scholarly journals Current application and future perspectives of molecular typing methods to study Clostridium difficile infections

2013 ◽  
Vol 18 (4) ◽  
Author(s):  
C W Knetsch ◽  
T D Lawley ◽  
M P Hensgens ◽  
J Corver ◽  
M W Wilcox ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Molecular Typing ◽  
Variable Number Tandem Repeat ◽  
Data Interpretation ◽  
Global Changes ◽  
Complex Data ◽  
Spatial And Temporal Patterns ◽  
Typing Method ◽  
Current Application ◽  
Pcr Ribotyping

Molecular typing is an essential tool to monitor Clostridium difficile infections and outbreaks within healthcare facilities. Molecular typing also plays a key role in defining the regional and global changes in circulating C. difficile types. The patterns of C. difficile types circulating within Europe (and globally) remain poorly understood, although international efforts are under way to understand the spatial and temporal patterns of C. difficile types. A complete picture is essential to properly investigate type-specific risk factors for C. difficile infections (CDI) and track long-range transmission. Currently, conventional agarose gel-based polymerase chain reaction (PCR) ribotyping is the most common typing method used in Europe to type C. difficile. Although this method has proved to be useful to study epidemiology on local, national and European level, efforts are made to replace it with capillary electrophoresis PCR ribotyping to increase pattern recognition, reproducibility and interpretation. However, this method lacks sufficient discriminatory power to study outbreaks and therefore multilocus variable-number tandem repeat analysis (MLVA) has been developed to study transmission between humans, animals and food. Sequence-based methods are increasingly being used for C. difficile fingerprinting/typing because of their ability to discriminate between highly related strains, the ease of data interpretation and transferability of data. The first studies using whole-genome single nucleotide polymorphism typing of healthcare-associated C. difficile within a clinically relevant timeframe are very promising and, although limited to select facilities because of complex data interpretation and high costs, these approaches will likely become commonly used over the coming years.

scholarly journals Molecular Typing of Mycoplasma genitalium-Positive Specimens Discriminates between Persistent and Recurrent Infections in Cases of Treatment Failure and Supports Contact Tracing

2019 ◽  
Vol 7 (12) ◽  
pp. 609 ◽  
Author(s):  
Luis Piñeiro ◽  
Pedro Idigoras ◽  
Gustavo Cilla
Keyword(s):  
Molecular Typing ◽  
Variable Number Tandem Repeat ◽  
Mycoplasma Genitalium ◽  
Variable Number ◽  
Contact Tracing ◽  
Polymorphism Analysis ◽  
Recurrent Infections ◽  
Transmitted Infection ◽  
Typing Method ◽  
Sexually Transmitted

Mycoplasma genitalium causes a sexually transmitted infection that sometimes persists or recurs despite adequate antibiotic treatment. Between 2014 and 2018, molecular typing was applied to 75 M. genitalium-positive samples from 48 patients with repeated infection and/or couples/groups of other infected sexual contacts. MG191 adhesin, MG309 lipoprotein, and the rRNA operon were amplified, sequenced, and typed using phylogenetic, variable number tandem repeat, and single-nucleotide polymorphism analysis, respectively. Amplicons were obtained in 74/75 samples, and the combination of locus patterns gave 44 different genetic profiles (discriminatory index of 0.987), with 43 considering only MG191 and MG309. Interestingly, 15/17 patients who presented a first sample sensitive and a second resistant to macrolides had the same genetic variant in the samples (persistence of the same strain). In 2/17 patients, discordant variants (one mixed infection and one recurrence due to incomplete contact tracing) were detected. In 31 additional not related and randomly distributed samples, MG191 typing obtained 23 different genotypes, with no appreciable clustering over time. The typing method allowed persistent and recurrent infections to be distinguished, indicating that macrolide resistance-associated mutations mostly developed during treatment. To detect these secondary resistant strains, prevent reinfections, and improve the control of M. genitalium infections, tests of cure and contact tracing of sexual partners should be mandatory.

scholarly journals 473. Molecular Typing of Clostridium difficile: Concordance Between PCR-Ribotyping and Multilocus Sequence Typing (MLST)

2018 ◽  
Vol 5 (suppl_1) ◽  
pp. S176-S176 ◽  
Author(s):  
Xiong Wang ◽  
Stacy Holzbauer ◽  
Kelly Pung ◽  
Maria Bye ◽  
Michelle Adamczyk ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Molecular Typing ◽  
Multilocus Sequence Typing ◽  
Pcr Ribotyping

scholarly journals Characterization of Clostridium difficile isolates using capillary gel electrophoresis-based PCR ribotyping

