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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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Krych Ł, Castro-Mejía JL, Forero-Junco LM, Moesby DN, Mikkelsen MB, Rasmussen MA, Sykulski M, Nielsen DS. DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq. Commun Biol 2019; 2:369. [PMID: 31633060 PMCID: PMC6787052 DOI: 10.1038/s42003-019-0617-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 09/17/2019] [Indexed: 11/10/2022] Open
Abstract
Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.
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Affiliation(s)
- Łukasz Krych
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
- GenXone S.A., 60-476 Poznań, Poland
| | - Josué L. Castro-Mejía
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Laura M. Forero-Junco
- Computational Biology and Microbial Ecology, Department of Biological Sciences, Universidad de los Andes, Bogotá, Colombia
| | - Daniel N. Moesby
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Morten B. Mikkelsen
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
| | - Morten A. Rasmussen
- Chemometrics and Analytical Technology, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Dennis S. Nielsen
- Food Microbiology and Fermentation, Department of Food Science, University of Copenhagen, 1958 Frederiksberg C, Denmark
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3
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Rodriguez C, Van Broeck J, Taminiau B, Delmée M, Daube G. Clostridium difficile infection: Early history, diagnosis and molecular strain typing methods. Microb Pathog 2016; 97:59-78. [PMID: 27238460 DOI: 10.1016/j.micpath.2016.05.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 04/18/2016] [Accepted: 05/02/2016] [Indexed: 01/05/2023]
Abstract
Recognised as the leading cause of nosocomial antibiotic-associated diarrhoea, the incidence of Clostridium difficile infection (CDI) remains high despite efforts to improve prevention and reduce the spread of the bacterium in healthcare settings. In the last decade, many studies have focused on the epidemiology and rapid diagnosis of CDI. In addition, different typing methods have been developed for epidemiological studies. This review explores the history of C. difficile and the current scope of the infection. The variety of available laboratory tests for CDI diagnosis and strain typing methods are also examined.
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Affiliation(s)
- C Rodriguez
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.
| | - J Van Broeck
- Belgian Reference Centre for Clostridium Difficile (NRC), Pôle de microbiologie médicale, Université Catholique de Louvain, Brussels, Belgium
| | - B Taminiau
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - M Delmée
- Belgian Reference Centre for Clostridium Difficile (NRC), Pôle de microbiologie médicale, Université Catholique de Louvain, Brussels, Belgium
| | - G Daube
- Food Science Department, FARAH, Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
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4
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Gebreyes WA, Adkins PRF. The use of pulsed-field gel electrophoresis for genotyping of Clostridium difficile. Methods Mol Biol 2015; 1301:95-101. [PMID: 25862051 DOI: 10.1007/978-1-4939-2599-5_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Genotyping approaches are important for tracking infectious agents and can be used for various purposes. Pulsed-Field Gel Electrophoresis (PFGE) is among the highly discriminatory genotyping approaches commonly used for characterizing Clostridium difficile. Other genotyping methods used for C. difficile include Ribotyping, Restriction Endonuclease Assay (REA), Multilocus Variable Number Tandem Repeats (VNTR) Assay, and others. PFGE has a high discriminatory power, high reproducibility, and typeability. We utilized PFGE for typing C. difficile isolates of porcine and human origin. We used a macrorestriction fragment analysis of an intact genomic DNA using SmaI, a rare cutting restriction endonuclease. Using a Contour-Clamped Homogeneous Electric Field (CHEF) system with running conditions of 120° angle; initial switch time of 5 s; final switch time of 40 s with a run time of 18 h in a low-melting temperature agarose (Seakem Gold); and 0.5× TBE circulated in the CHEF system at 6 V/cm [CDC (2014) Pulsenet. http://www.cdc.gov/pulsenet/index.html . Accessed 22 Aug 2014] supported by 14 °C cooling module, we were able to separate very large DNA fragments (up to 2 Mb).
