar to that of the φCD38-2 phage. In the present study, we investigated the mechanisms underlying the φNCKUH-21-mediated regulation of the pathogenicity and the PaLoc genes expression in the lysogenized C. difficile strain R20291. The carriage of φNCKUH-21 in R20291 cells substantially enhanced toxin production, bacterial motility, biofilm formation, and spore germination in vitro. Subsequent mouse studies revealed that the lysogenized R20291 strain caused a more severe infection than the wild-type strain. We screened three φNCKUH-21 genes encoding DNA-binding proteins to check their effects on PaLoc genes expression. The overexpression of NCKUH-21_03890, annotated as a transcriptional regulator (phage transcriptional regulator X, PtrX), considerably enhanced toxin production, biofilm formation, and bacterial motility of R20291. Transcriptome analysis further confirmed that the overexpression of ptrX led to the upregulation of the expression of toxin genes, flagellar genes, and csrA. In the ptrX-overexpressing R20291 strain, PtrX influenced the expression of flagellar genes and the sigma factor gene sigD, possibly through an increased flagellar phase ON configuration ratio.
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Affiliation(s)
- Jun-Jia Gong
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - I-Hsiu Huang
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, OK 74107, USA
| | - Marcia Shu-Wei Su
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Si-Xuan Xie
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Yong Liu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Rung Huang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yuan-Pin Hung
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shang-Rung Wu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Oral Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Jane Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan; Center for Clinical Medicine Research, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jenn-Wei Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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4
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Marvaud JC, Bouttier S, Saunier J, Kansau I. Clostridioides difficile Flagella. Int J Mol Sci 2024; 25:2202. [PMID: 38396876 PMCID: PMC10889297 DOI: 10.3390/ijms25042202] [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: 01/16/2024] [Revised: 02/04/2024] [Accepted: 02/09/2024] [Indexed: 02/25/2024] Open
Abstract
Clostridioides difficile is an important pathogen for humans with a lead in nosocomial infection, but it is also more and more common in communities. Our knowledge of the pathology has historically been focused on the toxins produced by the bacteria that remain its major virulence factors. But the dysbiosis of the intestinal microbiota creating the conditions for the colonization appears to be fundamental for our understanding of the disease. Colonization implies several steps for the bacteria that do or do not use their capacity of motility with the synthesis of flagella. In this review, we focus on the current understanding of different topics on the C. difficile flagellum, ranging from its genetic organization to the vaccinal interest in it.
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Affiliation(s)
- Jean-Christophe Marvaud
- Institut MICALIS, INRAE, AgroParisTech, Equipe Bactéries Pathogènes et Santé, Faculté de Pharmacie, Université Paris-Saclay, 91400 Orsay, France (I.K.)
| | - Sylvie Bouttier
- Institut MICALIS, INRAE, AgroParisTech, Equipe Bactéries Pathogènes et Santé, Faculté de Pharmacie, Université Paris-Saclay, 91400 Orsay, France (I.K.)
| | - Johanna Saunier
- Matériaux et Santé, Faculté de pharmacie, Université Paris Saclay, 91400 Orsay, France
| | - Imad Kansau
- Institut MICALIS, INRAE, AgroParisTech, Equipe Bactéries Pathogènes et Santé, Faculté de Pharmacie, Université Paris-Saclay, 91400 Orsay, France (I.K.)
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5
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Vuotto C, Donelli G, Buckley A, Chilton C. Clostridioides difficile Biofilm. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:249-272. [PMID: 38175479 DOI: 10.1007/978-3-031-42108-2_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile infection (CDI), previously Clostridium difficile infection, is a symptomatic infection of the large intestine caused by the spore-forming anaerobic, gram-positive bacterium Clostridioides difficile. CDI is an important healthcare-associated disease worldwide, characterized by high levels of recurrence, morbidity, and mortality. CDI is observed at a higher rate in immunocompromised patients after antimicrobial therapy, with antibiotics disrupting the commensal microbiota and promoting C. difficile colonization of the gastrointestinal tract.A rise in clinical isolates resistant to multiple antibiotics and the reduced susceptibility to the most commonly used antibiotic molecules have made the treatment of CDI more complicated, allowing the persistence of C. difficile in the intestinal environment.Gut colonization and biofilm formation have been suggested to contribute to the pathogenesis and persistence of C. difficile. In fact, biofilm growth is considered as a serious threat because of the related antimicrobial tolerance that makes antibiotic therapy often ineffective. This is the reason why the involvement of C. difficile biofilm in the pathogenesis and recurrence of CDI is attracting more and more interest, and the mechanisms underlying biofilm formation of C. difficile as well as the role of biofilm in CDI are increasingly being studied by researchers in the field.Findings on C. difficile biofilm, possible implications in CDI pathogenesis and treatment, efficacy of currently available antibiotics in treating biofilm-forming C. difficile strains, and some antimicrobial alternatives under investigation will be discussed here.
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Affiliation(s)
- Claudia Vuotto
- Microbial Biofilm Laboratory, IRCCS Fondazione Santa Lucia, Rome, Italy.
| | | | - Anthony Buckley
- Microbiome and Nutritional Sciences Group, School of Food Science & Nutrition, University of Leeds, Leeds, UK
| | - Caroline Chilton
- Healthcare Associated Infection Research Group, Section of Molecular Gastroenterology, Leeds Institute for Medical Research at St James, University of Leeds, Leeds, UK
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6
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Azrad M, Abu-Rahmoun L, Hamo Z, Peretz A. Associations of motility and auto-aggregation with biofilm-formation capacity levels in Clostridioidesdifficile. Microb Pathog 2024; 186:106490. [PMID: 38061667 DOI: 10.1016/j.micpath.2023.106490] [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: 09/10/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 01/02/2024]
Abstract
Clostridioides difficile (C. difficile) is responsible for one of the most common nosocomial infections worldwide. This work assessed associations between biofilm-formation capacity levels of C. difficile and cell viability, motility, flagella, motility and auto-aggregation in 118 clinical isolates. Biofilm production was assessed by the crystal violet method. Cell viability was determined by BacTiter-Glo™ Microbial Cell Viability Assay and live-imaging microscopy. Expression levels of LuxS, Cwp84, Spo0A, PilA, and FliC were measured by real-time PCR. Motility was visually assessed in agar tubes. Auto-aggregation levels were determined by OD600 measurements. Out of 118 isolates, 66 (56 %) were biofilm producers, with most being strong or moderate producers. Cell viability, motility and auto-aggregation positively correlated with biofilm-production capacity (p = 0.0001, p = 0.036 and p < 0.0001, respectively). Positive associations were found between pilA, fliC and luxS expression levels and biofilm-production capacity (p = 0.04, p = 0.01, p = 0.036, respectively). This is the first report of associations between biofilm-formation capacity and cell viability, pilA, fliC, and luxS gene expression, auto-aggregation and motility. These correlations should be further explored to expand knowledge on the regulation of C. difficile biofilm formation, and pathogenesis, which will have notable implications on treatment options.
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Affiliation(s)
- Maya Azrad
- Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Israel
| | | | - Zohar Hamo
- Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Israel
| | - Avi Peretz
- Clinical Microbiology Laboratory, Tzafon Medical Center, Poriya, Israel; Azrieli Faculty of Medicine, Bar Ilan University, Safed, Israel.
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7
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Mi Y, He Y, Mi J, Huang Y, Fan H, Song L, An X, Xu S, Li M, Tong Y. Genetic and Phenotypic Analysis of Phage-Resistant Mutant Fitness Triggered by Phage-Host Interactions. Int J Mol Sci 2023; 24:15594. [PMID: 37958578 PMCID: PMC10648725 DOI: 10.3390/ijms242115594] [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: 09/28/2023] [Revised: 10/16/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
The emergence of phage-resistant bacterial strains is one of the biggest challenges for phage therapy. However, the emerging phage-resistant bacteria are often accompanied by adaptive trade-offs, which supports a therapeutic strategy called "phage steering". The key to phage steering is to guide the bacterial population toward an evolutionary direction that is favorable for treatment. Thus, it is important to systematically investigate the impacts of phages targeting different bacterial receptors on the fitness of the bacterial population. Herein, we employed 20 different phages to impose strong evolutionary pressure on the host Pseudomonas aeruginosa PAO1 and examined the genetic and phenotypic responses of their phage-resistant mutants. Among these strains with impaired adsorptions, four types of mutations associated with bacterial receptors were identified, namely, lipopolysaccharides (LPSs), type IV pili (T4Ps), outer membrane proteins (OMPs), and exopolysaccharides (EPSs). PAO1, responding to LPS- and EPS-dependent phage infections, mostly showed significant growth impairment and virulence attenuation. Most mutants with T4P-related mutations exhibited a significant decrease in motility and biofilm formation ability, while the mutants with OMP-related mutations required the lowest fitness cost out of the bacterial populations. Apart from fitness costs, PAO1 strains might lose their resistance to antibiotics when counteracting with phages, such as the presence of large-fragment mutants in this study, which may inspire the usage of phage-antibiotic combination strategies. This work provides methods that leverage the merits of phage resistance relative to obtaining therapeutically beneficial outcomes with respect to phage-steering strategies.
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Affiliation(s)
- Yanze Mi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Yile He
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Jinhui Mi
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Yunfei Huang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Shan Xu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; (Y.M.); (Y.H.); (J.M.); (Y.H.); (H.F.); (L.S.); (X.A.); (S.X.)
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China
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8
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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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9
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Li R, Ling B, Zeng J, Wang X, Yang N, Fan L, Guo G, Li X, Yan F, Zheng J. A nosocomial Pseudomonas aeruginosa ST3495 isolated from a wild Burmese python (Python bivittatus) with suppurative pneumonia and bacteremia in Hainan, China. Braz J Microbiol 2023; 54:2403-2412. [PMID: 37344655 PMCID: PMC10484839 DOI: 10.1007/s42770-023-01038-7] [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: 11/17/2022] [Accepted: 06/07/2023] [Indexed: 06/23/2023] Open
Abstract
Pseudomonas aeruginosa is a common infectious agent associated with respiratory diseases in boas and pythons, however, the histopathology, resistance and virulence are yet described for this species. In this study, we investigated a dying Burmese python rescued from tropical rainforest in Hainan. Clinical signs were open-mouthed breathing, abnormal shedding and anorexia. Abundant yellow mucopurulent secretions were observed in highly ectatic segmental bronchi by postmortem. Histopathological lesions included systemic pneumonia, enteritis, nephritis and carditis. P. aeruginosa was the only species isolated from heart blood, kidney, trachea and lung. The phenotype analysis demonstrated that the isolates had strong biofilm, and were sensitive to amikacin, spectinomycin, ciprofloxacin, norfloxacin and polymyxin B, moreover, the LD50 of the most virulent isolate was 2.22×105 cfu/mL in a zebrafish model. Molecular epidemiological analysis revealed that the isolates belonged to sequence type 3495, the common gene patterns were toxA + exoSYT + phzIM + plcHN in virulence and catB + blaTEM + ant (3'')-I+ tetA in resistance. This study highlights that P. aeruginosa should be worth more attention in wildlife conservation and raise the public awareness for the cross infection and cross spread between animals and human.
