Back to Search
Start Over
Application of high-throughput sequencing to measure the performance of commonly used selective cultivation methods for the foodborne pathogen Campylobacter
- Source :
- FEMS Microbiology Ecology. 79:327-336
- Publication Year :
- 2011
- Publisher :
- Oxford University Press (OUP), 2011.
-
Abstract
- Campylobacter is an important foodborne human pathogen, which has traditionally been studied using a variety of selective cultivation methods. Here we use next-generation sequencing to ask the following: (i) how selective are commonly used Campylobacter cultivation methods relative to the initial sample and (ii) how do the specificity and sensitivity of these methods compare with one another? To answer these questions, we used 16S rRNA tagged-pyrosequencing to sequence directly from a pooled fecal sample representing a c. 16,000 bird poultry flock and compared these data to exhaustive sequencing of colonies formed after plating. We compared five commonly used media [Cefex, Cape Town, modified cefoperazone charcoal deoxycholate agar (mCCDA), Campy-Line agar (CLA), and Campy-CVA agar (CVA)], two incubation atmospheres (10% CO(2), 5% O(2), 85% N(2) and 10% CO(2), 10% H(2), 80% N(2)), and two incubation temperatures (37 and 42 °C). Analysis of 404,104 total sequence reads, including 19 472 total fecal reads, revealed Campylobacter represented only a small proportion (0.04%) of sequences present in the feces, but 88-97% of sequences from each media type. Incubation atmosphere had little effect on recovery, but a significant difference in media specificity (more non-Campylobacter OTUs; P = 0.028) was found at 42 vs. 37 °C. The most common non-Campylobacter sequence type was Proteus, which ranged from 0.04% of sequences (mCCDA) to 10.8% (Cape Town). High-throughput sequencing provides a novel and powerful approach to measure the performance of selective media, which remain widely used for research and regulatory purposes.
- Subjects :
- Veterinary medicine
food.ingredient
medicine.disease_cause
Sensitivity and Specificity
Applied Microbiology and Biotechnology
Microbiology
Feces
South Africa
food
medicine
Humans
Agar
Incubation
Bacteriological Techniques
Ecology
biology
Campylobacter
biology.organism_classification
16S ribosomal RNA
High-Throughput Screening Assays
Proteus
Food Microbiology
Pyrosequencing
Flock
Subjects
Details
- ISSN :
- 01686496
- Volume :
- 79
- Database :
- OpenAIRE
- Journal :
- FEMS Microbiology Ecology
- Accession number :
- edsair.doi.dedup.....b64b7409df4e1ea52b03b7dca42dbc63