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Affiliation(s)
- Wondwossen A Gebreyes
- Department of Veterinary Preventive Medicine, Infectious Diseases Molecular Epidemiology Laboratory, The Ohio State University, Columbus, OH, USA,
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5
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Cohen SH, Gerding DN, Johnson S, Kelly CP, Loo VG, McDonald LC, Pepin J, Wilcox MH. Clinical Practice Guidelines for Clostridium difficile Infection in Adults: 2010 Update by the Society for Healthcare Epidemiology of America (SHEA) and the Infectious Diseases Society of America (IDSA). Infect Control Hosp Epidemiol 2015; 31:431-55. [PMID: 20307191 DOI: 10.1086/651706] [Citation(s) in RCA: 2180] [Impact Index Per Article: 242.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Since publication of the Society for Healthcare Epidemiology of America position paper onClostridium difficileinfection in 1995, significant changes have occurred in the epidemiology and treatment of this infection.C. difficileremains the most important cause of healthcare-associated diarrhea and is increasingly important as a community pathogen. A more virulent strain ofC. difficilehas been identified and has been responsible for more-severe cases of disease worldwide. Data reporting the decreased effectiveness of metronidazole in the treatment of severe disease have been published. Despite the increasing quantity of data available, areas of controversy still exist. This guideline updates recommendations regarding epidemiology, diagnosis, treatment, and infection control and environmental management.
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Affiliation(s)
- Stuart H Cohen
- Department of Internal Medicine, Division of Infectious and Immunologic Diseases, University of California Davis Medical Center, Sacramento, California, USA
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6
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Dingle TC, MacCannell DR. Molecular Strain Typing and Characterisation of Toxigenic Clostridium difficile. METHODS IN MICROBIOLOGY 2015. [DOI: 10.1016/bs.mim.2015.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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An overview of various typing methods for clinical epidemiology of the emerging pathogen Stenotrophomonas maltophilia. Diagn Microbiol Infect Dis 2014; 81:219-26. [PMID: 25592000 DOI: 10.1016/j.diagmicrobio.2014.11.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2014] [Revised: 10/28/2014] [Accepted: 11/08/2014] [Indexed: 11/24/2022]
Abstract
Typing of bacterial isolates has been used for decades to study local outbreaks as well as in national and international surveillances for monitoring newly emerging resistant clones. Despite being recognized as a nosocomial pathogen, the precise modes of transmission of Stenotrophomonas maltophilia in health care settings are unknown. Due to the high genetic diversity observed among S. maltophilia clinical isolates, the typing results might be better interpreted if also environmental strains were included. This could help to identify preventative measures to be designed and implemented for decreasing the possibility of outbreaks and nosocomial infections. In this review, we attempt to provide an overview on the most common typing methods used for clinical epidemiology of S. maltophilia strains, such as PCR-based fingerprinting analyses, pulsed-field gel electrophoresis, multilocus variable number tandem repeat analysis, and multilocus sequence type. Application of the proteomic-based mass spectrometry by matrix-assisted laser desorption ionization-time of flight is also described. Improvements of typing methods already in use have to be achieved to facilitate S. maltophilia infection control at any level. In the near future, when novel Web-based platforms for rapid data processing and analysis will be available, whole genome sequencing technologies will likely become a highly powerful tool for outbreak investigations and surveillance studies in routine clinical practices.
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Extended multilocus variable-number tandem-repeat analysis of Clostridium difficile correlates exactly with ribotyping and enables identification of hospital transmission. J Clin Microbiol 2011; 49:3523-30. [PMID: 21849691 DOI: 10.1128/jcm.00546-11] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PCR ribotyping is currently used in many countries for epidemiological investigation to track transmission and to identify emerging variants of Clostridium difficile. Although PCR ribotyping differentiates over 300 types, it is not always sufficiently discriminatory for epidemiological investigations particularly for common ribotypes, e.g., ribotypes 027, 106, and 017. Multilocus variable-number tandem-repeat analysis (MLVA) is a highly discriminatory molecular subtyping method that has been applied to a number of bacterial species for high-level subtyping. Two MLVA typing schemes for C. difficile have been previously published, each utilizing seven variable-number tandem-repeat (VNTR) loci on the genome with four loci common to both schemes. Although these schemes are good genotyping methods with the ability to discriminate between isolates, they do not identify the ribotype. We show here that increasing the number of VNTR loci to 15, creating the extended MLVA (eMLVA) scheme, we have successfully subtyped all clinically significant ribotypes while still clustering isolates in concordance with PCR ribotyping. The eMLVA scheme developed here provides insight into the genetic diversity of the C. difficile population at both global and cross-infection clusters in patient levels, with the possibility of replacing PCR ribotyping.