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Affiliation(s)
- Roushan Li
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
- School of Animal Science and Technology, Hainan University, Haikou, 570228, China
| | - Bo Ling
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Jifeng Zeng
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
- School of Animal Science and Technology, Hainan University, Haikou, 570228, China
- One health institute, Hainan university, Haikou, 570228, China
| | - Xin Wang
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Nuo Yang
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Lixia Fan
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Guiying Guo
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
- School of Science, Hainan University, Haikou, 570228, China
| | - Xuesong Li
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China
- One health institute, Hainan university, Haikou, 570228, China
| | - Fei Yan
- Biological and Chemical Engineering College, Panzhihua University, Panzhihua, 617000, China
| | - Jiping Zheng
- Lab of Microbial Engineering (Infection and Immunity), School of Life Sciences, Hainan University, Haikou, 570228, China.
- One health institute, Hainan university, Haikou, 570228, China.
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10
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Perry EK, Tan MW. Bacterial biofilms in the human body: prevalence and impacts on health and disease. Front Cell Infect Microbiol 2023; 13:1237164. [PMID: 37712058 PMCID: PMC10499362 DOI: 10.3389/fcimb.2023.1237164] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023] Open
Abstract
Bacterial biofilms can be found in most environments on our planet, and the human body is no exception. Consisting of microbial cells encased in a matrix of extracellular polymers, biofilms enable bacteria to sequester themselves in favorable niches, while also increasing their ability to resist numerous stresses and survive under hostile circumstances. In recent decades, biofilms have increasingly been recognized as a major contributor to the pathogenesis of chronic infections. However, biofilms also occur in or on certain tissues in healthy individuals, and their constituent species are not restricted to canonical pathogens. In this review, we discuss the evidence for where, when, and what types of biofilms occur in the human body, as well as the diverse ways in which they can impact host health under homeostatic and dysbiotic states.
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Affiliation(s)
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech, South San Francisco, CA, United States
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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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12
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Vo N, Sidner BS, Yu Y, Piepenbrink KH. Type IV Pilus-Mediated Inhibition of Acinetobacter baumannii Biofilm Formation by Phenothiazine Compounds. Microbiol Spectr 2023; 11:e0102323. [PMID: 37341603 PMCID: PMC10433872 DOI: 10.1128/spectrum.01023-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 05/26/2023] [Indexed: 06/22/2023] Open
Abstract
Infections by pathogenic Acinetobacter species represent a significant burden on the health care system, despite their relative rarity, due to the difficulty of treating infections through oral antibiotics. Multidrug resistance is commonly observed in clinical Acinetobacter infections and multiple molecular mechanisms have been identified for this resistance, including multidrug efflux pumps, carbapenemase enzymes, and the formation of bacterial biofilm in persistent infections. Phenothiazine compounds have been identified as a potential inhibitor of type IV pilus production in multiple Gram-negative bacterial species. Here, we report the ability of two phenothiazines to inhibit type IV pilus-dependent surface (twitching) motility and biofilm formation in multiple Acinetobacter species. Biofilm formation was inhibited in both static and continuous flow models at micromolar concentrations without significant cytotoxicity, suggesting that type IV pilus biogenesis was the primary molecular target for these compounds. These results suggest that phenothiazines may be useful lead compounds for the development of biofilm dispersal agents against Gram-negative bacterial infections. IMPORTANCE Acinetobacter infections are a growing burden on health care systems worldwide due to increasing antimicrobial resistance through multiple mechanisms. Biofilm formation is an established mechanism of antimicrobial resistance, and its inhibition has the potential to potentiate the use of existing drugs against pathogenic Acinetobacter. Additionally, as discussed in the manuscript, anti-biofilm activity by phenothiazines has the potential to help to explain their known activity against other bacteria, including Staphylococcus aureus and Mycobacterium tuberculosis.
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Affiliation(s)
- Nam Vo
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Benjamin S. Sidner
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Yafan Yu
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kurt H. Piepenbrink
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
- Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
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13
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Ouyang Z, Zhao H, Zhao M, Yang Y, Zhao J. Type IV pili are involved in phenotypes associated with Clostridioides difficile pathogenesis. Crit Rev Microbiol 2023:1-9. [PMID: 37452617 DOI: 10.1080/1040841x.2023.2235002] [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: 03/13/2023] [Revised: 05/23/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Clostridioides difficile is a Gram-positive, spore-forming, rod-shaped, obligate anaerobe that is the leading cause of antibiotic-associated diarrhea. Type IV pili (T4P) are elongated appendages on the surface of C. difficile that are polymerized from many pilin proteins. T4P play an important role in C. difficile adherence and particularly in its persistence in the host intestine. Recent studies have shown that T4P promote C. difficile aggregation, surface motility, and biofilm formation, which may enhance its pathogenicity. Additionally, the second messenger cyclic diguanylate increases pilA1 transcript abundance, indirectly promoting T4P-mediated aggregation, surface motility, and biofilm formation of C. difficile. This review summarizes recent advances in C. difficile T4P research and the physiological activities of T4P in the context of C. difficile pathogenesis.
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Affiliation(s)
- Zirou Ouyang
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Hanlin Zhao
- Department of Medical Laboratory, Hebei North University, Zhangjiakou, Hebei Province, China
| | - Min Zhao
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
| | - Yaxuan Yang
- School of Public Health, The University of Queensland, Brisbane, Queensland, Australia
| | - Jianhong Zhao
- Hebei Provincial Center for Clinical Laboratories, The Second Hospital of Hebei Medical University, Shijiazhuang City, Hebei Province, China
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14
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Sidner B, Lerma A, Biswas B, Ronish LA, McCullough H, Auchtung JM, Piepenbrink KH. Flagellin is essential for initial attachment to mucosal surfaces by Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.19.541533. [PMID: 37292962 PMCID: PMC10245794 DOI: 10.1101/2023.05.19.541533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Mucins are glycoproteins which can be found in host cell membranes and as a gelatinous surface formed from secreted mucins. Mucosal surfaces in mammals form a barrier to invasive microbes, particularly bacteria, but are a point of attachment for others. Clostridioides difficile is anaerobic bacterium which colonizes the mammalian GI tract and is a common cause of acute GI inflammation leading to a variety of negative outcomes. Although C. difficile toxicity stems from secreted toxins, colonization is a prerequisite for C. difficile disease. While C. difficile is known to associate with the mucus layer and underlying epithelium, the mechanisms underlying these interactions that facilitate colonization are less well-understood. To understand the molecular mechanisms by which C. difficile interacts with mucins, we used ex vivo mucosal surfaces to test the ability of C. difficile to bind to mucins from different mammalian tissues. We found significant differences in C. difficile adhesion based upon the source of mucins, with highest levels of binding observed to mucins purified from the human colonic adenocarcinoma line LS174T and lowest levels of binding to porcine gastric mucin. We also observed that defects in adhesion by mutants deficient in flagella, but not type IV pili. These results imply that interactions between host mucins and C. difficile flagella facilitate the initial host attachment of C. difficile to host cells and secreted mucus.
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15
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Auria E, Hunault L, England P, Monot M, Pipoli Da Fonseca J, Matondo M, Duchateau M, Tremblay YDN, Dupuy B. The cell wall lipoprotein CD1687 acts as a DNA binding protein during deoxycholate-induced biofilm formation in Clostridioides difficile. NPJ Biofilms Microbiomes 2023; 9:24. [PMID: 37169797 PMCID: PMC10175255 DOI: 10.1038/s41522-023-00393-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023] Open
Abstract
The ability of bacterial pathogens to establish recurrent and persistent infections is frequently associated with their ability to form biofilms. Clostridioides difficile infections have a high rate of recurrence and relapses and it is hypothesized that biofilms are involved in its pathogenicity and persistence. Biofilm formation by C. difficile is still poorly understood. It has been shown that specific molecules such as deoxycholate (DCA) or metronidazole induce biofilm formation, but the mechanisms involved remain elusive. In this study, we describe the role of the C. difficile lipoprotein CD1687 during DCA-induced biofilm formation. We showed that the expression of CD1687, which is part of an operon within the CD1685-CD1689 gene cluster, is controlled by multiple transcription starting sites and some are induced in response to DCA. Only CD1687 is required for biofilm formation and the overexpression of CD1687 is sufficient to induce biofilm formation. Using RNAseq analysis, we showed that CD1687 affects the expression of transporters and metabolic pathways and we identified several potential binding partners by pull-down assay, including transport-associated extracellular proteins. We then demonstrated that CD1687 is surface exposed in C. difficile, and that this localization is required for DCA-induced biofilm formation. Given this localization and the fact that C. difficile forms eDNA-rich biofilms, we confirmed that CD1687 binds DNA in a non-specific manner. We thus hypothesize that CD1687 is a component of the downstream response to DCA leading to biofilm formation by promoting interaction between the cells and the biofilm matrix by binding eDNA.
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Affiliation(s)
- Emile Auria
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | - Lise Hunault
- Institut Pasteur, Université Paris-Cité, INSERM UMR1222, Unit of Antibodies in Therapy and Pathology, Paris, France
- Sorbonne Université, INSERM, CNRS, Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), F-75013, Paris, France
| | - Patrick England
- Plateforme de Biophysique Moléculaire, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Marc Monot
- Plateforme Technologique Biomics, Institut Pasteur, Paris, France
| | | | | | | | - Yannick D N Tremblay
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Bruno Dupuy
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France.
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16
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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 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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17
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Öztürk FY, Darcan C, Kariptaş E. The Determination, Monitoring, Molecular Mechanisms and Formation of Biofilm in E. coli. Braz J Microbiol 2023; 54:259-277. [PMID: 36577889 PMCID: PMC9943865 DOI: 10.1007/s42770-022-00895-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Accepted: 12/16/2022] [Indexed: 12/30/2022] Open
Abstract
Biofilms are cell assemblies embedded in an exopolysaccharide matrix formed by microorganisms of a single or many different species. This matrix in which they are embedded protects the bacteria from external influences and antimicrobial effects. The biofilm structure that microorganisms form to protect themselves from harsh environmental conditions and survive is found in nature in many different environments. These environments where biofilm formation occurs have in common that they are in contact with fluids. The gene expression of bacteria in complex biofilm differs from that of bacteria in the planktonic state. The differences in biofilm cell expression are one of the effects of community life. Means of quorum sensing, bacteria can act in coordination with each other. At the same time, while biofilm formation provides many benefits to bacteria, it has positive and negative effects in many different areas. Depending on where they occur, biofilms can cause serious health problems, contamination risks, corrosion, and heat and efficiency losses. However, they can also be used in water treatment plants, bioremediation, and energy production with microbial fuel cells. In this review, the basic steps of biofilm formation and biofilm regulation in the model organism Escherichia coli were discussed. Finally, the methods by which biofilm formation can be detected and monitored were briefly discussed.
