Genome sequencing of multidrug resistant novel Clostridium sp. BL8 reveals its potential for pathogenicity
- Nachiket Prakash Marathe†1, 3,
- Sudarshan Anand Shetty†1,
- Vikram B Lanjekar2,
- Mandar Hemant Rasane1,
- Dilip R Ranade2 and
- Yogesh S Shouche1, 4Email author
© Marathe et al.; licensee BioMed Central Ltd. 2014
Received: 21 May 2014
Accepted: 13 July 2014
Published: 18 July 2014
The human gut microbiome is important for maintaining the health status of the host. Clostridia are key members of the human gut microbiome, carrying out several important functions in the gut environment. Hence understanding the role of different Clostridium species isolated from human gut is essential. The present study was aimed at investigating the role of novel Clostridium sp. isolate BL8 in human gut using genome sequencing as a tool.
The genome analysis of Clostridium sp. BL8 showed the presence of several adaptive features like bile resistance, presence of sensory and regulatory systems, presence of oxidative stress managing systems and presence of membrane transport systems. The genome of Clostridium sp. BL8 consists of a wide variety of virulence factors like phospholipase C (alpha toxin), hemolysin, aureolysin and exfoliative toxin A, as well as adhesion factors, proteases, Type IV secretion system and antibiotic resistance genes. In vitro antibiotic sensitivity testing showed that Clostridium sp. BL8 was resistant to 11 different tested antibiotics belonging to 6 different classes. The cell cytotoxicity assay confirmed the cytotoxic effect of Clostridium sp. BL8 cells, which killed 40% of the Vero cells after 4 hrs of incubation.
Clostridium sp. BL8 has adapted for survival in human gut environment, with presence of different adaptive features. The presence of several virulence factors and cell cytotoxic activity indicate that Clostridium sp. BL8 has a potential to cause infections in humans, however further in vivo studies are necessary to ascertain this fact.
KeywordsClostridium Virulence Antibiotic resistance Ion Torrent PGM™
The human gut is an intricate environment which harbors a large variety of microorganisms. The interaction between the host and the gut microbiome has an effect on the host health. The human gut microbiome is dominated by two bacterial phyla, Firmicutes and Bacteroidetes[1, 2]. The Firmicutes population in the gut is dominated by the genus Clostridium. Clostridia start to colonize the human gut from the first month of life. Clostridium species in the gut play vital roles in degradation of food products, production of vitamins and short chain fatty acids, maintaining gut homeostasis and shaping the mucosal immune system. Recent studies have shown that Clostridia are reduced in abundance in inflammatory conditions such as inflammatory bowel disease (IBD), which leads to the dysbiosis further leading to inflammation . Thus, Clostridia are key members of the human gut microbiome.
Although this is true, some pathogenic Clostridium species like C. difficile, C. perfringens and C. tetani have been described. These organisms cause fatal infections like colitis, gangrene and tetanus respectively [3–5]. Hence, understanding the role of Clostridium species isolated from the human gut is of paramount importance. In this study, we carried out genome sequencing of a novel Clostridium species (isolate BL8), isolated from the stool sample of a healthy Indian individual, in order to decipher the potential role of this organism in the human gut ecosystem. Our study demonstrates that Clostridium sp BL8 has a potential to cause infections in humans and lays basis for further studies to characterize this potential novel pathogen.
Material and methods
Genomic DNA extraction and 16S rRNA gene PCR and antibiotic sensitivity
Genomic DNA extraction and 16S rRNA gene sequencing was carried out as described earlier . The antibiotic sensitivity of Clostridium sp. BL8 was carried out using antibiotic discs purchased from HiMedia laboratories, Mumbai following the CLSI guidelines .
Genome sequencing and bioinformatic analysis
The genome sequencing using an Ion Torrent PGM™ and bioinformatic analysis was carried out using the methodology described by Shetty et al. .
The cell cytotoxicity assay was carried out by microculture tetrazolium (MTT) assay as described earlier . Briefly: 96-well microplate was seeded with 100 μl medium containing 10,000 Vero cells in suspension. After 24 hr incubation and attachment, the cells were treated with 100 μl of 1 × 105Clostridium sp. BL8 cell suspension or 100 μl cell free supernatant for 2 hrs and 4 hrs respectively, in triplicates. Cell suspension buffer and sterile culture medium were used as controls. Cell viability was determined by adding tetrazolium salt (5 mg/ml) (Sigma Aldrich, USA). After 3 hours of incubation at 37°C, media was removed and precipitated formazan was dissolve in 100 μl of DMSO. Absorbance was taken at 570 nm using an ELISA plate reader Spectra MAX250 (Molecular Devices, USA).
