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Abad-Fau A, Sevilla E, Martín-Burriel I, Moreno B, Bolea R. Update on Commonly Used Molecular Typing Methods for Clostridioides difficile. Microorganisms 2023; 11:1752. [PMID: 37512924 PMCID: PMC10384772 DOI: 10.3390/microorganisms11071752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Eloísa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
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Neoh HM, Tan XE, Sapri HF, Tan TL. Pulsed-field gel electrophoresis (PFGE): A review of the "gold standard" for bacteria typing and current alternatives. INFECTION GENETICS AND EVOLUTION 2019; 74:103935. [PMID: 31233781 DOI: 10.1016/j.meegid.2019.103935] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 12/01/2022]
Abstract
Pulsed-field gel electrophoresis (PFGE) is considered the "gold standard" for bacteria typing. The method involves enzyme restriction of bacteria DNA, separation of the restricted DNA bands using a pulsed-field electrophoresis chamber, followed by clonal assignment of bacteria based on PFGE banding patterns. Various PFGE protocols have been developed for typing different bacteria, leading it to be one of the most widely used methods for phylogenetic studies, food safety surveillance, infection control and outbreak investigations. On the other hand, as PFGE is lengthy and labourious, several PCR-based typing methods can be used as alternatives for research purposes. Recently, matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and whole genome sequencing (WGS) have also been proposed for bacteria typing. In fact, as WGS provides more information, such as antimicrobial resistance and virulence of the tested bacteria in comparison to PFGE, more and more laboratories are currently transitioning from PFGE to WGS for bacteria typing. Nevertheless, PFGE will remain an affordable and relevant technique for small laboratories and hospitals in years to come.
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Affiliation(s)
- Hui-Min Neoh
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, Malaysia.
| | - Xin-Ee Tan
- Department of Infection and Immunity, School of Medicine, Jichi Medical University, Japan
| | - Hassriana Fazilla Sapri
- Department of Medical Microbiology & Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
| | - Toh Leong Tan
- Department of Emergency Medicine, Faculty of Medicine, Universiti Kebangsaan Malaysia, Malaysia
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How to: molecular investigation of a hospital outbreak. Clin Microbiol Infect 2018; 25:688-695. [PMID: 30287413 DOI: 10.1016/j.cmi.2018.09.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 09/19/2018] [Accepted: 09/23/2018] [Indexed: 12/11/2022]
Abstract
BACKGROUND Studying hospital outbreaks by using molecular tools, i.e. synthesizing the molecular epidemiology data to its appropriate clinical-epidemiologic context, is crucial in order to identify infection source, infer transmission dynamics, appropriately allocate prevention resources and implement control measures. Whole-genome sequencing (WGS) of pathogens has become the reference standard, as it is becoming more accessible and affordable. Consequently, sequencing of the full pathogen genome via WGS and major progress in fit-for-purpose genomic data analysis tools and interpretation is revolutionizing the field of outbreak investigations in hospitals. Metagenomics is an additional evolving field that might become commonly used in the future for outbreak investigations. Nevertheless, practitioners are frequently limited in terms of WGS or metagenomics, especially for local outbreak analyses, as a result of costs or logistical considerations, reduced or lack of locally available resources and/or expertise. As a result, traditional approaches, including pulsed-field gel electrophoresis, repetitive-element palindromic PCR and multilocus sequence typing, along with other typing methods, are still widely used. AIMS To provide practitioners with evidenced-based action plans for usage of the various typing techniques in order to investigate the molecular epidemiology of nosocomial outbreaks, of clinically significant pathogens in acute-care hospitals. SOURCES PubMed search with relevant keywords along with personal collection of relevant publications. CONTENT Representative case scenarios and critical review of the relevant scientific literature. IMPLICATIONS The review provides practical action plans to manage molecular epidemiologic investigations of outbreaks caused by clinically significant nosocomial pathogens, while prioritizing the use and timely integration of the various methodologies.