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Affiliation(s)
- Fırat Yavuz Öztürk
- Department of Molecular Biology and Genetic, Faculty of Arts and Science, Bilecik Seyh Edebali University, Bilecik, Turkey.
| | - Cihan Darcan
- Department of Molecular Biology and Genetic, Faculty of Arts and Science, Bilecik Seyh Edebali University, Bilecik, Turkey
| | - Ergin Kariptaş
- Department of Medical Microbiology, Faculty of Medicine, Samsun University, Samsun, Turkey
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18
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Cheng JKJ, Unnikrishnan M. Clostridioides difficile infection: traversing host-pathogen interactions in the gut. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36848200 DOI: 10.1099/mic.0.001306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
C. difficile is the primary cause for nosocomial infective diarrhoea. For a successful infection, C. difficile must navigate between resident gut bacteria and the harsh host environment. The perturbation of the intestinal microbiota by broad-spectrum antibiotics alters the composition and the geography of the gut microbiota, deterring colonization resistance, and enabling C. difficile to colonize. This review will discuss how C. difficile interacts with and exploits the microbiota and the host epithelium to infect and persist. We provide an overview of C. difficile virulence factors and their interactions with the gut to aid adhesion, cause epithelial damage and mediate persistence. Finally, we document the host responses to C. difficile, describing the immune cells and host pathways that are associated and triggered during C. difficile infection.
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Affiliation(s)
- Jeffrey K J Cheng
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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19
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Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus. mBio 2022; 13:e0268822. [PMID: 36374038 PMCID: PMC9765702 DOI: 10.1128/mbio.02688-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Hydrocephalus, the leading indication for childhood neurosurgery worldwide, is particularly prevalent in low- and middle-income countries. Hydrocephalus preceded by an infection, or postinfectious hydrocephalus, accounts for up to 60% of hydrocephalus in these areas. Since many children with hydrocephalus suffer poor long-term outcomes despite surgical intervention, prevention of hydrocephalus remains paramount. Our previous studies implicated a novel bacterial pathogen, Paenibacillus thiaminolyticus, as a causal agent of neonatal sepsis and postinfectious hydrocephalus in Uganda. Here, we report the isolation of three P. thiaminolyticus strains, Mbale, Mbale2, and Mbale3, from patients with postinfectious hydrocephalus. We constructed complete genome assemblies of the clinical isolates as well as the nonpathogenic P. thiaminolyticus reference strain and performed comparative genomic and proteomic analyses to identify potential virulence factors. All three isolates carry a unique beta-lactamase gene, and two of the three isolates exhibit resistance in culture to the beta-lactam antibiotics penicillin and ampicillin. In addition, a cluster of genes carried on a mobile genetic element that encodes a putative type IV pilus operon is present in all three clinical isolates but absent in the reference strain. CRISPR-mediated deletion of the gene cluster substantially reduced the virulence of the Mbale strain in mice. Comparative proteogenomic analysis identified various additional potential virulence factors likely acquired on mobile genetic elements in the virulent strains. These results provide insight into the emergence of virulence in P. thiaminolyticus and suggest avenues for the diagnosis and treatment of this novel bacterial pathogen. IMPORTANCE Postinfectious hydrocephalus, a devastating sequela of neonatal infection, is associated with increased childhood mortality and morbidity. A novel bacterial pathogen, Paenibacillus thiaminolyticus, is highly associated with postinfectious hydrocephalus in an African cohort. Whole-genome sequencing, RNA sequencing, and proteomics of clinical isolates and a reference strain in combination with CRISPR editing identified type IV pili as a critical virulence factor for P. thiaminolyticus infection. Acquisition of a type IV pilus-encoding mobile genetic element critically contributed to converting a nonpathogenic strain of P. thiaminolyticus into a pathogen capable of causing devastating diseases. Given the widespread presence of type IV pilus in pathogens, the presence of the type IV pilus operon could serve as a diagnostic and therapeutic target in P. thiaminolyticus and related bacteria.
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20
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Morais MLGDS, Santos MGC, Costa CL, Martins CS, Leitão RFDC, de Melo Pacífico D, Quesada-Gómez C, Castelo Branco D, Ferreira EDO, Brito GADC. Comparative biofilm-forming ability between Clostridioides difficile strains isolated in Latin America and the epidemic NAP1/027 strain. Front Cell Infect Microbiol 2022; 12:1033698. [PMID: 36619751 PMCID: PMC9815708 DOI: 10.3389/fcimb.2022.1033698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/07/2022] [Indexed: 12/03/2022] Open
Abstract
Introduction One of the challenges in treating Clostridioides difficile infection (CDI) is that the bacterium forms biofilms, a critical virulence mechanism known to promote antibiotic resistance and, as a result, consequently, a higher recurrence of the disease. The goal of this study was to compare the ability of three MLST Clade 2 strains to form a biofilm in vitro: ICC-45 (ribotype SLO231/UK[CE]821), a ST41 toxinotype IXb isolated in Brazil; and two epidemic NAP1/027/ST01 strains: NAP1/027/ST01 (LIBA5756), isolated during a 2010 outbreak in Costa Rica and the reference epidemic strain NAP1/027/ST01 (R20291); and ATCC700057, a non-toxigenic strain. Methods The ability of strains to form biofilm was evaluated using crystal violet staining. In addition, samples were stained with the Film Tracer biofilm matrix (Invitrogen®) and the biofilm matrix thickness was measured using confocal microscopy. The matrix architecture was determined using Scanning electron microscop. Confocal microscopy was used to detect the presence of toxin A (tcdA) using an anti-Clostridioides difficile TcdA antibody. The expression of virulence genes (tcdA, tcdB, tcdC, cdtB, spo0A, slpA, cwp66 and cwp84) was examined, as well as the effect of antibiotics metronidazole (MTZ) and vancomycin (VAN) on biofilm growth. Results All of the strains tested formed a moderate biofilm with 1.1 <DO570nm>3.5. After 72h, biofilm biomass of the NAP1/027/ST01 epidemic strains (LIBA5756 and R20291) was significantly higher than ICC-45 and ATCC 700057 biofilms, as confirmed by electron and confocal microscopy. At 120h, the LIBA5756 biofilm biomass decreased compared to other strains. The toxigenic strains R20291 or LIBA 5756 had higher expression of genes tcdA, tcdB, tcdC, cdtA, slpA and spo0A than ICC-45, but there were no significant differences in the expression levels of cdtB, cwp66 and cwp84. In epidemic strains, VAN and MTZ inhibited biofilm formation; however, in the ICC-45 strain, MIC concentrations of VAN and MIC and 4MIC of MTZ did not inhibit biofilm formation. Conclusion The three MLST Clade 2 isolated from different rybotipes, two of which were isolated from Latin America, are competent biofilm-forming bacteria, indicating their ability to induce C. difficile infection recurrence, making treatment difficult.
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Affiliation(s)
- Maria Luana Gaudencio dos Santos Morais
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil,Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Mayara Gilde Castro Santos
- Laboratório de Biologia de Anaeróbios, Instituto de Microbiologia Paulo de Góes Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cecília Leite Costa
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil,Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Conceição Silva Martins
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Dvison de Melo Pacífico
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Carlos Quesada-Gómez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Débora Castelo Branco
- Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Eliane de Oliveira Ferreira
- Laboratory of Bacteriology, Department of Pathology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Gerly Anne de Castro Brito
- Department of Morphology, Faculty of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil,*Correspondence: Gerly Anne de Castro Brito,
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21
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Analysis of biofilm production and expression of adhesion structures of circulating Clostridioides difficile strains from Mexico. ENFERMEDADES INFECCIOSAS Y MICROBIOLOGIA CLINICA (ENGLISH ED.) 2022; 40:445-448. [PMID: 36195408 DOI: 10.1016/j.eimce.2021.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 01/25/2021] [Indexed: 06/16/2023]
Abstract
INTRODUCTION Clostridioides difficile biofilms are believed to protect the pathogen from antibiotics, in addition to potentially contributing to recurrent infections. METHODOLOGY Biofilm production of 102 C. difficile isolates was determined using the crystal violet staining technique, and detachment assays were performed. The expression levels of cwp84 and slpA genes were evaluated by real-time PCR on selected isolates. RESULTS More than 70% of isolates (75/102) were strong biofilm producers, and the highest detachment of biofilm was achieved with the proteinase K treatment (>90%). The overall mean expression of cwp84 was higher in RT027 than in RT001 (p=0.003); among strong biofilm-producing strains, the slpA expression was lower in RT027 than in RT001 (p<0.000). CONCLUSIONS Proteins seem to have an important role in the biofilm's initial adherence and maturation. slpA and cwp84 are differentially expressed by C. difficile ribotype and biofilm production level.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Clinical, Pharmaceutical, and Biological Sciences, Hatfield, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Monterrey, N.L., Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Monterrey, N.L., Mexico.
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22
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Ronish LA, Sidner B, Yu Y, Piepenbrink KH. Recognition of extracellular DNA by type IV pili promotes biofilm formation by Clostridioides difficile. J Biol Chem 2022; 298:102449. [PMID: 36064001 PMCID: PMC9556784 DOI: 10.1016/j.jbc.2022.102449] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 11/15/2022] Open
Abstract
Clostridioides difficile is a Gram-positive bacillus, which is a frequent cause of gastrointestinal infections triggered by the depletion of the gut microbiome. Because of the frequent recurrence of these infections after antibiotic treatment, mechanisms of C. difficile persistence and recurrence, including biofilm formation, are of increasing interest. Previously, our group and others found that type IV pili, filamentous helical appendages polymerized from protein subunits, promoted microcolony and biofilm formation in C. difficile. In Gram-negative bacteria, the ability of type IV pili to mediate bacterial self-association has been explained through interactions between the pili of adjacent cells, but type IV pili from several Gram-negative species are also required for natural competence through DNA uptake. Here, we report the ability of two C. difficile pilin subunits, PilJ and PilW, to bind to DNA in vitro, as well as the defects in biofilm formation in the pilJ and pilW gene-interruption mutants. Additionally, we have resolved the X-ray crystal structure of PilW, which we use to model possible structural mechanisms for the formation of C. difficile biofilm through interactions between type IV pili and the DNA of the extracellular matrix. Taken together, our results provide further insight into the relationship between type IV pilus function and biofilm formation in C. difficile and, more broadly, suggest that DNA recognition by type IV pili and related structures may have functional importance beyond DNA uptake for natural competence.
