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Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing
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| Zeitschriftentitel: | Journal of Medical Microbiology |
|---|---|
| Personen und Körperschaften: | , , , , , , |
| In: | Journal of Medical Microbiology, 55, 2006, 8, S. 1061-1070 |
| Format: | E-Article |
| Sprache: | Englisch |
| veröffentlicht: |
Microbiology Society
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| Schlagwörter: |
| author_facet |
Price, Erin P. Thiruvenkataswamy, Venugopal Mickan, Lance Unicomb, Leanne Rios, Rosa E. Huygens, Flavia Giffard, Philip M. Price, Erin P. Thiruvenkataswamy, Venugopal Mickan, Lance Unicomb, Leanne Rios, Rosa E. Huygens, Flavia Giffard, Philip M. |
|---|---|
| author |
Price, Erin P. Thiruvenkataswamy, Venugopal Mickan, Lance Unicomb, Leanne Rios, Rosa E. Huygens, Flavia Giffard, Philip M. |
| spellingShingle |
Price, Erin P. Thiruvenkataswamy, Venugopal Mickan, Lance Unicomb, Leanne Rios, Rosa E. Huygens, Flavia Giffard, Philip M. Journal of Medical Microbiology Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing Microbiology (medical) General Medicine Microbiology |
| author_sort |
price, erin p. |
| spelling |
Price, Erin P. Thiruvenkataswamy, Venugopal Mickan, Lance Unicomb, Leanne Rios, Rosa E. Huygens, Flavia Giffard, Philip M. 0022-2615 1473-5644 Microbiology Society Microbiology (medical) General Medicine Microbiology http://dx.doi.org/10.1099/jmm.0.46460-0 <jats:p>This investigation describes the development of a generally applicable, bioinformatics-driven, single-nucleotide polymorphism (SNP) genotyping assay for the common bacterial gastrointestinal pathogen<jats:italic>Campylobacter jejuni</jats:italic>. SNPs were identified<jats:italic>in silico</jats:italic>using the program ‘Minimum SNPs’, which selects for polymorphisms providing the greatest resolution of bacterial populations based on Simpson's index of diversity (<jats:italic>D</jats:italic>). The high-<jats:italic>D</jats:italic>SNPs identified in this study were derived from the combined<jats:italic>C. jejuni</jats:italic>/<jats:italic>Campylobacter coli</jats:italic>multilocus sequence typing (MLST) database. Seven SNPs were found that provided a<jats:italic>D</jats:italic>of 0.98 compared with full MLST characterization, based on 959 sequence types (STs). The seven high-<jats:italic>D</jats:italic>SNPs were interrogated using allele-specific real-time PCR (AS kinetic PCR), which negates the need for expensive labelled primers or probes and requires minimal assay optimization. The total turnaround time of the SNP typing assay was approximately 2 h. Concurrently, 69<jats:italic>C. jejuni</jats:italic>isolates were subjected to MLST and flagellin A short variable region (<jats:italic>flaA</jats:italic>SVR) sequencing and combined with a population of 84<jats:italic>C. jejuni</jats:italic>and<jats:italic>C. coli</jats:italic>isolates previously characterized by these methods. Within this collection of 153 isolates, 19<jats:italic>flaA</jats:italic>SVR types (<jats:italic>D</jats:italic>=0.857) were identified, compared with 40 different STs (<jats:italic>D</jats:italic>=0.939). When MLST and<jats:italic>flaA</jats:italic>SVR sequencing were used in combination, the discriminatory power was increased to 0.959. In comparison, SNP typing of the 153 isolates alone provided a<jats:italic>D</jats:italic>of 0.920 and was unable to resolve a small number of unrelated isolates. However, addition of the<jats:italic>flaA</jats:italic>SVR locus to the SNP typing procedure increased the resolving power to 0.952 and clustered isolates similarly to MLST/<jats:italic>flaA</jats:italic>SVR. This investigation has shown that a seven-member<jats:italic>C. jejuni</jats:italic>SNP typing assay, used in combination with sequencing of the<jats:italic>flaA</jats:italic>SVR, efficiently discriminates<jats:italic>C. jejuni</jats:italic>isolates.</jats:p> Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing Journal of Medical Microbiology |
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Microbiology Society, 2006 |
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Journal of Medical Microbiology |
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| title |
Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_unstemmed |
Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_full |
Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_fullStr |
Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_full_unstemmed |
Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_short |
Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_sort |