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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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Evidence of a clonal expansion of Streptococcus pneumoniae serotype 19A in adults as in children assessed by the DiversiLab® system. Eur J Clin Microbiol Infect Dis 2014; 33:2067-73. [DOI: 10.1007/s10096-014-2148-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 04/28/2014] [Indexed: 11/26/2022]
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Comparison between phage-open-reading frame typing and automated repetitive-sequence-based PCR for typing MRSA isolates. J Antibiot (Tokyo) 2014; 67:565-9. [DOI: 10.1038/ja.2014.41] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 02/20/2014] [Accepted: 03/11/2014] [Indexed: 11/08/2022]
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Corbellini S, Piccinelli G, De Francesco MA, Ravizzola G, Bonfanti C. Molecular epidemiology of Clostridium difficile strains from nosocomial-acquired infections. Folia Microbiol (Praha) 2013; 59:173-9. [PMID: 24081935 DOI: 10.1007/s12223-013-0281-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2013] [Accepted: 09/19/2013] [Indexed: 12/18/2022]
Abstract
The purpose of this study is to analyze isolates of Clostridium difficile from patients with nosocomial acquired infection in respect to their molecular type and antimicrobial susceptibility. Fifty-nine randomly selected clinical isolates were characterized. Molecular typing was performed by rep-PCR (DiversiLab). Isolates were tested by disk diffusion towards 11 different antibiotics. All isolates were susceptible to metronidazole and vancomycin. Fifty five (93 %) isolates were resistant to erythromycin and fifty six (95 %) exhibited resistance to both clindamycin and moxifloxacin. Twenty rep-PCR types were identified, but most clinical isolates formed four major rep-PCR clusters (A1 24/59, 40 %; A2 20/59, 33 %; A3 5/59, 8 %; A4 3/59, 5 %). These results show high genetic variability, which demonstrate clearly the complexity of the strains of C. difficile and also show an increasing rate of resistance to fluoroquinolones in our region emphasizing the importance of implementing surveillance programs in order to prevent further spread of resistance in C. difficile.
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Affiliation(s)
- Silvia Corbellini
- Institute of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, P. le Spedali Civili, 1, 25123, Brescia, Italy
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Lukinmaa-Åberg S, Horsma J, Pasanen T, Mero S, Aulu L, Vaara M, Siitonen A, Antikainen J. Applicability of DiversiLab repetitive sequence-based PCR method in epidemiological typing of enterohemorrhagic Escherichia coli (EHEC). Foodborne Pathog Dis 2013; 10:632-8. [PMID: 23692078 DOI: 10.1089/fpd.2012.1411] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Enterohemorrhagic Escherichia coli (EHEC) causes diarrhea, often with severe complications. Rapid and discriminatory typing of EHEC using advanced molecular methods is needed for determination of the genetic relatedness of clones responsible for foodborne outbreaks and for finding out the transmission sources of the outbreaks. This study evaluated the potential of DiversiLab, a semiautomated repetitive sequence-based polymerase chain reaction method for the genotyping of EHEC strains. A set of 52 EHEC strains belonging to 15 O:H serotypes was clustered into 10 DiversiLab groups. All of the O157 strains and one O55 strain were classified into the same group based on a 90% similarity threshold. The other serotypes were classified to their own DiversiLab group, with the exception of one R:H(-) strain that was grouped with O5:H(-) strains. In addition, O26 and O111 strains were grouped together but ultimately subdivided according to their O-serotypes based on a 95% similarity threshold. The O104 strain, which was associated with a major outbreak of hemolytic uremic syndrome in Germany in May 2011, was also classified independently. The DiversiLab performed well in identifying isolates, but the discriminatory power of the repetitive sequence-based polymerase chain reaction method was lower than that of pulsed-field gel electrophoresis. Analysis of 15 enteropathogenic E. coli (EPEC) strains revealed that some EPEC strains clustered together with EHEC strains. Therefore, the DiversiLab system cannot be used to discriminate between these pathogroups. In conclusion, DiversiLab is a rapid and easy system for the primary exclusion of unrelated EHEC strains based on their serotypes, but more discriminatory methods, such as pulsed-field gel electrophoresis, are needed for accurate typing of the EHEC strains.