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Affiliation(s)
- Leslie A Ronish
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Ben Sidner
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Yafan Yu
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Kurt H Piepenbrink
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA; Center for Integrated Biomolecular Communication, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
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23
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Prevalence of Type IV Pili-Mediated Twitching Motility in Streptococcus sanguinis Strains and Its Impact on Biofilm Formation and Host Adherence. Appl Environ Microbiol 2022; 88:e0140322. [PMID: 36094177 PMCID: PMC9499025 DOI: 10.1128/aem.01403-22] [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: 11/20/2022] Open
Abstract
Type IV pili (Tfp) are known to mediate several biological activities, including surface-dependent twitching motility. Although a pil gene cluster for Tfp biosynthesis is found in all sequenced Streptococcus sanguinis strains, Tfp-mediated twitching motility is less commonly detected. Upon examining 81 clinical strains, 39 strains generated twitching zones on blood agar plates (BAP), while 27 strains displayed twitching on Todd-Hewitt (TH) agar. Although BAP appears to be more suitable for the development of twitching zones, 5 strains exhibited twitching motility only on TH agar, indicating that twitching motility is not only strain specific but also sensitive to growth media. Furthermore, different twitching phenotypes were observed in strains expressing comparable levels of pilT, encoding the retraction ATPase, suggesting that the twitching phenotype on agar plates is regulated by multiple factors. By using a PilT-null and a pilin protein-null derivative (CHW02) of twitching-active S. sanguinis CGMH010, we found that Tfp retraction was essential for biofilm stability. Further, biofilm growth was amplified in CHW02 in the absence of shearing force, indicating that S. sanguinis may utilize other ligands for biofilm formation in the absence of Tfp. Similar to SK36, Tfp from CGMH010 were required for colonization of host cells, but PilT only marginally affected adherence and only in the twitching-active strain. Taken together, the results suggest that Tfp participates in host cell adherence and that Tfp retraction facilitates biofilm stability. IMPORTANCE Although the gene clusters encoding Tfp are commonly present in Streptococcus sanguinis, not all strains express surface-dependent twitching motility on agar surfaces. Regardless of whether the Tfp could drive motility, Tfp can serve as a ligand for the colonization of host cells. Though many S. sanguinis strains lack twitching activity, motility can enhance biofilm stability in a twitching-active strain; thus, perhaps motility provides little or no advantage to the survival of bacteria within dental plaque. Rather, Tfp retraction could provide additional advantages for the bacteria to establish infections outside the oral cavity.
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Venturini C, Petrovic Fabijan A, Fajardo Lubian A, Barbirz S, Iredell J. Biological foundations of successful bacteriophage therapy. EMBO Mol Med 2022; 14:e12435. [PMID: 35620963 PMCID: PMC9260219 DOI: 10.15252/emmm.202012435] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/13/2022] [Accepted: 04/19/2022] [Indexed: 12/20/2022] Open
Abstract
Bacteriophages (phages) are selective viral predators of bacteria. Abundant and ubiquitous in nature, phages can be used to treat bacterial infections (phage therapy), including refractory infections and those resistant to antibiotics. However, despite an abundance of anecdotal evidence of efficacy, significant hurdles remain before routine implementation of phage therapy into medical practice, including a dearth of robust clinical trial data. Phage-bacterium interactions are complex and diverse, characterized by co-evolution trajectories that are significantly influenced by the environments in which they occur (mammalian body sites, water, soil, etc.). An understanding of the molecular mechanisms underpinning these dynamics is essential for successful clinical translation. This review aims to cover key aspects of bacterium-phage interactions that affect bacterial killing by describing the most relevant published literature and detailing the current knowledge gaps most likely to influence therapeutic success.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Sydney, NSW, Australia
| | - Aleksandra Petrovic Fabijan
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Alicia Fajardo Lubian
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia
| | - Stefanie Barbirz
- Department of Medicine, Science Faculty, MSB Medical School Berlin, Berlin, Germany
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW, Australia.,Faculty of Health and Medicine, School of Medicine, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia.,Westmead Hospital, Western Sydney Local Health District, Westmead, NSW, Australia
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25
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Abstract
Type IV pili (T4P) are retractable multifunctional nanofibers present on the surface of numerous bacterial and archaeal species. Their importance to microbiology is difficult to overstate. The scientific journey leading to our current understanding of T4P structure and function has included many innovative research milestones. Although multiple T4P reviews over the years have emphasized recent advances, we find that current reports often omit many of the landmark discoveries in this field. Here, we attempt to highlight chronologically the most important work on T4P, from the discovery of pili to the application of sophisticated contemporary methods, which has brought us to our current state of knowledge. As there remains much to learn about the complex machine that assembles and retracts T4P, we hope that this review will increase the interest of current researchers and inspire innovative progress.
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Krishnakumar R, Ruffing AM. OperonSEQer: A set of machine-learning algorithms with threshold voting for detection of operon pairs using short-read RNA-sequencing data. PLoS Comput Biol 2022; 18:e1009731. [PMID: 34986143 PMCID: PMC8765615 DOI: 10.1371/journal.pcbi.1009731] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/18/2022] [Accepted: 12/07/2021] [Indexed: 11/19/2022] Open
Abstract
Operon prediction in prokaryotes is critical not only for understanding the regulation of endogenous gene expression, but also for exogenous targeting of genes using newly developed tools such as CRISPR-based gene modulation. A number of methods have used transcriptomics data to predict operons, based on the premise that contiguous genes in an operon will be expressed at similar levels. While promising results have been observed using these methods, most of them do not address uncertainty caused by technical variability between experiments, which is especially relevant when the amount of data available is small. In addition, many existing methods do not provide the flexibility to determine the stringency with which genes should be evaluated for being in an operon pair. We present OperonSEQer, a set of machine learning algorithms that uses the statistic and p-value from a non-parametric analysis of variance test (Kruskal-Wallis) to determine the likelihood that two adjacent genes are expressed from the same RNA molecule. We implement a voting system to allow users to choose the stringency of operon calls depending on whether your priority is high recall or high specificity. In addition, we provide the code so that users can retrain the algorithm and re-establish hyperparameters based on any data they choose, allowing for this method to be expanded as additional data is generated. We show that our approach detects operon pairs that are missed by current methods by comparing our predictions to publicly available long-read sequencing data. OperonSEQer therefore improves on existing methods in terms of accuracy, flexibility, and adaptability. Bacteria and archaea, single-cell organisms collectively known as prokaryotes, live in all imaginable environments and comprise the majority of living organisms on this planet. Prokaryotes play a critical role in the homeostasis of multicellular organisms (such as animals and plants) and ecosystems. In addition, bacteria can be pathogenic and cause a variety of diseases in these same hosts and ecosystems. In short, understanding the biology and molecular functions of bacteria and archaea and devising mechanisms to engineer and optimize their properties are critical scientific endeavors with significant implications in healthcare, agriculture, manufacturing, and climate science among others. One major molecular difference between unicellular and multicellular organisms is the way they express genes–multicellular organisms make individual RNA molecules for each gene while, prokaryotes express operons (i.e., a group of genes coding functionally related proteins) in contiguous polycistronic RNA molecules. Understanding which genes exist within operons is critical for elucidating basic biology and for engineering organisms. In this work, we use a combination of statistical and machine learning-based methods to use next-generation sequencing data to predict operon structure across a range of prokaryotes. Our method provides an easily implemented, robust, accurate, and flexible way to determine operon structure in an organism-agnostic manner using readily available data.
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Affiliation(s)
- Raga Krishnakumar
- Systems Biology Department, Sandia National Laboratories, Livermore, California, United States of America
- * E-mail:
| | - Anne M. Ruffing
- Molecular and Microbiology Department, Sandia National Laboratories, Albuquerque, New Mexico, United States of America
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27
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Schupack DA, Mars RAT, Voelker DH, Abeykoon JP, Kashyap PC. The promise of the gut microbiome as part of individualized treatment strategies. Nat Rev Gastroenterol Hepatol 2022; 19:7-25. [PMID: 34453142 PMCID: PMC8712374 DOI: 10.1038/s41575-021-00499-1] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/14/2021] [Indexed: 02/07/2023]
Abstract
Variability in disease presentation, progression and treatment response has been a central challenge in medicine. Although variability in host factors and genetics are important, it has become evident that the gut microbiome, with its vast genetic and metabolic diversity, must be considered in moving towards individualized treatment. In this Review, we discuss six broad disease groups: infectious disease, cancer, metabolic disease, cardiovascular disease, autoimmune or inflammatory disease, and allergic and atopic diseases. We highlight current knowledge on the gut microbiome in disease pathogenesis and prognosis, efficacy, and treatment-related adverse events and its promise for stratifying existing treatments and as a source of novel therapies. The Review is not meant to be comprehensive for each disease state but rather highlights the potential implications of the microbiome as a tool to individualize treatment strategies in clinical practice. Although early, the outlook is optimistic but challenges need to be overcome before clinical implementation, including improved understanding of underlying mechanisms, longitudinal studies with multiple data layers reflecting gut microbiome and host response, standardized approaches to testing and reporting, and validation in larger cohorts. Given progress in the microbiome field with concurrent basic and clinical studies, the microbiome will likely become an integral part of clinical care within the next decade.
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Affiliation(s)
- Daniel A Schupack
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Ruben A T Mars
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Dayne H Voelker
- Division of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Jithma P Abeykoon
- Division of Hematology and Oncology, Mayo Clinic, Rochester, MN, USA
| | - Purna C Kashyap
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA.
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, MN, USA.
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Tremblay YD, Dupuy B. The blueprint for building a biofilm the Clostridioides difficile way. Curr Opin Microbiol 2021; 66:39-45. [PMID: 34933207 DOI: 10.1016/j.mib.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/25/2021] [Accepted: 12/06/2021] [Indexed: 11/27/2022]
Abstract
Clostridioides difficile is an opportunistic pathogen that causes by a high rate of recurrent infections. Persistence in the gastrointestinal tract is thought to be mediated by sporulation and/or biofilm formation. There is an increase interest in C. difficile biofilm formation and recent findings have provided a framework to model surface-attached biofilm formation. For in vitro biofilm formation, C. difficile must undergo a metabolic reprogramming as it enters stationary phase. This helps maintain long-term viability and increases responsiveness to signals leading to biofilm formation. Metabolic reprogramming and biofilm formation requires several regulatory factors and these overlap with the sporulation cascade. Despite recent advances, further research is needed to answer outstanding questions in the field.
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Affiliation(s)
- Yannick Dn Tremblay
- Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France; Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada.
| | - Bruno Dupuy
- Institut Pasteur, Université de Paris, UMR-CNRS 2001, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France.