genotyping of campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaa short variable region sequencing |
| topic |
Microbiology (medical) General Medicine Microbiology |
| url |
http://dx.doi.org/10.1099/jmm.0.46460-0 |
| publishDate |
2006 |
| physical |
1061-1070 |
| description |
<jats:p>This investigation describes the development of a generally applicable, bioinformatics-driven, single-nucleotide polymorphism (SNP) genotyping assay for the common bacterial gastrointestinal pathogen<jats:italic>Campylobacter jejuni</jats:italic>. SNPs were identified<jats:italic>in silico</jats:italic>using the program ‘Minimum SNPs’, which selects for polymorphisms providing the greatest resolution of bacterial populations based on Simpson's index of diversity (<jats:italic>D</jats:italic>). The high-<jats:italic>D</jats:italic>SNPs identified in this study were derived from the combined<jats:italic>C. jejuni</jats:italic>/<jats:italic>Campylobacter coli</jats:italic>multilocus sequence typing (MLST) database. Seven SNPs were found that provided a<jats:italic>D</jats:italic>of 0.98 compared with full MLST characterization, based on 959 sequence types (STs). The seven high-<jats:italic>D</jats:italic>SNPs were interrogated using allele-specific real-time PCR (AS kinetic PCR), which negates the need for expensive labelled primers or probes and requires minimal assay optimization. The total turnaround time of the SNP typing assay was approximately 2 h. Concurrently, 69<jats:italic>C. jejuni</jats:italic>isolates were subjected to MLST and flagellin A short variable region (<jats:italic>flaA</jats:italic>SVR) sequencing and combined with a population of 84<jats:italic>C. jejuni</jats:italic>and<jats:italic>C. coli</jats:italic>isolates previously characterized by these methods. Within this collection of 153 isolates, 19<jats:italic>flaA</jats:italic>SVR types (<jats:italic>D</jats:italic>=0.857) were identified, compared with 40 different STs (<jats:italic>D</jats:italic>=0.939). When MLST and<jats:italic>flaA</jats:italic>SVR sequencing were used in combination, the discriminatory power was increased to 0.959. In comparison, SNP typing of the 153 isolates alone provided a<jats:italic>D</jats:italic>of 0.920 and was unable to resolve a small number of unrelated isolates. However, addition of the<jats:italic>flaA</jats:italic>SVR locus to the SNP typing procedure increased the resolving power to 0.952 and clustered isolates similarly to MLST/<jats:italic>flaA</jats:italic>SVR. This investigation has shown that a seven-member<jats:italic>C. jejuni</jats:italic>SNP typing assay, used in combination with sequencing of the<jats:italic>flaA</jats:italic>SVR, efficiently discriminates<jats:italic>C. jejuni</jats:italic>isolates.</jats:p> |
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| author | Price, Erin P., Thiruvenkataswamy, Venugopal, Mickan, Lance, Unicomb, Leanne, Rios, Rosa E., Huygens, Flavia, Giffard, Philip M. |
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| description | <jats:p>This investigation describes the development of a generally applicable, bioinformatics-driven, single-nucleotide polymorphism (SNP) genotyping assay for the common bacterial gastrointestinal pathogen<jats:italic>Campylobacter jejuni</jats:italic>. SNPs were identified<jats:italic>in silico</jats:italic>using the program ‘Minimum SNPs’, which selects for polymorphisms providing the greatest resolution of bacterial populations based on Simpson's index of diversity (<jats:italic>D</jats:italic>). The high-<jats:italic>D</jats:italic>SNPs identified in this study were derived from the combined<jats:italic>C. jejuni</jats:italic>/<jats:italic>Campylobacter coli</jats:italic>multilocus sequence typing (MLST) database. Seven SNPs were found that provided a<jats:italic>D</jats:italic>of 0.98 compared with full MLST characterization, based on 959 sequence types (STs). The seven high-<jats:italic>D</jats:italic>SNPs were interrogated using allele-specific real-time PCR (AS kinetic PCR), which negates the need for expensive labelled primers or probes and requires minimal assay optimization. The total turnaround time of the SNP typing assay was approximately 2 h. Concurrently, 69<jats:italic>C. jejuni</jats:italic>isolates were subjected to MLST and flagellin A short variable region (<jats:italic>flaA</jats:italic>SVR) sequencing and combined with a population of 84<jats:italic>C. jejuni</jats:italic>and<jats:italic>C. coli</jats:italic>isolates previously characterized by these methods. Within this collection of 153 isolates, 19<jats:italic>flaA</jats:italic>SVR types (<jats:italic>D</jats:italic>=0.857) were identified, compared with 40 different STs (<jats:italic>D</jats:italic>=0.939). When MLST and<jats:italic>flaA</jats:italic>SVR sequencing were used in combination, the discriminatory power was increased to 0.959. In comparison, SNP typing of the 153 isolates alone provided a<jats:italic>D</jats:italic>of 0.920 and was unable to resolve a small number of unrelated isolates. However, addition of the<jats:italic>flaA</jats:italic>SVR locus to the SNP typing procedure increased the resolving power to 0.952 and clustered isolates similarly to MLST/<jats:italic>flaA</jats:italic>SVR. This investigation has shown that a seven-member<jats:italic>C. jejuni</jats:italic>SNP typing assay, used in combination with sequencing of the<jats:italic>flaA</jats:italic>SVR, efficiently discriminates<jats:italic>C. jejuni</jats:italic>isolates.</jats:p> |
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| spelling | Price, Erin P. Thiruvenkataswamy, Venugopal Mickan, Lance Unicomb, Leanne Rios, Rosa E. Huygens, Flavia Giffard, Philip M. 0022-2615 1473-5644 Microbiology Society Microbiology (medical) General Medicine Microbiology http://dx.doi.org/10.1099/jmm.0.46460-0 <jats:p>This investigation describes the development of a generally applicable, bioinformatics-driven, single-nucleotide polymorphism (SNP) genotyping assay for the common bacterial gastrointestinal pathogen<jats:italic>Campylobacter jejuni</jats:italic>. SNPs were identified<jats:italic>in silico</jats:italic>using the program ‘Minimum SNPs’, which selects for polymorphisms providing the greatest resolution of bacterial populations based on Simpson's index of diversity (<jats:italic>D</jats:italic>). The high-<jats:italic>D</jats:italic>SNPs identified in this study were derived from the combined<jats:italic>C. jejuni</jats:italic>/<jats:italic>Campylobacter coli</jats:italic>multilocus sequence typing (MLST) database. Seven SNPs were found that provided a<jats:italic>D</jats:italic>of 0.98 compared with full MLST characterization, based on 959 sequence types (STs). The seven high-<jats:italic>D</jats:italic>SNPs were interrogated using allele-specific real-time PCR (AS kinetic PCR), which negates the need for expensive labelled primers or probes and requires minimal assay optimization. The total turnaround time of the SNP typing assay was approximately 2 h. Concurrently, 69<jats:italic>C. jejuni</jats:italic>isolates were subjected to MLST and flagellin A short variable region (<jats:italic>flaA</jats:italic>SVR) sequencing and combined with a population of 84<jats:italic>C. jejuni</jats:italic>and<jats:italic>C. coli</jats:italic>isolates previously characterized by these methods. Within this collection of 153 isolates, 19<jats:italic>flaA</jats:italic>SVR types (<jats:italic>D</jats:italic>=0.857) were identified, compared with 40 different STs (<jats:italic>D</jats:italic>=0.939). When MLST and<jats:italic>flaA</jats:italic>SVR sequencing were used in combination, the discriminatory power was increased to 0.959. In comparison, SNP typing of the 153 isolates alone provided a<jats:italic>D</jats:italic>of 0.920 and was unable to resolve a small number of unrelated isolates. However, addition of the<jats:italic>flaA</jats:italic>SVR locus to the SNP typing procedure increased the resolving power to 0.952 and clustered isolates similarly to MLST/<jats:italic>flaA</jats:italic>SVR. This investigation has shown that a seven-member<jats:italic>C. jejuni</jats:italic>SNP typing assay, used in combination with sequencing of the<jats:italic>flaA</jats:italic>SVR, efficiently discriminates<jats:italic>C. jejuni</jats:italic>isolates.</jats:p> Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing Journal of Medical Microbiology |
| spellingShingle | Price, Erin P., Thiruvenkataswamy, Venugopal, Mickan, Lance, Unicomb, Leanne, Rios, Rosa E., Huygens, Flavia, Giffard, Philip M., Journal of Medical Microbiology, Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing, Microbiology (medical), General Medicine, Microbiology |
| title | Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_full | Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_fullStr | Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_full_unstemmed | Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_short | Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| title_sort | genotyping of campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaa short variable region sequencing |
| title_unstemmed | Genotyping of Campylobacter jejuni using seven single-nucleotide polymorphisms in combination with flaA short variable region sequencing |
| topic | Microbiology (medical), General Medicine, Microbiology |
| url | http://dx.doi.org/10.1099/jmm.0.46460-0 |