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Affiliation(s)
- Susanna Lukinmaa-Åberg
- Bacteriology Unit, Department of Infectious Disease Surveillance and Control, National Institute for Health and Welfare THL, Helsinki, Finland
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Abstract
The medical records of 84 patients with stool cultures positive for Clostridium difficile during the period August 2007 to June 2009 were retrospectively reviewed. A case of confirmed (toxigenic)C. difficile infection (CDI) was defined by the presence of symptoms (fever, diarrhoea, abdominal discomfort or distension, ileus) and the presence of toxigenic C. difficile. Patients with compatible clinical symptoms and stool cultures positive for non-toxigenic C. difficile isolates were defined as probable (non-toxigenic) CDI cases. Of these 84 patients, 50 (59.5%) were diagnosed as confirmed CDI and 34 (40.5%) as probable CDI. Thirteen (15.5%) of the 84 patients died during their hospital stay. Usage of proton pump inhibitors was a significant independent risk factor for CDI (OR 3.21, P=0.014). Of the 50 isolates associated with confirmed CDI, seven (8.3%) carried binary toxin genes (cdtAB), and six (7.1%) had a deletion in the tcdC gene. The mortality rate in confirmed CDI patients with isolates exhibiting deletion in the tcdC gene (2/6, 33.3%), those with isolates harbouring binary toxin genes (2/7, 28.6%), and those with isolates containing mutations in gyrA (2/7, 28.6%) and gyrB (1/2, 50%) was higher than the overall mortality rate (10/50, 20%) in patients with confirmed CDI.
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Hirvonen JJ, Pasanen T, Tissari P, Salmenlinna S, Vuopio J, Kaukoranta SS. Outbreak analysis and typing of MRSA isolates by automated repetitive-sequence-based PCR in a region with multiple strain types causing epidemics. Eur J Clin Microbiol Infect Dis 2012; 31:2935-42. [DOI: 10.1007/s10096-012-1644-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Accepted: 05/09/2012] [Indexed: 11/30/2022]
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Mattila E, Uusitalo-Seppälä R, Wuorela M, Lehtola L, Nurmi H, Ristikankare M, Moilanen V, Salminen K, Seppälä M, Mattila PS, Anttila VJ, Arkkila P. Fecal transplantation, through colonoscopy, is effective therapy for recurrent Clostridium difficile infection. Gastroenterology 2012; 142:490-6. [PMID: 22155369 DOI: 10.1053/j.gastro.2011.11.037] [Citation(s) in RCA: 263] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/20/2011] [Revised: 11/16/2011] [Accepted: 11/27/2011] [Indexed: 12/14/2022]
Abstract
BACKGROUND & AIMS Treatment of recurrent Clostridium difficile infection (CDI) with antibiotics leads to recurrences in up to 50% of patients. We investigated the efficacy of fecal transplantation in treatment of recurrent CDI. METHODS We reviewed records from 70 patients with recurrent CDI who had undergone fecal transplantation. Fecal transplantation was performed at colonoscopy by infusing fresh donor feces into cecum. Before transplantation, the patients had whole-bowel lavage with polyethylene glycol solution. Clinical failure was defined as persistent or recurrent symptoms and signs, and a need for new therapy. RESULTS During the first 12 weeks after fecal transplantation, symptoms resolved in all patients who did not have strain 027 C difficile infections. Of 36 patients with 027 C difficile infection, 32 (89%) had a favorable response; all 4 nonresponders had a pre-existing serious condition, caused by a long-lasting diarrheal disease or comorbidity and subsequently died of colitis. During the first year after transplantation, 4 patients with an initial favorable response had a relapse after receiving antibiotics for unrelated causes; 2 were treated successfully with another fecal transplantation and 2 with antibiotics for CDI. Ten patients died of unrelated illnesses within 1 year after transplantation. No immediate complications of fecal transplantation were observed. CONCLUSIONS Fecal transplantation through colonoscopy seems to be an effective treatment for recurrent CDI and also for recurrent CDI caused by the virulent C difficile 027 strain.
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Affiliation(s)
- Eero Mattila
- Department of Infectious Diseases, Helsinki University Central Hospital, Helsinki, Finland.