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Metabolic adaption to extracellular pyruvate triggers biofilm formation in Clostridioides difficile. THE ISME JOURNAL 2021; 15:3623-3635. [PMID: 34155333 PMCID: PMC8630010 DOI: 10.1038/s41396-021-01042-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile infections are associated with gut microbiome dysbiosis and are the leading cause of hospital-acquired diarrhoea. The infectious process is strongly influenced by the microbiota and successful infection relies on the absence of specific microbiota-produced metabolites. Deoxycholate and short-chain fatty acids are microbiota-produced metabolites that limit the growth of C. difficile and protect the host against this infection. In a previous study, we showed that deoxycholate causes C. difficile to form strongly adherent biofilms after 48 h. Here, our objectives were to identify and characterize key molecules and events required for biofilm formation in the presence of deoxycholate. We applied time-course transcriptomics and genetics to identify sigma factors, metabolic processes and type IV pili that drive biofilm formation. These analyses revealed that extracellular pyruvate induces biofilm formation in the presence of deoxycholate. In the absence of deoxycholate, pyruvate supplementation was sufficient to induce biofilm formation in a process that was dependent on pyruvate uptake by the membrane protein CstA. In the context of the human gut, microbiota-generated pyruvate is a metabolite that limits pathogen colonization. Taken together our results suggest that pyruvate-induced biofilm formation might act as a key process driving C. difficile persistence in the gut.
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30
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Meza-Torres J, Auria E, Dupuy B, Tremblay YDN. Wolf in Sheep's Clothing: Clostridioides difficile Biofilm as a Reservoir for Recurrent Infections. Microorganisms 2021; 9:1922. [PMID: 34576818 PMCID: PMC8470499 DOI: 10.3390/microorganisms9091922] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/07/2021] [Indexed: 12/21/2022] Open
Abstract
The microbiota inhabiting the intestinal tract provide several critical functions to its host. Microorganisms found at the mucosal layer form organized three-dimensional structures which are considered to be biofilms. Their development and functions are influenced by host factors, host-microbe interactions, and microbe-microbe interactions. These structures can dictate the health of their host by strengthening the natural defenses of the gut epithelium or cause disease by exacerbating underlying conditions. Biofilm communities can also block the establishment of pathogens and prevent infectious diseases. Although these biofilms are important for colonization resistance, new data provide evidence that gut biofilms can act as a reservoir for pathogens such as Clostridioides difficile. In this review, we will look at the biofilms of the intestinal tract, their contribution to health and disease, and the factors influencing their formation. We will then focus on the factors contributing to biofilm formation in C. difficile, how these biofilms are formed, and their properties. In the last section, we will look at how the gut microbiota and the gut biofilm influence C. difficile biofilm formation, persistence, and transmission.
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Affiliation(s)
- Jazmin Meza-Torres
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Emile Auria
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
| | - Yannick D. N. Tremblay
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, UMR-CNRS 2001, Université de Paris, 25 rue du Docteur Roux, 75724 Paris, France; (J.M.-T.); (E.A.)
- Health Sciences Building, Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Rd, Saskatoon, SK S7N 5E5, Canada
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31
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Abstract
Clostridiodes difficile (C. difficile) was ranked an “urgent threat” by the Centers for Disease Control and Prevention (CDC) in 2019. C. difficile infection (CDI) is the most common healthcare-associated infection (HAI) in the United States of America as well as the leading cause of antibiotic-associated gastrointestinal disease. C. difficile is a gram-positive, rod-shaped, spore-forming, anaerobic bacterium that causes infection of the epithelial lining of the gut. CDI occurs most commonly after disruption of the human gut microflora following the prolonged use of broad-spectrum antibiotics. However, the recurrent nature of this disease has led to the hypothesis that biofilm formation may play a role in its pathogenesis. Biofilms are sessile communities of bacteria protected from extracellular stresses by a matrix of self-produced proteins, polysaccharides, and extracellular DNA. Biofilm regulation in C. difficile is still incompletely understood, and its role in disease recurrence has yet to be fully elucidated. However, many factors have been found to influence biofilm formation in C. difficile, including motility, adhesion, and hydrophobicity of the bacterial cells. Small changes in one of these systems can greatly influence biofilm formation. Therefore, the biofilm regulatory system would need to coordinate all these systems to create optimal biofilm-forming physiology under appropriate environmental conditions. The coordination of these systems is complex and multifactorial, and any analysis must take into consideration the influences of the stress response, quorum sensing (QS), and gene regulation by second messenger molecule cyclic diguanosine monophosphate (c-di-GMP). However, the differences in biofilm-forming ability between C. difficile strains such as 630 and the “hypervirulent” strain, R20291, make it difficult to assign a “one size fits all” mechanism to biofilm regulation in C. difficile. This review seeks to consolidate published data regarding the regulation of C. difficile biofilms in order to identify gaps in knowledge and propose directions for future study. Clostridioides difficile (C. difficile) is an opportunistic bacterial pathogen that causes infection of the human gut epithelium following disruption of the normal gut microflora, usually by broad-spectrum antibiotics. C. difficile infection (CDI) is recurrent in 20% to 30% of cases and can lead to significant health-related complications such as pseudomembranous colitis and, in severe cases, death. The impact and cost of this pathogen on healthcare systems are significant, and some aspects of the pathogen’s lifestyle in the host are, as yet, unknown. It is hypothesised that C. difficile exists in the gut as a biofilm due to the infection’s severity and recurrent nature. The biofilm mode of bacterial growth can protect the cells from external factors such as antibiotic treatment, physiological processes, and the immune system. However, biofilm regulation in C. difficile is not yet fully characterised, and in this review, we consolidate published primary research on C. difficile biofilm regulation to gain a comprehensive overview of the factors involved and how they may interact to enable biofilm development within a host.
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Samrot AV, Abubakar Mohamed A, Faradjeva E, Si Jie L, Hooi Sze C, Arif A, Chuan Sean T, Norbert Michael E, Yeok Mun C, Xiao Qi N, Ling Mok P, Kumar SS. Mechanisms and Impact of Biofilms and Targeting of Biofilms Using Bioactive Compounds-A Review. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:839. [PMID: 34441045 PMCID: PMC8401077 DOI: 10.3390/medicina57080839] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 08/10/2021] [Indexed: 12/31/2022]
Abstract
Biofilms comprising aggregates of microorganisms or multicellular communities have been a major issue as they cause resistance against antimicrobial agents and biofouling. To date, numerous biofilm-forming microorganisms have been identified, which have been shown to result in major effects including biofouling and biofilm-related infections. Quorum sensing (which describes the cell communication within biofilms) plays a vital role in the regulation of biofilm formation and its virulence. As such, elucidating the various mechanisms responsible for biofilm resistance (including quorum sensing) will assist in developing strategies to inhibit and control the formation of biofilms in nature. Employing biological control measures (such as the use of bioactive compounds) in targeting biofilms is of great interest since they naturally possess antimicrobial activity among other favorable attributes and can also possibly act as potent antibiofilm agents. As an effort to re-establish the current notion and understanding of biofilms, the present review discuss the stages involved in biofilm formation, the factors contributing to its development, the effects of biofilms in various industries, and the use of various bioactive compounds and their strategies in biofilm inhibition.
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Affiliation(s)
- Antony V. Samrot
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Amira Abubakar Mohamed
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Etel Faradjeva
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Lee Si Jie
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Chin Hooi Sze
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Akasha Arif
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Tan Chuan Sean
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Emmanuel Norbert Michael
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Chua Yeok Mun
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Ng Xiao Qi
- School of Bioscience, Faculty of Medicine, Bioscience and Nursing, MAHSA University, Jenjarom 42610, Selangor, Malaysia; (A.A.M.); (E.F.); (L.S.J.); (C.H.S.); (A.A.); (T.C.S.); (E.N.M.); (C.Y.M.); (N.X.Q.)
| | - Pooi Ling Mok
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Suresh S. Kumar
- Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Department of Biotechnology, Bharath Institute of Higher Education and Research, Agharam Road Selaiyur, Chennai 600 073, Tamil Nadu, India
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Brauer M, Lassek C, Hinze C, Hoyer J, Becher D, Jahn D, Sievers S, Riedel K. What's a Biofilm?-How the Choice of the Biofilm Model Impacts the Protein Inventory of Clostridioides difficile. Front Microbiol 2021; 12:682111. [PMID: 34177868 PMCID: PMC8225356 DOI: 10.3389/fmicb.2021.682111] [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: 03/17/2021] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
The anaerobic pathogen Clostridioides difficile is perfectly equipped to survive and persist inside the mammalian intestine. When facing unfavorable conditions C. difficile is able to form highly resistant endospores. Likewise, biofilms are currently discussed as form of persistence. Here a comprehensive proteomics approach was applied to investigate the molecular processes of C. difficile strain 630Δerm underlying biofilm formation. The comparison of the proteome from two different forms of biofilm-like growth, namely aggregate biofilms and colonies on agar plates, revealed major differences in the formation of cell surface proteins, as well as enzymes of its energy and stress metabolism. For instance, while the obtained data suggest that aggregate biofilm cells express both flagella, type IV pili and enzymes required for biosynthesis of cell-surface polysaccharides, the S-layer protein SlpA and most cell wall proteins (CWPs) encoded adjacent to SlpA were detected in significantly lower amounts in aggregate biofilm cells than in colony biofilms. Moreover, the obtained data suggested that aggregate biofilm cells are rather actively growing cells while colony biofilm cells most likely severely suffer from a lack of reductive equivalents what requires induction of the Wood-Ljungdahl pathway and C. difficile’s V-type ATPase to maintain cell homeostasis. In agreement with this, aggregate biofilm cells, in contrast to colony biofilm cells, neither induced toxin nor spore production. Finally, the data revealed that the sigma factor SigL/RpoN and its dependent regulators are noticeably induced in aggregate biofilms suggesting an important role of SigL/RpoN in aggregate biofilm formation.
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Affiliation(s)
- Madita Brauer
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Lassek
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Christian Hinze
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Juliane Hoyer
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dörte Becher
- Department for Microbial Proteomics, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Institute of Microbiology, Technische Universität Braunschweig, Braunschweig, Germany
| | - Susanne Sievers
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
| | - Katharina Riedel
- Department for Microbial Physiology and Molecular Biology, Institute of Microbiology, University of Greifswald, Greifswald, Germany
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Wang Y, Gao H, F Wells G. Integrated omics analyses reveal differential gene expression and potential for cooperation between denitrifying polyphosphate and glycogen accumulating organisms. Environ Microbiol 2021; 23:3274-3293. [PMID: 33769674 DOI: 10.1111/1462-2920.15486] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 03/02/2021] [Accepted: 03/24/2021] [Indexed: 01/06/2023]
Abstract
Unusually high accumulation of the potent greenhouse gas nitrous oxide (N2 O) has previously been documented in denitrifying biological phosphorus (P) removal bioprocesses, but the roles of differential denitrification gene expression patterns and ecological interactions between key functional groups in driving these emissions are not well understood. To address these knowledge gaps, we applied genome-resolved metagenomics and metatranscriptomics to a denitrifying bioprocess enriched in as-yet-uncultivated denitrifying polyphosphate accumulating organisms (PAOs) affiliated with Candidatus Accumulibacter. The six transcriptionally most active populations in the community included three co-occurring Accumulibacter strains affiliated with clades IF (a novel clade identified in this study), IA and IC, a competing glycogen accumulating organism (GAO) affiliated with Competibacteraceae (GAO1), a Gammaproteobacteria PR6 and an Anaerolineae CH7. Strongly elevated expression of nitrite reductase genes compared to nitrous oxide reductase genes was observed in the overall community and in Accumulibacter populations, suggesting a strong role for differential gene expression in driving N2 O accumulation. Surprisingly, while ~90% of the nirS gene transcripts were expressed by the three co-occurring PAO populations, ~93% of the norB gene transcripts were expressed by GAO1 and ~75% of the norZ gene transcripts were mapped to PR6 and several other non-PAO flanking populations. This suggests the potential for cooperation between flanking populations and PAOs in reducing denitrification intermediates. Such cooperation may benefit the community by reducing the accumulation of toxic nitric oxide.