The isolate used in the study
Genomic features of Clostridium sp. BL8
The assembled genome of Clostridium sp. BL8 was 4,776,227 bp with an average coverage of 37×. This Whole Genome Shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession AUPA00000000. The list of all proteins annotated by RAST server is represented in Additional file 1: Table S1.
The genome of Clostridium sp. BL8 revealed the presence of adaptive features like bile resistance, presence of sensory and regulatory systems, presence of oxidative stress managing systems and presence of membrane transport systems. All these features are important for the survival of Clostridium sp. BL8 in the human gut .
Resistance to antibiotics
Antibiotic resistance genes detected in Clostridium sp. BL8 genome
Resistance tested against
Response regulator for bacitracin transporter BceR
bacitracin ABC transporter, ATP-binding protein
Metal-dependent beta-lactamase PhnP
Beta-lactamase (EC 22.214.171.124)
Ribosome protection-type tetracycline resistance proteins
Tetracycline efflux pump TetA
Zwittermicin A resistance protein ZmaR
Vancomycin B-type resistance protein VanW
Quinolone resistance protein
Erythromycin esterase type II
Horizontal gene transfer between pathogens and human commensals is an important factor for the dissemination of antibiotic resistance . BL8 genome has mobile genetic elements like integrase and transposes such as IS1380-Spn, ISSod4, IS1294, IS3/IS911, IS110 and IS4. Type IV secretion system are important for transfer of DNA and secretion of proteins in bacteria . BL8 genome encodes for type IV secretion system with presence of PilABC and PilMNO proteins and pilus regulator PilR. These systems would enable exchange of DNA between BL8 and other gut commensals.
Genes coding for virulence factors
The virulence genes were categorized into two categories 1) toxins, 2) exoenzyme, adhesins and others. 1) Toxins and hemolysins: C. perfringens is known to produce alpha toxin (Phospholipase C) which is responsible for myonecrosis eventually causing gangrene . Phospholipase C (EC 126.96.36.199) was detected in the genome of BL8 suggesting that it has a potential to cause muscle necrosis. The genes coding for hemolysin and hemolysin III were also detected in BL8 genome. All these genes are important virulence factors for C. perfringens. Proteins similar to aureolysin and exfoliative toxin A of Stahpyhlococcus were also detected in BL8 genome. Exfoliative toxin A is known as ‘epidermolytic toxins’ which cleaves upper epidermal layer of skin, while aureolysin is a known complement inhibitor [12, 13]. Both these genes are important for S. aureus pathogenesis.
2) Exoenzymes, adhensins and others: Secreted enzymes like proteases and serine proteases degrade host extracellular matrix allowing the entry of pathogens in the tissue, thus are important factors for virulence in bacterial pathogens. Secreted proteins like prepilin peptidase, HtrA family serine proteases, subtilisin-type proteinase, peptidase M23B were detected in BL8 genome. All these proteins play an important role in pathogenesis of various pathogens like Legionella pneumophila, Streptococcus pyogenes, Streptococcus suis, Pseudomonas aeruginosa, Salmonella typhimurium, Campylobacter jejuni and Helicobacter pylori [14–18].
Along with secreted proteins the genome of BL8 had myosin reactive antigen, which is reported to be important for virulence in Shigella flexneri. BL8 genome also contains platelet-activating factor acetylhydrolase and iron ABC uptake transporter similar to anthrachelin. The platelet-activating factor acetylhydrolase is a proinflammatory enzyme required for virulence, while anthrachelin is essential for virulence of Bacillus anthracis[20, 21]. Fibronectin/fibrinogen-binding protein, adhensins are important for adhesion and colonization of the pathogen on wound tissue and blood clots . Genes coding for both these factors were present in the genome of BL8. To aid the regulations of these genes, several transcriptional regulators belonging to AraC, DeoR, GntR, LysR, MarR and TetR families were detected in the genome of BL8. All these regulators have been reported to be important in the regulation of several virulence genes in pathogens [22, 23]. The presence of all these virulence genes and regulatory factors suggests that Clostridium sp. BL8 has a high potential for pathogenicity.