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Comparison of a commercially available repetitive-element PCR system (DiversiLab) with PCR ribotyping for typing of clostridium difficile strains. J Clin Microbiol 2011; 49:3352-4. [PMID: 21775548 DOI: 10.1128/jcm.00324-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study compared a repetitive-element PCR (rep-PCR) method (DiversiLab system) to PCR ribotyping. The discriminatory power of rep-PCR was 0.997. Among the PCR ribotype 027 isolates tested, different rep types could be distinguished. rep-PCR showed a higher discriminatory power than PCR ribotyping. Nevertheless, this method requires technical skill, and visual interpretation of rep-PCR fingerprint patterns may be difficult.
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Clinical Clostridium difficile: clonality and pathogenicity locus diversity. PLoS One 2011; 6:e19993. [PMID: 21625511 PMCID: PMC3098275 DOI: 10.1371/journal.pone.0019993] [Citation(s) in RCA: 136] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/08/2011] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile infection (CDI) is an important cause of mortality and morbidity in healthcare settings. The major virulence determinants are large clostridial toxins, toxin A (tcdA) and toxin B (tcdB), encoded within the pathogenicity locus (PaLoc). Isolates vary in pathogenicity from hypervirulent PCR-ribotypes 027 and 078 with high mortality, to benign non-toxigenic strains carried asymptomatically. The relative pathogenicity of most toxigenic genotypes is still unclear, but may be influenced by PaLoc genetic variant. This is the largest study of C. difficile molecular epidemiology performed to date, in which a representative collection of recent isolates (n = 1290) from patients with CDI in Oxfordshire, UK, was genotyped by multilocus sequence typing. The population structure was described using NeighborNet and ClonalFrame. Sequence variation within toxin B (tcdB) and its negative regulator (tcdC), was mapped onto the population structure. The 69 Sequence Types (ST) showed evidence for homologous recombination with an effect on genetic diversification four times lower than mutation. Five previously recognised genetic groups or clades persisted, designated 1 to 5, each having a strikingly congruent association with tcdB and tcdC variants. Hypervirulent ST-11 (078) was the only member of clade 5, which was divergent from the other four clades within the MLST loci. However, it was closely related to the other clades within the tcdB and tcdC loci. ST-11 (078) may represent a divergent formerly non-toxigenic strain that acquired the PaLoc (at least) by genetic recombination. This study focused on human clinical isolates collected from a single geographic location, to achieve a uniquely high density of sampling. It sets a baseline of MLST data for future comparative studies investigating genotype virulence potential (using clinical severity data for these isolates), possible reservoirs of human CDI, and the evolutionary origins of hypervirulent strains.
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Characterization of cases of Clostridium difficile infection (CDI) presenting at an emergency room: molecular and clinical features differentiate community-onset hospital-associated and community-associated CDI in a tertiary care hospital. J Clin Microbiol 2011; 49:2161-5. [PMID: 21471341 DOI: 10.1128/jcm.02330-10] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Definition of community-onset, hospital-acquired Clostridium difficile infection (CO-HA-CDI) is difficult in patients presenting with diarrhea at hospitals or outpatient clinics, especially 4 to 12 weeks after the last discharge. We performed C. difficile stool culture for 272 diarrheic patients visiting the emergency room (ER) between January 2006 and June 2010. C. difficile was isolated from 36 cases (13.2%), and isolation rates increased year by year, from 10.1% in 2008 to 12.4% in 2009 and 16.7% in 2010. Among 32 toxin-positive isolates, 13 (40.6%) and 19 (59.4%) were associated with CO-HA-CDI and community-acquired CDI (CA-CDI), respectively, if cases with CDI diagnosed within 12 weeks after discharge were considered hospital associated. The majority (70%) of CO-HA-CDI cases occurred within 2 weeks after hospital discharge, although the interval from discharge to onset of symptoms was as long as 10 weeks. We found via tcdA and tcdB and repetitive sequence PCR analysis, that toxin A-positive/toxin B-positive isolates were the most prevalent in both CO-HA-CDI (53.8%) and CA-CDI (94.7%) cases. Toxin A-negative/toxin B-positive isolates were also still highly associated with HA-CDI cases but were also observed in CA-CDI cases. Younger age, fewer underlying diseases, lack of prior antibiotic use, and genetic diversity of isolates in repetitive sequence PCR were the main characteristics in CA-CDI cases visiting the ER.