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Affiliation(s)
- Yubo Wang
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - Han Gao
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
| | - George F Wells
- Department of Civil and Environmental Engineering, Northwestern University, Evanston, IL, USA
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Engevik MA, Engevik AC, Engevik KA, Auchtung JM, Chang-Graham AL, Ruan W, Luna RA, Hyser JM, Spinler JK, Versalovic J. Mucin-Degrading Microbes Release Monosaccharides That Chemoattract Clostridioides difficile and Facilitate Colonization of the Human Intestinal Mucus Layer. ACS Infect Dis 2021; 7:1126-1142. [PMID: 33176423 DOI: 10.1021/acsinfecdis.0c00634] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
It is widely accepted that the pathogen Clostridioides difficile exploits an intestinal environment with an altered microbiota, but the details of these microbe-microbe interactions are unclear. Adherence and colonization of mucus has been demonstrated for several enteric pathogens and it is possible that mucin-associated microbes may be working in concert with C. difficile. We showed that C. difficile ribotype-027 adheres to MUC2 glycans and using fecal bioreactors, we identified that C. difficile associates with several mucin-degrading microbes. C. difficile was found to chemotax toward intestinal mucus and its glycan components, demonstrating that C. difficile senses the mucus layer. Although C. difficile lacks the glycosyl hydrolases required to degrade mucin glycans, coculturing C. difficile with the mucin-degrading Akkermansia muciniphila, Bacteroides thetaiotaomicron, and Ruminococcus torques allowed C. difficile to grow in media that lacked glucose but contained purified MUC2. Collectively, these studies expand our knowledge on how intestinal microbes support C. difficile.
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Affiliation(s)
- Melinda A. Engevik
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Amy C. Engevik
- Department of Surgery, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
- Epithelial Biology Center, Vanderbilt University School of Medicine, Nashville Tennessee 37232, United States
| | - Kristen A. Engevik
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer M. Auchtung
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln Nebraska 68588, United States
| | - Alexandra L. Chang-Graham
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Wenly Ruan
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Ruth Ann Luna
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - Joseph M. Hyser
- Department of Molecular Virology and Microbiology, Baylor College of Medicine Houston Texas 77030, United States
| | - Jennifer K. Spinler
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
| | - James Versalovic
- Department of Pathology & Immunology, Baylor College of Medicine Houston Texas 77030, United States
- Department of Pathology, Texas Children’s Hospital Houston Texas 77030, United States
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Analysis of biofilm production and expression of adhesion structures of circulating Clostridioides difficile strains from Mexico. Enferm Infecc Microbiol Clin 2021; 40:S0213-005X(21)00042-2. [PMID: 33714640 DOI: 10.1016/j.eimc.2021.01.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 01/21/2023]
Abstract
INTRODUCTION Clostridioides difficile biofilms are believed to protect the pathogen from antibiotics, in addition to potentially contributing to recurrent infections. METHODOLOGY Biofilm production of 102 C. difficile isolates was determined using the crystal violet staining technique, and detachment assays were performed. The expression levels of cwp84 and slpA genes were evaluated by real-time PCR on selected isolates. RESULTS More than 70% of isolates (75/102) were strong biofilm producers, and the highest detachment of biofilm was achieved with the proteinase K treatment (>90%). The overall mean expression of cwp84 was higher in RT027 than in RT001 (p=0.003); among strong biofilm-producing strains, the slpA expression was lower in RT027 than in RT001 (p<0.000). CONCLUSIONS Proteins seem to have an important role in the biofilm's initial adherence and maturation. slpA and cwp84 are differentially expressed by C. difficile ribotype and biofilm production level.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Clinical, Pharmaceutical, and Biological Sciences, Hatfield, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Monterrey, N.L., Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Monterrey, N.L., Mexico.
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37
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Lebov JF, Bohannan BJM. Msh Pilus Mutations Increase the Ability of a Free-Living Bacterium to Colonize a Piscine Host. Genes (Basel) 2021; 12:genes12020127. [PMID: 33498301 PMCID: PMC7909257 DOI: 10.3390/genes12020127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/12/2021] [Accepted: 01/18/2021] [Indexed: 02/07/2023] Open
Abstract
Symbioses between animals and bacteria are ubiquitous. To better understand these relationships, it is essential to unravel how bacteria evolve to colonize hosts. Previously, we serially passaged the free-living bacterium, Shewanella oneidensis, through the digestive tracts of germ-free larval zebrafish (Danio rerio) to uncover the evolutionary changes involved in the initiation of a novel symbiosis with a vertebrate host. After 20 passages, we discovered an adaptive missense mutation in the mshL gene of the msh pilus operon, which improved host colonization, increased swimming motility, and reduced surface adhesion. In the present study, we determined that this mutation was a loss-of-function mutation and found that it improved zebrafish colonization by augmenting S. oneidensis representation in the water column outside larvae through a reduced association with environmental surfaces. Additionally, we found that strains containing the mshL mutation were able to immigrate into host digestive tracts at higher rates per capita. However, mutant and evolved strains exhibited no evidence of a competitive advantage after colonizing hosts. Our results demonstrate that bacterial behaviors outside the host can play a dominant role in facilitating the onset of novel host associations.
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Affiliation(s)
- Jarrett F. Lebov
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA;
- Correspondence:
| | - Brendan J. M. Bohannan
- Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403-5289, USA;
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38
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Muhammad MH, Idris AL, Fan X, Guo Y, Yu Y, Jin X, Qiu J, Guan X, Huang T. Beyond Risk: Bacterial Biofilms and Their Regulating Approaches. Front Microbiol 2020; 11:928. [PMID: 32508772 PMCID: PMC7253578 DOI: 10.3389/fmicb.2020.00928] [Citation(s) in RCA: 247] [Impact Index Per Article: 61.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/20/2020] [Indexed: 12/24/2022] Open
Abstract
Bacterial biofilms are complex surface attached communities of bacteria held together by self-produced polymer matrixs mainly composed of polysaccharides, secreted proteins, and extracellular DNAs. Bacterial biofilm formation is a complex process and can be described in five main phases: (i) reversible attachment phase, where bacteria non-specifically attach to surfaces; (ii) irreversible attachment phase, which involves interaction between bacterial cells and a surface using bacterial adhesins such as fimbriae and lipopolysaccharide (LPS); (iii) production of extracellular polymeric substances (EPS) by the resident bacterial cells; (iv) biofilm maturation phase, in which bacterial cells synthesize and release signaling molecules to sense the presence of each other, conducing to the formation of microcolony and maturation of biofilms; and (v) dispersal/detachment phase, where the bacterial cells depart biofilms and comeback to independent planktonic lifestyle. Biofilm formation is detrimental in healthcare, drinking water distribution systems, food, and marine industries, etc. As a result, current studies have been focused toward control and prevention of biofilms. In an effort to get rid of harmful biofilms, various techniques and approaches have been employed that interfere with bacterial attachment, bacterial communication systems (quorum sensing, QS), and biofilm matrixs. Biofilms, however, also offer beneficial roles in a variety of fields including applications in plant protection, bioremediation, wastewater treatment, and corrosion inhibition amongst others. Development of beneficial biofilms can be promoted through manipulation of adhesion surfaces, QS and environmental conditions. This review describes the events involved in bacterial biofilm formation, lists the negative and positive aspects associated with bacterial biofilms, elaborates the main strategies currently used to regulate establishment of harmful bacterial biofilms as well as certain strategies employed to encourage formation of beneficial bacterial biofilms, and highlights the future perspectives of bacterial biofilms.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Tianpei Huang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops & Key Laboratory of Biopesticide and Chemical Biology of Ministry of Education, College of Life Sciences & College of Plant Protection & International College, Fujian Agriculture and Forestry University, Fuzhou, China
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39
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Ligthart K, Belzer C, de Vos WM, Tytgat HLP. Bridging Bacteria and the Gut: Functional Aspects of Type IV Pili. Trends Microbiol 2020; 28:340-348. [PMID: 32298612 DOI: 10.1016/j.tim.2020.02.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 01/31/2020] [Accepted: 02/10/2020] [Indexed: 12/14/2022]
Abstract
Cell-surface-located proteinaceous appendages, such as flagella and fimbriae or pili, are ubiquitous in bacterial communities. Here, we focus on conserved type IV pili (T4P) produced by bacteria in the intestinal tract, one of the most densely populated human ecosystems. Computational analysis revealed that approximately 30% of known intestinal bacteria are predicted to produce T4P. To rationalize how T4P allow intestinal bacteria to interact with their environment, other microbiota members, and host cells, we review their established role in gut commensals and pathogens with respect to adherence, motility, and biofilm formation, as well as protein secretion and DNA uptake. This work indicates that T4P are widely spread among the known members of the intestinal microbiota and that their contribution to human health might be underestimated.
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Affiliation(s)
- Kate Ligthart
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Clara Belzer
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands; Research Program Human Microbiome, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands.
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40
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Crawshaw AD, Baslé A, Salgado PS. A practical overview of molecular replacement: Clostridioides difficile PilA1, a difficult case study. Acta Crystallogr D Struct Biol 2020; 76:261-271. [PMID: 32133990 PMCID: PMC7057214 DOI: 10.1107/s2059798320000467] [Citation(s) in RCA: 3] [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: 10/25/2019] [Accepted: 01/14/2020] [Indexed: 12/02/2022] Open
Abstract
Many biologists are now routinely seeking to determine the three-dimensional structures of their proteins of choice, illustrating the importance of this knowledge, but also of the simplification and streamlining of structure-determination processes. Despite the fact that most software packages offer simple pipelines, for the non-expert navigating the outputs and understanding the key aspects can be daunting. Here, the structure determination of the type IV pili (TFP) protein PilA1 from Clostridioides difficile is used to illustrate the different steps involved, the key decision criteria and important considerations when using the most common pipelines and software. Molecular-replacement pipelines within CCP4i2 are presented to illustrate the more commonly used processes. Previous knowledge of the biology and structure of TFP pilins, particularly the presence of a long, N-terminal α-helix required for pilus formation, allowed informed decisions to be made during the structure-determination strategy. The PilA1 structure was finally successfully determined using ARCIMBOLDO and the ab initio MR strategy used is described.