Clostridium sp. BL8 seems to have adapted for survival in the human gut environment, with presence of different adaptive features. Clostridium sp. BL8 genome showed presence of an array virulence factors encountered in different pathogens, suggesting that it has a high potential to cause infections in humans. This study thus, lays the basis for further in vivo and in vitro studies that are necessary to decipher the pathogenesis of infections that can be caused by a novel potential pathogen Clostridium sp. BL8 and guide in the treatment of these infections.
The authors are thankful to the Department of Biotechnology (DBT), Government of India, New Delhi, for funding (Microbial Culture Collection project, grant no: BT/PR10054/NDB/52/94/2007). Nachiket Marathe acknowledges Council of Scientific and Industrial Research (CSIR), New Delhi, for fellowship.
- Shetty SA, Marathe NP, Shouche YS: Opportunities and challenges for gut microbiome studies in the Indian population. Microbiome. 2013, 1 (1): 24-10.1186/2049-2618-1-24.PubMed CentralView ArticlePubMedGoogle Scholar
- Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A: Commensal Clostridia: leading players in the maintenance of gut homeostasis. Gut pathogens. 2013, 14: 31-33.Google Scholar
- Vincent C, Stephens DA, Loo VG, Edens TJ, Behr MA, Dewar K, Manges AR: Reductions in intestinal Clostridiales precede the development of nosocomial Clostridium difficile infection. Microbiome. 2013, 1 (1): 18-10.1186/2049-2618-1-18.PubMed CentralView ArticlePubMedGoogle Scholar
- Shimizu T, Ohtani K, Hirakawa H, Ohshima K, Yamashita A, Shiba T, Ogasawara N, Hattori M, Kuhara S, Hayashi H: Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci. 2002, 99 (2): 996-1001. 10.1073/pnas.022493799.PubMed CentralView ArticlePubMedGoogle Scholar
- Brüggemann H, Bäumer S, Fricke WF, Wiezer A, Liesegang H, Decker I, Herzberg C, Martinez-Arias R, Merkl R, Henne A, Gottschalk G: The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci. 2003, 100 (3): 1316-1321. 10.1073/pnas.0335853100.PubMed CentralView ArticlePubMedGoogle Scholar
- Marathe N, Shetty S, Lanjekar V, Ranade D, Shouche Y: Changes in human gut flora with age: an Indian familial study. BMC Microbiol. 2012, 12 (1): 222-10.1186/1471-2180-12-222.PubMed CentralView ArticlePubMedGoogle Scholar
- Clinical and Laboratory Standards Institute (CLSI): Methods for antimicrobial susceptibility testing of anaerobic bacteria; approved standard- seventh edition M11-A7.In CLSI. PA, USA: Wayne; 2007.Google Scholar
- Shetty SA, Marathe NP, Lanjekar V, Ranade D, Shouche YS: Comparative Genome Analysis of Megasphaera sp. Reveals Niche Specialization and Its Potential Role in the Human Gut. PLoS One. 2013, 8 (11): e79353-10.1371/journal.pone.0079353.PubMed CentralView ArticlePubMedGoogle Scholar
- Marathe NP, Rasane MH, Kumar H, Patwardhan AA, Shouche YS, Diwanay SS: In vitro antibacterial activity of Tabernaemontana alternifolia (Roxb) stem bark aqueous extracts against clinical isolates of methicillin resistant Staphylococcus aureus. Ann Clin Microbiol Antimicrob. 2013, 12 (1): 26-10.1186/1476-0711-12-26.PubMed CentralView ArticlePubMedGoogle Scholar
- Salyers AA, Gupta A, Wang Y: Human intestinal bacteria as reservoirs for antibiotic resistance genes. Trends Microbiol. 2004, 12 (9): 412-416. 10.1016/j.tim.2004.07.004.View ArticlePubMedGoogle Scholar
- Wallden K, Rivera-Calzada A, Waksman G: Type IV secretion systems: versatility and diversity in function. Cell Microbiol. 2010, 12 (9): 1203-1212. 10.1111/j.1462-5822.2010.01499.x.PubMed CentralView ArticlePubMedGoogle Scholar