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10
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Green LM, Worthington T, Hilton AC, Lambert PA. Genetic characterization of clinical isolates of Clostridium difficile using an optimized RAPD protocol and PCR ribotyping reveals strain diversity between two tertiary referral Trusts in the West Midlands, UK. J Med Microbiol 2011; 60:1287-1291. [PMID: 21511887 DOI: 10.1099/jmm.0.030999-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Epidemiological investigations of Clostridium difficile often focus on differences between separate geographical areas. In this investigation, two populations of C. difficile recovered from separate tertiary referral Trusts within the West Midlands, UK, were characterized using both PCR ribotyping and an optimized RAPD (random amplification of polymorphic DNA) protocol. The PCR ribotyping and RAPD methodologies identified differences between the two C. difficile populations, in both the prevalence and the diversity of types identified. The use of PCR ribotyping in conjunction with RAPD further categorized different types within defined PCR ribotypes, identifying different types within the same PCR ribotype and therefore providing a greater discriminatory power than either of the methods when used alone. The differences observed in this study between the two Trusts in the distribution of both RAPD 'type' and PCR ribotype demonstrate the diversity that is present amongst isolates of C. difficile within a relatively small geographical area and warrants a need for further investigation into the local epidemiology of C. difficile.
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Affiliation(s)
- Lauren M Green
- Aston University, School of Life & Health Sciences, Aston Triangle, Birmingham B4 7ET, UK
| | - Tony Worthington
- Aston University, School of Life & Health Sciences, Aston Triangle, Birmingham B4 7ET, UK
| | - Anthony C Hilton
- Aston University, School of Life & Health Sciences, Aston Triangle, Birmingham B4 7ET, UK
| | - Peter A Lambert
- Aston University, School of Life & Health Sciences, Aston Triangle, Birmingham B4 7ET, UK
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Solomon K, Murray S, Scott L, McDermott S, Drudy D, Martin A, O'Donoghue C, Skally M, Burns K, Fenelon L, Fitzpatrick F, Kyne L, Fanning S. An investigation of the subtype diversity of clinical isolates of Irish Clostridium difficile ribotypes 027 and 078 by repetitive-extragenic palindromic PCR. J Med Microbiol 2011; 60:1080-1087. [PMID: 21459905 DOI: 10.1099/jmm.0.029983-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A repetitive-extragenic palindromic PCR (rep-PCR) subtyping method (DiversiLab) in conjunction with ribotyping, toxinotyping and antimicrobial-susceptibility testing was used to detect subtypes within Clostridium difficile ribotypes 027 and 078. Clinical isolates of ribotypes 027 (toxinotype III) (n = 30) and 078 (toxinotype V) (n = 23) were provided by health-care facilities across the Republic of Ireland over 2 months in 2006 and 1 month in 2009. Ribotype 027 isolates were significantly more related to each other (9 different subtype profiles) when compared to ribotype 078 isolates (14 different profiles) (P = 0.001; cut-off >90 % similarity). Almost half of ribotype 078 isolates (45.5 %) showed no relationship to each other. The clonality of ribotype 027 isolates suggests effective adaptation to the human niche, whereas the considerable genetic diversity within ribotype 078 isolates suggests that they may have originated from a variety of sources. Subtyping correlated well with antimicrobial susceptibility, in particular clindamycin susceptibility for ribotype 027, but diverse antimicrobial-susceptibility profiles were seen in ribotype 078 isolates, even within a single health-care facility. Between 2006 and 2009, a change in the predominant subtype of ribotype 027 was seen, with the recent clone representing half of all ribotype 027 isolates studied. This strain exhibited 89 % similarity to a rep-PCR profile of the North American NAP-1 strain.
