| Title |
Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes
|
|---|---|
| Published in |
Microbial Ecology, February 2018
|
| DOI | 10.1007/s00248-018-1155-7 |
| Pubmed ID | |
| Authors |
Adriana Cabal, Se-Ran Jun, Piroon Jenjaroenpun, Visanu Wanchai, Intawat Nookaew, Thidathip Wongsurawat, Mary J. Burgess, Atul Kothari, Trudy M. Wassenaar, David W. Ussery |
| Abstract |
Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients. |
X Demographics
The data shown below were collected from the profiles of 5 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| India | 1 | 20% |
| Unknown | 4 | 80% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 3 | 60% |
| Scientists | 1 | 20% |
| Practitioners (doctors, other healthcare professionals) | 1 | 20% |
Mendeley readers
The data shown below were compiled from readership statistics for 59 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 59 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 9 | 15% |
| Researcher | 8 | 14% |
| Student > Master | 6 | 10% |
| Other | 4 | 7% |
| Professor | 4 | 7% |
| Other | 15 | 25% |
| Unknown | 13 | 22% |
| Readers by discipline | Count | As % |
|---|---|---|
| Biochemistry, Genetics and Molecular Biology | 17 | 29% |
| Immunology and Microbiology | 6 | 10% |
| Agricultural and Biological Sciences | 6 | 10% |
| Medicine and Dentistry | 4 | 7% |
| Environmental Science | 2 | 3% |
| Other | 9 | 15% |
| Unknown | 15 | 25% |
Attention Score in Context
This research output has an Altmetric Attention Score of 3. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 18 February 2018.
All research outputs
#13,140,583
of 23,498,099 outputs
Outputs from Microbial Ecology
#1,134
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Outputs of similar age
#208,282
of 448,666 outputs
Outputs of similar age from Microbial Ecology
#28
of 45 outputs
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