Comparison of Whole-Genome Sequencing and Molecular-Epidemiological Techniques for<i>Clostridium difficile</i>Strain Typing

Dominguez, Samuel R.; Anderson, Lydia; Kotter, Cassandra V.; Littlehorn, Cynthia A.; Arms, Lesley E.; Dowell, Elaine; Todd, James K.; Frank, Daniel N.

doi:10.1093/jpids/piv020

Cited by 13 publications

(10 citation statements)

References 12 publications

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“…When analyzing a large number of isolates, however, it is an expensive typing methodology, especially with Sanger sequencing costs which are generally in the range of £3-to-£5 per read depending on the service provider. As the costs of NGS have continued to fall, and are comparable per isolate to MLST, rapid and high quality WGS analysis of bacterial strains is now increasing common for epidemiological investigations [ 73 , 74 ].…”

Section: Newer Molecular Typing Methodologies For Propiomentioning

confidence: 99%

Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?

McDowell

2017

Microorganisms

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The Gram-positive, anaerobic bacterium Propionibacterium acnes forms part of the normal microbiota on human skin and mucosal surfaces. While normally associated with skin health, P. acnes is also an opportunistic pathogen linked with a range of human infections and clinical conditions. Over the last decade, our knowledge of the intraspecies phylogenetics and taxonomy of this bacterium has increased tremendously due to the introduction of DNA typing schemes based on single and multiple gene loci, as well as whole genomes. Furthermore, this work has led to the identification of specific lineages associated with skin health and human disease. In this review we will look back at the introduction of DNA sequence typing of P. acnes based on recA and tly loci, and then describe how these methods provided a basic understanding of the population genetic structure of the bacterium, and even helped characterize the grapevine-associated lineage of P. acnes, known as P. acnes type Zappe, which appears to have undergone a host switch from humans-to-plants. Particular limitations of recA and tly sequence typing will also be presented, as well as a detailed discussion of more recent, higher resolution, DNA-based methods to type P. acnes and investigate its evolutionary history in greater detail.

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Section: Newer Molecular Typing Methodologies For Propiomentioning

confidence: 99%

Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?

McDowell

2017

Microorganisms

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“…Similarly, the Centres for Disease Control (CDC) and collaborators have implemented the “ Listeria Whole-Genome Sequencing Project” for all Listeria isolates in the United States [ 63 ]. WGS provides higher-resolution data (WGS can detect insertion, deletion and recombination events in genome sequences, as well as single nucleotide polymorphisms (SNPs)) compared to typing methods such as pulse-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and serotyping, enabling improved identification of an outbreak source and potential transmission events [ 64 ]. Numerous studies have demonstrated the effectiveness of WGS for analysing and tracking outbreaks of clinically relevant pathogens, such as Staphylococcus aureus , Acinetobacter baumannii , Klebsiella pneumoniae and Pseudomonas aeruginosa [ 65 , 66 , 67 , 68 ].…”

Section: Whole-genome Sequencingmentioning

confidence: 99%

Advances in the Microbiome: Applications to Clostridium difficile Infection

Culligan

Sleator

2016

JCM

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Clostridium difficile is a major cause of morbidity and mortality worldwide, causing over 400,000 infections and approximately 29,000 deaths in the United States alone each year. C. difficile is the most common cause of nosocomial diarrhoea in the developed world, and, in recent years, the emergence of hyper-virulent (mainly ribotypes 027 and 078, sometimes characterised by increased toxin production), epidemic strains and an increase in the number of community-acquired infections has caused further concern. Antibiotic therapy with metronidazole, vancomycin or fidaxomicin is the primary treatment for C. difficile infection (CDI). However, CDI is unique, in that, antibiotic use is also a major risk factor for acquiring CDI or recurrent CDI due to disruption of the normal gut microbiota. Therefore, there is an urgent need for alternative, non-antibiotic therapeutics to treat or prevent CDI. Here, we review a number of such potential treatments which have emerged from advances in the field of microbiome research.

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“…First, this study involved only a pilot cohort and convenience samples collected for a previously conducted outbreak investigation. [ 9 , 21 ] Second, because of the cross-sectional study design, we cannot make any definitive claims of causation for any factors (i.e., chemotherapy, patient type, antibiotic usage, etc.) associated with dysbiosis.…”

Section: Discussionmentioning

confidence: 99%

“…difficile outbreak investigation, stool samples were collected from all patients admitted to the pediatric CCBD floor from October through December 2012. [ 9 , 21 ] Stool samples were tested for the C . difficile toxin B gene by PCR (Xpert C .…”

Section: Methodsmentioning

confidence: 99%

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients

et al. 2018

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Bloodstream infections (BSI) and Clostridium difficile infections (CDI) in pediatric oncology/hematology/bone marrow transplant (BMT) populations are associated with significant morbidity and mortality. The objective of this study was to explore possible associations between altered microbiome composition and the occurrence of BSI and CDI in a cohort of pediatric oncology patients. Stool samples were collected from all patients admitted to the pediatric oncology floor from Oct.–Dec. 2012. Bacterial profiles from patient stools were determined by bacterial 16S rRNA gene profiling. Differences in overall microbiome composition were assessed by a permutation-based multivariate analysis of variance test, while differences in the relative abundances of specific taxa were assessed by Kruskal-Wallis tests. At admission, 9 of 42 patients (21%) were colonized with C. difficile, while 6 of 42 (14%) subsequently developed a CDI. Furthermore, 3 patients (7%) previously had a BSI and 6 patients (14%) subsequently developed a BSI. Differences in overall microbiome composition were significantly associated with disease type (p = 0.0086), chemotherapy treatment (p = 0.018), BSI following admission from any cause (p < 0.0001) or suspected gastrointestinal organisms (p = 0.00043). No differences in baseline microbiota were observed between individuals who did or did not subsequently develop C. difficile infection. Additionally, multiple bacterial groups varied significantly between subjects with post-admission BSI compared with no BSI. Our results suggest that differences in gut microbiota not only are associated with type of cancer and chemotherapy, but may also be predictive of subsequent bloodstream infection.

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Comparison of Whole-Genome Sequencing and Molecular-Epidemiological Techniques forClostridium difficileStrain Typing

Cited by 13 publications

References 12 publications

Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?

Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt?

Advances in the Microbiome: Applications to Clostridium difficile Infection

Evaluation of bloodstream infections, Clostridium difficile infections, and gut microbiota in pediatric oncology patients

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