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Affiliation(s)
- K Solomon
- UCD Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - S Murray
- UCD Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - L Scott
- Department of Clinical Microbiology, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - S McDermott
- Department of Clinical Microbiology, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - D Drudy
- UCD Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - A Martin
- Department of Medicine for the Older Person, Mater Misericordiae University Hospital, Eccles Street, Dublin 7, Ireland
- UCD Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - C O'Donoghue
- Department of Medicine for the Older Person, Mater Misericordiae University Hospital, Eccles Street, Dublin 7, Ireland
- UCD Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - M Skally
- Health Protection and Surveillance Centre, Gardiner Street, Dublin 1, Ireland
- Department of Clinical Microbiology, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - K Burns
- Department of Clinical Microbiology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
| | - L Fenelon
- Department of Clinical Microbiology, St Vincent's University Hospital, Elm Park, Dublin 4, Ireland
| | - F Fitzpatrick
- Department of Clinical Microbiology, Beaumont Hospital, Beaumont Road, Dublin 9, Ireland
- Health Protection and Surveillance Centre, Gardiner Street, Dublin 1, Ireland
| | - L Kyne
- Department of Medicine for the Older Person, Mater Misericordiae University Hospital, Eccles Street, Dublin 7, Ireland
- UCD Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
| | - S Fanning
- UCD Veterinary Sciences Centre, University College Dublin, Belfield, Dublin 4, Ireland
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Pasanen T, Kotila S, Horsma J, Virolainen A, Jalava J, Ibrahem S, Antikainen J, Mero S, Tarkka E, Vaara M, Tissari P. Comparison of repetitive extragenic palindromic sequence-based PCR with PCR ribotyping and pulsed-field gel electrophoresis in studying the clonality of Clostridium difficile. Clin Microbiol Infect 2011; 17:166-75. [DOI: 10.1111/j.1469-0691.2010.03221.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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13
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Joshy L, Chaudhry R, Dhawan B. Detection and characterization of Clostridium difficile from patients with antibiotic-associated diarrhoea in a tertiary care hospital in North India. J Med Microbiol 2009; 58:1657-1659. [DOI: 10.1099/jmm.0.000125-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Lovely Joshy
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Benu Dhawan
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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15
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Lin CW, Chiou CS, Chang YC, Yang TC. Comparison of pulsed-field gel electrophoresis and three rep-PCR methods for evaluating the genetic relatedness of Stenotrophomonas maltophilia isolates. Lett Appl Microbiol 2009; 47:393-8. [PMID: 19146527 DOI: 10.1111/j.1472-765x.2008.02443.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS In this study, three facile repetitive-sequence PCR (rep-PCR) techniques have been compared with the pulsed-field gel electrophoresis (PFGE) method for differentiating the genetic relatedness of clinical Stenotrophomonas maltophilia isolates. METHODS AND RESULTS The dendrograms of 20 S. maltophilia isolates were constructed based on the data obtained from PFGE and three PCR-based methods, i.e. enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), BOX-PCR and repetitive extragenic palindromic-PCR (REP-PCR). When compared with PFGE, ERIC-PCR displayed a much lower discriminatory power, whereas BOX-PCR and REP-PCR had a comparable discriminatory power for close genetic-related isolates. CONCLUSION BOX-PCR and REP-PCR can be convenient and effective methods for evaluating the close genetic relatedness of clinical S. maltophilia isolates. SIGNIFICANCE AND IMPACT OF THE STUDY A rapid method for determining S. maltophilia's close genetic relatedness provides a convenient tool for understanding the epidemiology of S. maltophilia.
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Affiliation(s)
- C-W Lin
- Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung, Taiwan
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16
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Indra A, Huhulescu S, Schneeweis M, Hasenberger P, Kernbichler S, Fiedler A, Wewalka G, Allerberger F, Kuijper EJ. Characterization of Clostridium difficile isolates using capillary gel electrophoresis-based PCR ribotyping. J Med Microbiol 2008; 57:1377-1382. [PMID: 18927415 PMCID: PMC2884938 DOI: 10.1099/jmm.0.47714-0] [Citation(s) in RCA: 167] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have developed a Clostridium difficile PCR ribotyping method based on capillary gel electrophoresis and have compared it with conventional PCR ribotyping. A total of 146 C. difficile isolates were studied: five isolates were reference strains (PCR ribotypes 001, 014, 017, 027 and 053); 141 were clinical isolates comprising 39 Austrian PCR ribotypes collected in the period 2006–2007 at 25 Austrian healthcare facilities. Capillary gel electrophoresis yielded up to 11 fragments per isolate and 47 ribotype patterns. All but one of the five PCR ribotypes of reference strains were clearly reflected in the chromatograms of capillary-based typing. Capillary gel electrophoresis divided 24 isolates belonging to PCR ribotype type 014 into seven subgroups, whereas subtyping the same isolates using multiple-locus variable-number tandem-repeat analysis yielded three unrelated subgroups, without obvious correlation to sr subgroups. Using a web-based software program (http://webribo.ages.at), we were able to correctly identify these 014 isolates by simply allocating the seven subgroup patterns to one ribotype, i.e. to PCR ribotype 014. We consider capillary gel electrophoresis-based PCR ribotyping to be a way of overcoming the problems associated with inter-laboratory comparisons of typing results, while at the same time substantially diminishing the hands-on time for PCR ribotyping.