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Affiliation(s)
- Adam D. Crawshaw
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
| | - Arnaud Baslé
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
| | - Paula S. Salgado
- Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, England
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41
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The Impact of pH on Clostridioides difficile Sporulation and Physiology. Appl Environ Microbiol 2020; 86:AEM.02706-19. [PMID: 31811041 DOI: 10.1128/aem.02706-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 12/03/2019] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a pathogenic bacterium that infects the human colon to cause diarrheal disease. Growth of the bacterium is known to be dependent on certain bile acids, oxygen levels, and nutrient availability in the intestine, but how the environmental pH can influence C. difficile is mostly unknown. Previous studies indicated that C. difficile modulates the intestinal pH, and prospective cohort studies have found a strong association between a more alkaline fecal pH and C. difficile infection. Based on these data, we hypothesized that C. difficile physiology can be affected by various pH conditions. In this study, we investigated the impact of a range of pH conditions on C. difficile to assess potential effects on growth, sporulation, motility, and toxin production in the strains 630Δerm and R20291. We observed pH-dependent differences in sporulation rate, spore morphology, and viability. Sporulation frequency was lowest under acidic conditions, and differences in cell morphology were apparent at low pH. In alkaline environments, C. difficile sporulation was greater for strain 630Δerm, whereas R20291 produced relatively high levels of spores in a broad range of pH conditions. Rapid changes in pH during exponential growth impacted sporulation similarly among the strains. Furthermore, we observed an increase in C. difficile motility with increases in pH, and strain-dependent differences in toxin production under acidic conditions. The data demonstrate that pH is an important parameter that affects C. difficile physiology and may reveal relevant insights into the growth and dissemination of this pathogen.IMPORTANCE Clostridioides difficile is an anaerobic bacterium that causes gastrointestinal disease. C. difficile forms dormant spores which can survive harsh environmental conditions, allowing their spread to new hosts. In this study, we determine how intestinally relevant pH conditions impact C. difficile physiology in the two divergent strains, 630Δerm and R20291. Our data demonstrate that low pH conditions reduce C. difficile growth, sporulation, and motility. However, toxin production and spore morphology were differentially impacted in the two strains at low pH. In addition, we observed that alkaline environments reduce C. difficile growth, but increase cell motility. When pH was adjusted rapidly during growth, we observed similar impacts on both strains. This study provides new insights into the phenotypic diversity of C. difficile grown under diverse pH conditions present in the intestinal tract, and demonstrates similarities and differences in the pH responses of different C. difficile isolates.
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Epigenomic characterization of Clostridioides difficile finds a conserved DNA methyltransferase that mediates sporulation and pathogenesis. Nat Microbiol 2019; 5:166-180. [PMID: 31768029 PMCID: PMC6925328 DOI: 10.1038/s41564-019-0613-4] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 10/18/2019] [Indexed: 12/20/2022]
Abstract
Clostridioides difficile is a leading cause of health care-associated infections. Although significant progress has been made in the understanding of its genome, the epigenome of C. difficile and its functional impact has not been systematically explored. Here, we performed a comprehensive DNA methylome analysis of C. difficile using 36 human isolates and observed great epigenomic diversity. We discovered an orphan DNA methyltransferase with a well-defined specificity whose corresponding gene is highly conserved across our dataset and in all ∼300 global C. difficile genomes examined. Inactivation of the methyltransferase gene negatively impacted sporulation, a key step in C. difficile disease transmission, consistently supported by multi-omics data, genetic experiments, and a mouse colonization model. Further experimental and transcriptomic analysis also suggested that epigenetic regulation is associated with cell length, biofilm formation, and host colonization. These findings provide a unique epigenetic dimension to characterize medically relevant biological processes in this critical pathogen. This work also provides a set of methods for comparative epigenomics and integrative analysis, which we expect to be broadly applicable to bacterial epigenomics studies.
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43
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Pelicic V. Monoderm bacteria: the new frontier for type IV pilus biology. Mol Microbiol 2019; 112:1674-1683. [PMID: 31556183 PMCID: PMC6916266 DOI: 10.1111/mmi.14397] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2019] [Indexed: 12/11/2022]
Abstract
In the diverse world of bacterial pili, type IV pili (Tfp) are unique for two reasons: their multifunctionality and ubiquity. This latter feature offers an extraordinary possibility, that is, to perform comparative studies in evolutionarily distant species in order to improve our fragmentary understanding of Tfp biology. Regrettably, such potential has remained largely untapped, because, for 20 years, Tfp have only been characterised in diderm bacteria. However, recent studies of Tfp in monoderms have started closing the gap, revealing many interesting commonalities and a few significant differences, extending the frontiers of knowledge of Tfp biology. Here, I review the current state of the art of the Tfp field in monoderm bacteria and discuss resulting implications for our general understanding of the assembly and function of these widespread filamentous nanomachines.
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Affiliation(s)
- Vladimir Pelicic
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, UK
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44
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Maikova A, Peltier J, Boudry P, Hajnsdorf E, Kint N, Monot M, Poquet I, Martin-Verstraete I, Dupuy B, Soutourina O. Discovery of new type I toxin-antitoxin systems adjacent to CRISPR arrays in Clostridium difficile. Nucleic Acids Res 2019. [PMID: 29529286 PMCID: PMC5961336 DOI: 10.1093/nar/gky124] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Clostridium difficile, a major human enteropathogen, must cope with foreign DNA invaders and multiple stress factors inside the host. We have recently provided an experimental evidence of defensive function of the C. difficile CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system important for its survival within phage-rich gut communities. Here, we describe the identification of type I toxin-antitoxin (TA) systems with the first functional antisense RNAs in this pathogen. Through the analysis of deep-sequencing data, we demonstrate the general co-localization with CRISPR arrays for the majority of sequenced C. difficile strains. We provide a detailed characterization of the overlapping convergent transcripts for three selected TA pairs. The toxic nature of small membrane proteins is demonstrated by the growth arrest induced by their overexpression. The co-expression of antisense RNA acting as an antitoxin prevented this growth defect. Co-regulation of CRISPR-Cas and type I TA genes by the general stress response Sigma B and biofilm-related factors further suggests a possible link between these systems with a role in recurrent C. difficile infections. Our results provide the first description of genomic links between CRISPR and type I TA systems within defense islands in line with recently emerged concept of functional coupling of immunity and cell dormancy systems in prokaryotes.
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Affiliation(s)
- Anna Maikova
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia.,Peter the Great St.Petersburg Polytechnic University, Saint Petersburg 195251, Russia
| | - Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Pierre Boudry
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Eliane Hajnsdorf
- UMR8261 (CNRS-Univ. Paris Diderot, Sorbonne Paris Cité), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Nicolas Kint
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France.,Département de Microbiologie et d'infectiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, J1E 4K8, Sherbrooke, QC, Canada
| | - Isabelle Poquet
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,INRA, UMR1319 Micalis (Microbiologie de l'Alimentation au service de la Santé), Domaine de Vilvert, 78352, Jouy-en-Josas Cedex, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, 75724 Paris Cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, 75724 Paris Cedex 15, France.,Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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45
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Rizzato C, Torres J, Kasamatsu E, Camorlinga-Ponce M, Bravo MM, Canzian F, Kato I. Potential Role of Biofilm Formation in the Development of Digestive Tract Cancer With Special Reference to Helicobacter pylori Infection. Front Microbiol 2019; 10:846. [PMID: 31110496 PMCID: PMC6501431 DOI: 10.3389/fmicb.2019.00846] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 04/02/2019] [Indexed: 12/16/2022] Open
Abstract
Bacteria are highly social organisms that communicate via signaling molecules and can assume a multicellular lifestyle to build biofilm communities. Until recently, complications from biofilm-associated infection have been primarily ascribed to increased bacterial resistance to antibiotics and host immune evasion, leading to persistent infection. In this theory and hypothesis article we present a relatively new argument that biofilm formation has potential etiological role in the development of digestive tract cancer. First, we summarize recent new findings suggesting the potential link between bacterial biofilm and various types of cancer to build the foundation of our hypothesis. To date, evidence has been particularly convincing for colorectal cancer and its precursor, i.e., polyps, pointing to several key individual bacterial species, such as Bacteroides fragilis, Fusobacterium nucleatum, and Streptococcus gallolyticus subsp. Gallolyticus. Then, we further extend this hypothesis to one of the most common bacterial infection in humans, Helicobacter pylori (Hp), which is considered a major cause of gastric cancer. Thus far, there has been no direct evidence linking in vivo Hp gastric biofilm formation to gastric carcinogenesis. Yet, we synthesize the information to support an argument that biofilm associated-Hp is potentially more carcinogenic, summarizing biological characteristics of biofilm-associated bacteria. We also discuss mechanistic pathways as to how Hp or other biofilm-associated bacteria control biofilm formation and highlight recent findings on Hp genes that influence biofilm formation, which may lead to strain variability in biofilm formation. This knowledge may open a possibility of developing targeted intervention. We conclude, however, that this field is still in its infancy. To test the hypothesis rigorously and to link it ultimately to gastric pathologies (e.g., premalignant lesions and cancer), studies are needed to learn more about Hp biofilms, such as compositions and biological properties of extracellular polymeric substance (EPS), presence of non-Hp microbiome and geographical distribution of biofilms in relation to gastric gland types and structures. Identification of specific Hp strains with enhanced biofilm formation would be helpful not only for screening patients at high risk for sequelae from Hp infection, but also for development of new antibiotics to avoid resistance, regardless of its association with gastric cancer.