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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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Al Nakib M, Longo M, Tazi A, Billoet A, Raymond J, Trieu-Cuot P, Poyart C. Comparison of the Diversilab® system with multi-locus sequence typing and pulsed-field gel electrophoresis for the characterization of Streptococcus agalactiae invasive strains. J Microbiol Methods 2011; 85:137-42. [PMID: 21338630 DOI: 10.1016/j.mimet.2011.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 02/13/2011] [Accepted: 02/14/2011] [Indexed: 10/18/2022]
Abstract
Streptococcus agalactiae (or group B streptococcus; GBS) is a leading cause of neonatal morbidity and mortality in the developed countries. Several epidemiological typing tools have been developed for GBS to investigate the association between genotype and disease and to assess genetic variations within genogroups. This study compared the semi-automated repetitive sequence-based PCR Diversilab® system (DL) with MLST and pulsed field gel electrophoresis (PFGE) for determining the relatedness of invasive GBS strains. We analysed 179 unrelated GBS strains isolated from adult (n=108) and neonatal (n=71) invasive infections. By MLST, strains were resolved into 6 clonal complexes (CCs) including 23 sequence-types (STs), and 4 unique STs, whereas DL differentiated these isolates into 12 rep-PCR clusters (rPCs) and 9 unique rep-PCR types. The discriminatory power of both methods was similar, with Simpson's diversity indexes of 71.9% and 70.6%, respectively. However, their clustering concordance was low with Wallace concordance coefficients inferior to 0.4. PFGE was performed on 31 isolates representative of the most relevant DLrPCs clustered within the 3 major MLST CCs (CC-17, CC-23 and CC-1). As already observed with MLST, the concordance of DL with PFGE was low for all three CCs (Wallace coefficient <0.5), PFGE being more discriminative than rep-PCR. In summary, this work suggests that DL is less appropriate than MLST or PFGE to study GBS population genetic diversity.
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Affiliation(s)
- Malik Al Nakib
- Centre National de Référence des Streptocoques (CNR-Strep), Groupe Hospitalier Cochin-Hôtel Dieu-Broca Assistance Publique Hôpitaux de Paris, France
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Antimicrobial susceptibilities and molecular epidemiology of clinical isolates of Clostridium difficile in taiwan. Antimicrob Agents Chemother 2011; 55:1701-5. [PMID: 21263053 DOI: 10.1128/aac.01440-10] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The antimicrobial susceptibility and virulence factors of Clostridium difficile clinical isolates in Taiwan have not previously been reported. One hundred and thirteen isolates were collected from two major teaching hospitals in Taiwan from 2001 to 2009. Molecular typing was performed by an automated repetitive extragenic palindromic sequence-based PCR (rep-PCR) method (DiversiLab; Bacterial Barcodes, Inc., Athens, GA) and PCR ribotyping. Detection of tcdA, tcdB, cdtA, and cdtB genes was performed using a multiplex PCR assay, and gyrA and gyrB genes of moxifloxacin-nonsusceptible isolates were sequenced. All isolates were susceptible to vancomycin and metronidazole. Ninety-five (84%) isolates were susceptible to moxifloxacin, and the MIC(90) for nemonoxacin was 4 μg/ml. Tigecycline showed favorable antibacterial activity (MIC(90) of 0.06 μg/ml). Thirteen rep-PCR types were identified as a predominant rep-PCR type (type A; non-North American pulsed-field gel electrophoresis type 1 [NAP1], -NAP7, or -NAP8) accounting for 52.2% (59 isolates). Nine of 18 moxifloxacin-nonsusceptible isolates belonged to the rep-PCR type A. The rep-PCR type A and C isolates were distinct from NAP1 (ribotype 027) and NAP8 (ribotype 078) as determined by PCR ribotyping. Seventy-four (65%) isolates harbored tcdA and tcdB, and 15 (13%) harbored cdtAB encoding binary toxin. Eleven isolates had a gene deletion in tcdC, including a 39-bp deletion (9 isolates) and an 18-bp deletion (2). In conclusion, dissemination of a predominant C. difficile clone in southern and northern Taiwan was noted. However, no NAP1 (ribotype 027) isolate could be discovered in this study.
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