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Affiliation(s)
- A Indra
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - S Huhulescu
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | | | - P Hasenberger
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - S Kernbichler
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - A Fiedler
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - G Wewalka
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - F Allerberger
- Austrian Agency for Health and Food Safety (AGES), Vienna, Austria
| | - E J Kuijper
- Department of Medical Microbiology, Center of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
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Martin H, Willey B, Low DE, Staempfli HR, McGeer A, Boerlin P, Mulvey M, Weese JS. Characterization of Clostridium difficile strains isolated from patients in Ontario, Canada, from 2004 to 2006. J Clin Microbiol 2008; 46:2999-3004. [PMID: 18650360 PMCID: PMC2546775 DOI: 10.1128/jcm.02437-07] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 03/18/2008] [Accepted: 07/14/2008] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile is the bacterium most commonly surmised to cause antimicrobial- and hospital-associated diarrhea in developed countries worldwide, and such infections are thought to be increasing in frequency and severity. A laboratory-based study was carried out to characterize C. difficile strains isolated from persons in Ontario, Canada, during 2004 to 2006 according to toxin type (enterotoxin A, cytotoxin B, and binary toxin [CDT]), tcdC gene characterization, ribotyping, pulsed-field gel electrophoresis, and toxinotyping. Clostridium difficile was isolated from 1,080/1,152 (94%) samples from 21 diagnostic laboratories. Isolates with toxin profiles A(+) B(+) CDT(-), A(+) B(+) CDT(+), A(-) B(+) CDT(-), and A(-) B(+) CDT(+) accounted for 63%, 34%, 2.4%, and 0.6% of isolates, respectively. Alterations in tcdC were detected in six different ribotypes, including ribotype 027. A total of 39 different ribotypes were identified, with ribotype 027/North American pulsotype 1 (NAP1), an internationally recognized outbreak strain associated with severe disease, being the second most common ribotype (19% of isolates). Transient resistance to metronidazole was identified in 19 (1.8%) isolates. While a large number of ribotypes were found, a few predominated across the province. The high prevalence and wide distribution of ribotype 027/NAP1 are disconcerting in view of the severity of disease associated with it.
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Affiliation(s)
- H Martin
- Department of Clinical Studies, University of Guelph, Guelph, Ontario, Canada
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18
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Sadeghifard N, Gürtler V, Beer M, Seviour RJ. The mosaic nature of intergenic 16S-23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains. Appl Environ Microbiol 2006; 72:7311-23. [PMID: 16980415 PMCID: PMC1636144 DOI: 10.1128/aem.01179-06] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2006] [Accepted: 09/07/2006] [Indexed: 11/20/2022] Open
Abstract
Clostridium difficile is a major spore-forming environmental pathogen that causes serious health problems in patients undergoing antibiotic therapy. Consequently, reliable and sensitive methods for typing individual strains are required for epidemiological and environmental studies. Ribotyping is generally considered the best method, but it fails to account for sequence diversity which might exist in intergenic 16S-23S rRNA spacer regions (ISRs) within and among strains of this organism. Therefore, this study was undertaken to compare the sequence of each individual ISR in five strains of C. difficile to explore the extent of this diversity and see whether such information might provide the basis for more sensitive and discriminatory strain typing methods. After targeted PCR amplification, cloning, and sequencing, the diversity of the ISRs was used as a measure of rRNA operon copy number. In C. difficile strains 630, ATCC 43593, A, and B, 11, 11, 7, and 8 ISR length variants, respectively, were found (containing different combinations of sequence groups [i to xiii]), suggesting 11, 11, 7, and 8 rrn copies in the respective strains. Many ISRs of the same length differed markedly in their sequences, and some of these were restricted in occurrence to a single strain. Most of these ISRs did not contain any tRNA genes, and only single copies of the tRNA(Ala) gene were found in those that did. The presence of ISR sequence groups (i to xiii) varied between strains, with some found in one, two, three, four, or all five strains. We conclude that the intergenic 16S-23S rRNA spacer regions showed a high degree of diversity, not only among the rrn operons in different strains and different rrn copies in a single strain but also among ISRs of the same length. It appears that C. difficile ISRs vary more at the inter- and intragenic levels than those of other species as determined by empirical comparison of sequences. The precise characterization of these sequences has demonstrated a high level of mosaic sequence block rearrangements that are present or absent in multiple strain-variable rrn copies within and between five different strains of C. difficile.