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Affiliation(s)
- Cosmeri Rizzato
- Department of Translation Research and of New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Javier Torres
- Unidad de Investigación en Enfermedades Infecciosas, Unidades Médicas de Alta Especialidad Pediatría, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Elena Kasamatsu
- Instituto de Investigaciones en Ciencias de la Salud, National University of Asunción, Asunción, Paraguay
| | - Margarita Camorlinga-Ponce
- Unidad de Investigación en Enfermedades Infecciosas, Unidades Médicas de Alta Especialidad Pediatría, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Maria Mercedes Bravo
- Grupo de Investigación en Biología del Cáncer, Instituto Nacional de Cancerología, Bogotá, Colombia
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Ikuko Kato
- Department of Oncology and Pathology, Wayne State University School of Medicine, Detroit, MI, United States
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Arato V, Gasperini G, Giusti F, Ferlenghi I, Scarselli M, Leuzzi R. Dual role of the colonization factor CD2831 in Clostridium difficile pathogenesis. Sci Rep 2019; 9:5554. [PMID: 30944377 PMCID: PMC6447587 DOI: 10.1038/s41598-019-42000-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 03/12/2019] [Indexed: 01/01/2023] Open
Abstract
Clostridium difficile is a Gram-positive, anaerobic bacterium and the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis. C. difficile modulates its transition from a motile to a sessile lifestyle through a mechanism of riboswitches regulated by cyclic diguanosine monophosphate (c-di-GMP). Previously described as a sortase substrate positively regulated by c-di-GMP, CD2831 was predicted to be a collagen-binding protein and thus potentially involved in sessility. By overexpressing CD2831 in C. difficile and heterologously expressing it on the surface of Lactococcus lactis, here we further demonstrated that CD2831 is a collagen-binding protein, able to bind to immobilized collagen types I, III and V as well as native collagen produced by human fibroblasts. We also observed that the overexpression of CD2831 raises the ability to form biofilm on abiotic surface in both C. difficile and L. lactis. Notably, we showed that CD2831 binds to the collagen-like domain of the human complement component C1q, suggesting a role in preventing complement cascade activation via the classical pathway. This functional characterization places CD2831 in the Microbial Surface Components Recognizing Adhesive Matrix Molecule (MSCRAMMs) family, a class of virulence factors with a dual role in adhesion to collagen-rich tissues and in host immune evasion by binding to human complement components.
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Affiliation(s)
- Vanessa Arato
- Glaxo Smith Kline Vaccines, Via Fiorentina 1, 53100, Siena, Italy.,University of Padova, Department of Biomedical Sciences, 35131, Padua, Italy
| | - Gianmarco Gasperini
- GSK Vaccines Institute for Global Health (GVGH), Via Fiorentina 1, 53100, Siena, Italy
| | - Fabiola Giusti
- Glaxo Smith Kline Vaccines, Via Fiorentina 1, 53100, Siena, Italy
| | - Ilaria Ferlenghi
- Glaxo Smith Kline Vaccines, Via Fiorentina 1, 53100, Siena, Italy
| | - Maria Scarselli
- Glaxo Smith Kline Vaccines, Via Fiorentina 1, 53100, Siena, Italy
| | - Rosanna Leuzzi
- Glaxo Smith Kline Vaccines, Via Fiorentina 1, 53100, Siena, Italy.
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Molecular and Functional Analysis of the Type IV Pilus Gene Cluster in Streptococcus sanguinis SK36. Appl Environ Microbiol 2019; 85:AEM.02788-18. [PMID: 30635384 DOI: 10.1128/aem.02788-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/04/2019] [Indexed: 12/11/2022] Open
Abstract
Streptococcus sanguinis, dominant in the oral microbiome, is the only known streptococcal species possessing a pil gene cluster for the biosynthesis of type IV pili (Tfp). Although this cluster is commonly present in the genome of S. sanguinis, most of the strains do not express Tfp-mediated twitching motility. Thus, this study was designed to investigate the biological functions encoded by the cluster in the twitching-negative strain S. sanguinis SK36. We found that the cluster was transcribed as an operon, with three promoters located 5' to the cluster and one in the intergenic region between SSA_2307 and SSA_2305. Studies using promoter-cat fusion strains revealed that the transcription of the cluster was mainly driven by the distal 5' promoter, which is located more than 800 bases 5' to the first gene of the cluster, SSA_2318. Optimal expression of the cluster occurred at the early stationary growth phase in a CcpA-dependent manner, although a CcpA-binding consensus is absent in the promoter region. Expression of the cluster resulted in a short hairlike surface structure under transmission electron microscopy. Deletion of the putative pilin genes (SSA_2313 to SSA_2315) abolished the biosynthesis of this structure and significantly reduced the adherence of SK36 to HeLa and SCC-4 cells. Mutations in the pil genes downregulated biofilm formation by S. sanguinis SK36. Taken together, the results demonstrate that Tfp of SK36 are important for host cell adherence, but not for motility, and that expression of the pil cluster is subject to complex regulation.IMPORTANCE The proteins and assembly machinery of the type IV pili (Tfp) are conserved throughout bacteria and archaea, and yet the function of this surface structure differs from species to species and even from strain to strain. As seen in Streptococcus sanguinis SK36, the expression of the Tfp gene cluster results in a hairlike surface structure that is much shorter than the typical Tfp. This pilus is essential for the adherence of SK36 but is not involved in motility. Being a member of the highly diverse dental biofilm, perhaps S. sanguinis could more effectively utilize this structure to adhere to host cells and to interact with other microbes within the same niche.
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Cyclic Diguanylate Regulates Virulence Factor Genes via Multiple Riboswitches in Clostridium difficile. mSphere 2018; 3:3/5/e00423-18. [PMID: 30355665 PMCID: PMC6200980 DOI: 10.1128/msphere.00423-18] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In Clostridium difficile, the signaling molecule c-di-GMP regulates multiple processes affecting its ability to cause disease, including swimming and surface motility, biofilm formation, toxin production, and intestinal colonization. In this study, we used RNA-seq to define the transcriptional regulon of c-di-GMP in C. difficile. Many new targets of c-di-GMP regulation were identified, including multiple putative colonization factors. Transcriptional analyses revealed a prominent role for riboswitches in c-di-GMP signaling. Only a subset of the 16 previously predicted c-di-GMP riboswitches were functional in vivo and displayed potential variability in their response kinetics to c-di-GMP. This work underscores the importance of studying c-di-GMP riboswitches in a relevant biological context and highlights the role of the riboswitches in controlling gene expression in C. difficile. The intracellular signaling molecule cyclic diguanylate (c-di-GMP) regulates many processes in bacteria, with a central role in controlling the switch between motile and nonmotile lifestyles. Recent work has shown that in Clostridium difficile (also called Clostridioides difficile), c-di-GMP regulates swimming and surface motility, biofilm formation, toxin production, and intestinal colonization. In this study, we determined the transcriptional regulon of c-di-GMP in C. difficile, employing overexpression of a diguanylate cyclase gene to artificially manipulate intracellular c-di-GMP. Consistent with prior work, c-di-GMP regulated the expression of genes involved in swimming and surface motility. c-di-GMP also affected the expression of multiple genes encoding cell envelope proteins, several of which affected biofilm formation in vitro. A substantial proportion of the c-di-GMP regulon appears to be controlled either directly or indirectly via riboswitches. We confirmed the functionality of 11 c-di-GMP riboswitches, demonstrating their effects on downstream gene expression independent of the upstream promoters. The class I riboswitches uniformly functioned as “off” switches in response to c-di-GMP, while class II riboswitches acted as “on” switches. Transcriptional analyses of genes 3′ of c-di-GMP riboswitches over a broad range of c-di-GMP levels showed that relatively modest changes in c-di-GMP levels are capable of altering gene transcription, with concomitant effects on microbial behavior. This work expands the known c-di-GMP signaling network in C. difficile and emphasizes the role of the riboswitches in controlling known and putative virulence factors in C. difficile. IMPORTANCE In Clostridium difficile, the signaling molecule c-di-GMP regulates multiple processes affecting its ability to cause disease, including swimming and surface motility, biofilm formation, toxin production, and intestinal colonization. In this study, we used RNA-seq to define the transcriptional regulon of c-di-GMP in C. difficile. Many new targets of c-di-GMP regulation were identified, including multiple putative colonization factors. Transcriptional analyses revealed a prominent role for riboswitches in c-di-GMP signaling. Only a subset of the 16 previously predicted c-di-GMP riboswitches were functional in vivo and displayed potential variability in their response kinetics to c-di-GMP. This work underscores the importance of studying c-di-GMP riboswitches in a relevant biological context and highlights the role of the riboswitches in controlling gene expression in C. difficile.
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Poquet I, Saujet L, Canette A, Monot M, Mihajlovic J, Ghigo JM, Soutourina O, Briandet R, Martin-Verstraete I, Dupuy B. Clostridium difficile Biofilm: Remodeling Metabolism and Cell Surface to Build a Sparse and Heterogeneously Aggregated Architecture. Front Microbiol 2018; 9:2084. [PMID: 30258415 PMCID: PMC6143707 DOI: 10.3389/fmicb.2018.02084] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 08/14/2018] [Indexed: 12/11/2022] Open
Abstract
Clostridium difficile is an opportunistic entero-pathogen causing post-antibiotic and nosocomial diarrhea upon microbiota dysbiosis. Although biofilms could contribute to colonization, little is known about their development and physiology. Strain 630Δerm is able to form, in continuous-flow micro-fermentors, macro-colonies and submersed biofilms loosely adhesive to glass. According to gene expression data, in biofilm/planktonic cells, central metabolism is active and fuels fatty acid biosynthesis rather than fermentations. Consistently, succinate is consumed and butyrate production is reduced. Toxin A expression, which is coordinated to metabolism, is down-regulated, while surface proteins, like adhesins and the primary Type IV pili subunits, are over-expressed. C-di-GMP level is probably tightly controlled through the expression of both diguanylate cyclase-encoding genes, like dccA, and phosphodiesterase-encoding genes. The coordinated expression of genes controlled by c-di-GMP and encoding the putative surface adhesin CD2831 and the major Type IV pilin PilA1, suggests that c-di-GMP could be high in biofilm cells. A Bacillus subtilis SinR-like regulator, CD2214, and/or CD2215, another regulator co-encoded in the same operon as CD2214, control many genes differentially expressed in biofilm, and in particular dccA, CD2831 and pilA1 in a positive way. After growth in micro-titer plates and disruption, the biofilm is composed of robust aggregated structures where cells are embedded into a polymorphic material. The intact biofilm observed in situ displays a sparse, heterogeneous and high 3D architecture made of rods and micro-aggregates. The biofilm is denser in a mutant of both CD2214 and CD2215 genes, but it is not affected by the inactivation of neither CD2831 nor pilA1. dccA, when over-expressed, not only increases the biofilm but also triggers its architecture to become homogeneous and highly aggregated, in a way independent of CD2831 and barely dependent of pilA1. Cell micro-aggregation is shown to play a major role in biofilm formation and architecture. This thorough analysis of gene expression reprogramming and architecture remodeling in biofilm lays the foundation for a deeper understanding of this lifestyle and could lead to novel strategies to limit C. difficile spread.
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Affiliation(s)
- Isabelle Poquet
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France
| | - Laure Saujet
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Alexis Canette
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Marc Monot
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | | | - Jean-Marc Ghigo
- Unité de Génétique des Biofilms, Institut Pasteur, Paris, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Romain Briandet
- Micalis Institute, Institut National de la Recherche Agronomique, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bacteries Anaerobies, Institut Pasteur, Paris, France.,Sorbonne Paris Cité, Université Paris Diderot, Paris, France
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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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