2008 ◽  
Vol 57 (11) ◽  
pp. 1377-1382 ◽  
Author(s):  
A. Indra ◽  
S. Huhulescu ◽  
M. Schneeweis ◽  
P. Hasenberger ◽  
S. Kernbichler ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Gel Electrophoresis ◽  
Variable Number Tandem Repeat ◽  
Variable Number ◽  
Web Based ◽  
Healthcare Facilities ◽  
Capillary Gel Electrophoresis ◽  
Hands On ◽  
Pcr Ribotyping ◽  
Reference Strains

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.

scholarly journals 2428. Whole-genome Sequencing to Determine Clostridium difficile Transmission

2019 ◽  
Vol 6 (Supplement_2) ◽  
pp. S839-S839
Author(s):  
Victoria M Madigan ◽  
Glen Carter ◽  
Kirsty Buising ◽  
Benjamin Howden ◽  
Caroline Marshall
Keyword(s):  
Clostridium Difficile ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Molecular Typing ◽  
Clinical Epidemiology ◽  
Epidemiological Data ◽  
Whole Genome ◽  
Royal Melbourne Hospital ◽  
Hospital Patients ◽  
Pcr Ribotyping

Abstract Background Clostridium difficile is a major problem in healthcare institutions due to its substantial attributable morbidity, mortality and costs. Although traditionally recognized as a nosocomial infection, there is increasing evidence that hospital-based transmission may not be as common as previously thought. Whole-genome sequencing (WGS) has superior discriminatory ability than other previously used techniques for C. difficile typing. This study aimed to investigate whether WGS could help to elucidate C. difficile transmission patterns at The Royal Melbourne Hospital (RMH). Methods All C. difficile isolates (N = 138) identified in patients admitted to RMH from November 1, 2015 to October 31, 2016 had molecular typing performed by WGS, multilocus sequence typing (MLST) and PCR ribotyping. Clinical epidemiological data were collected for each episode so that patient locations could be examined together with molecular typing information to determine putative transmissions in the hospital. Results After combining molecular and clinical epidemiology, a picture of diverse C. difficile emerged. Only 7 (6%) of isolates appeared to have been transmitted from other hospital patients, according to combined WGS and patient location data. However, both PCR ribotyping (33%) and MLST (44%) had significantly higher proportions of putative transmissions in this cohort. Conclusion This finding has significant implications for the Infection Prevention team as efforts toward prevention of C. difficile infection may need to be redirected away from the current focus on prevention of nosocomial transmission. Future studies are needed to broaden understanding of C. difficile transmission dynamics so that other sources can be identified and targeted for intervention. Disclosures All authors: No reported disclosures.

scholarly journals Survey of diagnostic and typing capacity for Clostridium difficile infection in Europe, 2011 and 2014

2016 ◽  
Vol 21 (29) ◽  
Author(s):  
Sofie M van Dorp ◽  
Daan W Notermans ◽  
Jeroen Alblas ◽  
Petra Gastmeier ◽  
Silja Mentula ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Laboratory Diagnostics ◽  
Surveillance Network ◽  
Typing Method ◽  
Cross Sectional ◽  
Convenience Sample ◽  
Infection Surveillance ◽  
Pcr Ribotyping ◽  
National Capacity ◽  
And Control

Suboptimal laboratory diagnostics for Clostridium difficile infection (CDI) impedes its surveillance and control across Europe. We evaluated changes in local laboratory CDI diagnostics and changes in national diagnostic and typing capacity for CDI during the European C. difficile Infection Surveillance Network (ECDIS-Net) project, through cross-sectional surveys in 33 European countries in 2011 and 2014. In 2011, 126 (61%) of a convenience sample of 206 laboratories in 31 countries completed a survey on local diagnostics. In 2014, 84 (67%) of these 126 laboratories in 26 countries completed a follow-up survey. Among laboratories that participated in both surveys, use of CDI diagnostics deemed ‘optimal’ or ‘acceptable’ increased from 19% to 46% and from 10% to 15%, respectively (p  < 0.001). The survey of national capacity was completed by national coordinators of 31 and 32 countries in 2011 and 2014, respectively. Capacity for any C. difficile typing method increased from 22/31 countries in 2011 to 26/32 countries in 2014; for PCR ribotyping from 20/31 countries to 23/32 countries, and specifically for capillary PCR ribotyping from 7/31 countries to 16/32 countries. While our study indicates improved diagnostic capability and national capacity for capillary PCR ribotyping across European laboratories between 2011 and 2014, increased use of ‘optimal’ diagnostics should be promoted.

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