- Bukowski M, Wladyka B, Dubin G: Exfoliative toxins of Staphylococcus aureus. Toxins. 2010, 2 (5): 1148-1165. 10.3390/toxins2051148.PubMed CentralView ArticlePubMedGoogle Scholar
- Laarman AJ, Ruyken M, Malone CL, van Strijp JA, Horswill AR, Rooijakkers SH: Staphylococcus aureus metalloprotease aureolysin cleaves complement C3 to mediate immune evasion. J Immunol. 2011, 186 (11): 6445-6453. 10.4049/jimmunol.1002948.View ArticlePubMedGoogle Scholar
- Liles MR, Edelstein PH, Cianciotto NP: The prepilin peptidase is required for protein secretion by and the virulence of the intracellular pathogen Legionella pneumophila. Molecular microbiol. 1999, 31 (3): 959-970. 10.1046/j.1365-2958.1999.01239.x.View ArticleGoogle Scholar
- Lyon WR, Caparon MG: Role for serine protease HtrA (DegP) of Streptococcus pyogenes in the biogenesis of virulence factors SpeB and the hemolysin streptolysin S. Infect Immun. 2004, 72 (3): 1618-1625. 10.1128/IAI.72.3.1618-1625.2004.PubMed CentralView ArticlePubMedGoogle Scholar
- Bonifait L, de la Cruz D-PM, Vaillancourt K, Bart C, Slater J, Frenette M, Gottschalk M, Grenier D: The cell envelope subtilisin-like proteinase is a virulence determinant for Streptococcus suis. BMC Microbiol. 2010, 10 (1): 42-10.1186/1471-2180-10-42.PubMed CentralView ArticlePubMedGoogle Scholar
- Feinbaum RL, Urbach JM, Liberati NT, Djonovic S, Adonizio A, Carvunis AR, Ausubel FM: Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model. PLoS Pathog. 2012, 8 (7): e1002813-10.1371/journal.ppat.1002813.PubMed CentralView ArticlePubMedGoogle Scholar
- Pallen MJ, Wren BW: The HtrA family of serine proteases. Mol Microbiol. 1997, 26 (2): 209-221. 10.1046/j.1365-2958.1997.5601928.x.View ArticlePubMedGoogle Scholar
- Oaks EV, Turbyfill KR: Myosin-cross-reactive epitope of Shigella flexneri invasion plasmid antigen B. Infect Immun. 1992, 60 (2): 557-564.PubMed CentralPubMedGoogle Scholar
- Pawlowic MC, Zhang K: Leishmania parasites possess a platelet-activating factor acetylhydrolase important for virulence. Mol Biochem Parasitol. 2012, 186 (1): 11-20. 10.1016/j.molbiopara.2012.08.005.PubMed CentralView ArticlePubMedGoogle Scholar
- Cendrowski S, MacArthur W, Hanna P: Bacillus anthracis requires siderophore biosynthesis for growth in macrophages and mouse virulence. Mol Microbiol. 2004, 51 (2): 407-417. 10.1046/j.1365-2958.2003.03861.x.View ArticlePubMedGoogle Scholar
- Michaux C, Sanguinetti M, Reffuveille F, Auffray Y, Posteraro B, Gilmore MS, Hartke A, Giard JC: SlyA is a transcriptional regulator involved in the virulence of Enterococcus faecalis. Infect Immun. 2011, 79 (7): 2638-2645. 10.1128/IAI.01132-10.PubMed CentralView ArticlePubMedGoogle Scholar
- Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R: The TetR family of transcriptional repressors. Microbiol Mol Biol Rev. 2005, 69 (2): 326-356. 10.1128/MMBR.69.2.326-356.2005.PubMed CentralView ArticlePubMedGoogle Scholar
- Mahony DE, Gilliatt E, Dawson S, Stockdale E, Lee SH: Vero cell assay for rapid detection of Clostridium perfringens enterotoxin. Appl Environ Microbiol. 1989, 55 (9): 2141-2143.PubMed CentralPubMedGoogle Scholar
- Ferreira CEA, Nakano V, Avila-Campos MJ: Cytotoxicity and antimicrobial susceptibility of Clostridium difficile isolated from hospitalized children with acute diarrhea. Anaerobe. 2004, 10 (3): 171-177. 10.1016/j.anaerobe.2004.02.003.View ArticlePubMedGoogle Scholar
This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.