K-mer based prediction of Clostridioides difficile relatedness and ribotypes
Comparative analysis of Clostridioides difficile whole-genome sequencing (WGS) data enables fine scaled investigation of transmission and is increasingly becoming part of routine surveillance. However, these analyses are constrained by the computational requirements of the large volumes of data invo...
| Main Authors: | , , , |
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| Format: | Journal article |
| Language: | English |
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Microbiology Society
2022
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| _version_ | 1826307578644135936 |
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| author | Moore, M Wilcox, MH Walker, AS Eyre, D |
| author_facet | Moore, M Wilcox, MH Walker, AS Eyre, D |
| author_sort | Moore, M |
| collection | OXFORD |
| description | Comparative analysis of Clostridioides difficile whole-genome sequencing (WGS) data enables fine scaled investigation of transmission and is increasingly becoming part of routine surveillance. However, these analyses are constrained by the computational requirements of the large volumes of data involved. By decomposing WGS reads or assemblies into k-mers and using the dimensionality reduction technique MinHash, it is possible to rapidly approximate genomic distances without alignment. Here we assessed the performance of MinHash, as implemented by sourmash, in predicting single nucleotide differences between genomes (SNPs) and C. difficile ribotypes (RTs). For a set of 1,905 diverse C. difficile genomes (differing by 0-168,519 SNPs), using sourmash to screen for closely related genomes, at a sensitivity of 100% for pairs ≤10 SNPs, sourmash reduced the number of pairs from 1,813,560 overall to 161,934, i.e., by 91%, with a positive predictive value of 32% to correctly identify pairs ≤10 SNPs (maximum SNP distance 4,144). At a sensitivity of 95%, pairs were reduced by 94% to 108,266 and PPV increased to 45% (maximum SNP distance 1,009). Increasing the MinHash sketch size above 2000 produced minimal performance improvement. We also explored a MinHash similarity-based ribotype prediction method. Genomes with known ribotypes (n=3,937) were split into a training set (2,937) and test set (1,000) randomly. The training set was used to construct a sourmash index against which genomes from the test set were compared. If the closest 5 genomes in the index had the same ribotype this was taken to predict the searched genome’s ribotype. Using our MinHash ribotype index, predicted ribotypes were correct in 780/1000 (78%) genomes, incorrect in 20 (2%), and indeterminant in 200 (20%). Relaxing the classifier to 4/5 closest matches with the same RT improved the correct predictions to 87%. Using MinHash it is possible to subsample C. difficile genome k-mer hashes and use them to approximate small genomic differences within minutes, significantly reducing the search space for further analysis. |
| first_indexed | 2024-03-07T07:05:12Z |
| format | Journal article |
| id | oxford-uuid:bcaa8fa7-b90a-4275-9f12-b4fce61b14b0 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T07:05:12Z |
| publishDate | 2022 |
| publisher | Microbiology Society |
| record_format | dspace |
| spelling | oxford-uuid:bcaa8fa7-b90a-4275-9f12-b4fce61b14b02022-05-03T10:53:35ZK-mer based prediction of Clostridioides difficile relatedness and ribotypesJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:bcaa8fa7-b90a-4275-9f12-b4fce61b14b0EnglishSymplectic ElementsMicrobiology Society2022Moore, MWilcox, MHWalker, ASEyre, DComparative analysis of Clostridioides difficile whole-genome sequencing (WGS) data enables fine scaled investigation of transmission and is increasingly becoming part of routine surveillance. However, these analyses are constrained by the computational requirements of the large volumes of data involved. By decomposing WGS reads or assemblies into k-mers and using the dimensionality reduction technique MinHash, it is possible to rapidly approximate genomic distances without alignment. Here we assessed the performance of MinHash, as implemented by sourmash, in predicting single nucleotide differences between genomes (SNPs) and C. difficile ribotypes (RTs). For a set of 1,905 diverse C. difficile genomes (differing by 0-168,519 SNPs), using sourmash to screen for closely related genomes, at a sensitivity of 100% for pairs ≤10 SNPs, sourmash reduced the number of pairs from 1,813,560 overall to 161,934, i.e., by 91%, with a positive predictive value of 32% to correctly identify pairs ≤10 SNPs (maximum SNP distance 4,144). At a sensitivity of 95%, pairs were reduced by 94% to 108,266 and PPV increased to 45% (maximum SNP distance 1,009). Increasing the MinHash sketch size above 2000 produced minimal performance improvement. We also explored a MinHash similarity-based ribotype prediction method. Genomes with known ribotypes (n=3,937) were split into a training set (2,937) and test set (1,000) randomly. The training set was used to construct a sourmash index against which genomes from the test set were compared. If the closest 5 genomes in the index had the same ribotype this was taken to predict the searched genome’s ribotype. Using our MinHash ribotype index, predicted ribotypes were correct in 780/1000 (78%) genomes, incorrect in 20 (2%), and indeterminant in 200 (20%). Relaxing the classifier to 4/5 closest matches with the same RT improved the correct predictions to 87%. Using MinHash it is possible to subsample C. difficile genome k-mer hashes and use them to approximate small genomic differences within minutes, significantly reducing the search space for further analysis. |
| spellingShingle | Moore, M Wilcox, MH Walker, AS Eyre, D K-mer based prediction of Clostridioides difficile relatedness and ribotypes |
| title | K-mer based prediction of Clostridioides difficile relatedness and ribotypes |
| title_full | K-mer based prediction of Clostridioides difficile relatedness and ribotypes |
| title_fullStr | K-mer based prediction of Clostridioides difficile relatedness and ribotypes |
| title_full_unstemmed | K-mer based prediction of Clostridioides difficile relatedness and ribotypes |
| title_short | K-mer based prediction of Clostridioides difficile relatedness and ribotypes |
| title_sort | k mer based prediction of clostridioides difficile relatedness and ribotypes |
| work_keys_str_mv | AT moorem kmerbasedpredictionofclostridioidesdifficilerelatednessandribotypes AT wilcoxmh kmerbasedpredictionofclostridioidesdifficilerelatednessandribotypes AT walkeras kmerbasedpredictionofclostridioidesdifficilerelatednessandribotypes AT eyred kmerbasedpredictionofclostridioidesdifficilerelatednessandribotypes |