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Affiliation(s)
- Nourkhoda Sadeghifard
- Biotechnology Research Centre, La Trobe University, Bendigo, Victoria 3552, Australia
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MacCannell DR, Louie TJ, Gregson DB, Laverdiere M, Labbe AC, Laing F, Henwick S. Molecular analysis of Clostridium difficile PCR ribotype 027 isolates from Eastern and Western Canada. J Clin Microbiol 2006; 44:2147-52. [PMID: 16757612 PMCID: PMC1489423 DOI: 10.1128/jcm.02563-05] [Citation(s) in RCA: 140] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The prevalence and characteristics of PCR ribotype 027 strains of Clostridium difficile have come into question following recent outbreaks in Eastern Canada and elsewhere. In order to determine the distribution of this strain in other regions in Canada, we screened a bank of 1,419 isolates recovered from three different Canadian health regions between 2000 and 2004. Among isolates from a Montreal area hospital, PCR ribotype 027 strains represented 115/153 strains (75.2%) from 2003 to 2004, but ribotype 027 strains were absent in 2000 and 2001. In Calgary, by contrast, ribotype 027 rates have remained relatively stable over 4 years of surveillance, representing 51/685 (7.4%) hospital isolates and 62/373 (16.6%) strains from the community (P < 0.001). PCR ribotype 027 accounted for 8/135 (5.9%) hospital isolates in the Fraser Health Region in 2004. repetitive extragenic palindromic PCR was used to subtype a random selection of 027 isolates from each region. All 10 of the isolates from Quebec were of a single subtype, which was also dominant among isolates from Alberta (8/10 isolates) and British Columbia (6/8 isolates). Comparative sequencing of the tcdC repressor gene confirmed the documented 18-bp deletion and identified a second, single-base-pair deletion at position 117. Both deletions were conserved across all three provinces and were identified in a United Kingdom reference strain. The presence of a frameshift in the early portion of the tcdC gene implies serious functional disruption and may contribute to the hypervirulence of the 027 phenotype. PCR ribotype 027 strains appear to be widely distributed, to predate the Montreal outbreak, and to have measurable community presence in Western Canada.
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Affiliation(s)
- Duncan R MacCannell
- Department of Microbiology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada.
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Akerlund T, Svenungsson B, Lagergren A, Burman LG. Correlation of disease severity with fecal toxin levels in patients with Clostridium difficile-associated diarrhea and distribution of PCR ribotypes and toxin yields in vitro of corresponding isolates. J Clin Microbiol 2006; 44:353-8. [PMID: 16455883 PMCID: PMC1392646 DOI: 10.1128/jcm.44.2.353-358.2006] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We investigated in vivo and in vitro yields of toxins A and B from and PCR ribotypes of Clostridium difficile isolates from 164 patients with differing severities of C. difficile-associated diarrhea (CDAD) (patients were grouped as follows: <3 loose stools per day, n = 45; 3 to 10 per day, n = 97; >10 per day, n = 22). The median fecal toxin levels in each group were 0.5, 6.8, and 149 U/g feces (P < 0.001), respectively. Patients with severe diarrhea also had more-frequent occurrence of blood in stool and vomiting, but there was no association with fecal toxin levels per se. There was no correlation between fecal toxin level and toxin yield in vitro for the corresponding C. difficile isolate or between its PCR ribotype and disease severity. A broad range of toxin yields among isolates belonging to major PCR ribotypes indicated a presence of many subtypes. We hypothesize that bacterial and host factors that affect C. difficile toxin levels in feces are important determinants of symptoms in CDAD patients. An inverse correlation between toxin yield and spore count (r = 0.66) in stationary-phase cultures supported the notion that toxin production and sporulation represent opposite alternative survival strategies for C. difficile cells facing nutrient shortage.
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Affiliation(s)
- Thomas Akerlund
- Department of Bacteriology, Swedish Institute for Infectious Disease Control, S-17182, Solna, Sweden.
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