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In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings.

Aim: To evaluate direct plating methods for the estimation of Salmonella load in poultry carcass rinses. Methods and Results: Two direct plating tools, the spiral plate count method (SPCM) and the hydrophobic grid membrane filtration (HGMF) method, were adapted to support quantification of Salmonella during poultry processing. Test samples consisted of 180 broiler carcasses from a commercial abattoir, 60 from each of three points in the processing line [pre-inside‐outside bird wash (preIOBW), prechill and postchill]. The SPCM was used to estimate Salmonella load in pre-IOBW rinses, while HGMF was used to estimate Salmonella levels in prechill and postchill rinses. Carcass rinses were also evaluated for Salmonella prevalence by enrichment methods. Mean prevalences of Salmonella were 95%, 100% and 41AE7%, and the geometric mean loads were 3AE7 · 10 1 , 5AE6 · 10 0 and 5AE0 · 10 )2 CFU ml )1 for pre-IOBW, prechill and postchill rinses, respectively. Conclusions: The methods described are useful for estimating the concentration of viable and typical Salmonella in poultry carcass rinses. Significance and Impact of the Study: Direct plating enumeration methods can facilitate the monitoring of Salmonella load on poultry carcasses throughout the production process, and the evaluation of new processing intervention

Summary: A challenge in biodata analysis is to understand the underlying phenomena among many interactions in signaling pathways. Such study is formulated as the pathway enrichment analysis, which identifies relevant pathways functional enriched in high-throughput data. The question faced here is how to analyze different data types in a unified and integrative way by characterizing pathways that these data simultaneously reveal. To this end, we developed integrative Pathway Enrichment Analysis Platform, iPEAP, which handles transcriptomics, proteomics, metabolomics and GWAS data under a unified aggregation schema. iPEAP emphasizes on the ability to aggregate various pathway enrichment results generated in different high-throughput experiments, as well as the quantitative measurements of different ranking results, thus providing the first benchmark platform for integration, comparison and evaluation of multiple types of data and enrichment methods. Availability and implementation: iPEAP is freely available at http://www.tongji.edu.cn/∼qiliu/ipeap.html. Contact: qiliu@tongji.edu.cn or zwcao@tongji.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.

A collaborative study was conducted to validate new enrichment methods for the TECRA Listeria Visual Immunoassay (TLVIA). These new methods incorporate a newly formulated medium, TECRA Listeria Enrichment Broth, which does not contain the highly toxic antifungal agent, cycloheximide. The new procedures will provide an alternative to the enrichment procedures described in AOAC Method 995.22. Three food types (raw ground beef, lettuce, and ice cream) were analyzed in the United States, and 2 food types (cooked turkey and cooked fish fillets) were analyzed in Australasia. Thirty collaborators participated in the study, 16 in Australasia and 14 in the United States. With the exception of one batch of ground beef, comparison of the proportion of positive test portions (p ≥ 0.05) showed no significant difference between the TLVIA and the reference method for the 5 foods at 3 inoculation levels. For the one batch of naturally contaminated raw ground beef, the TLVIA gave significantly more confirmed positive results than the reference method.

AOAC Official Method 996.10, Assurance® Enzyme Immunoassay (EIA) for Escherichia coli O157:H7 (EHEC), was modified to incorporate a new enrichment protocol using BioControl EHEC8™ medium for testing raw and cooked beef. Foods were tested by EIA and the U.S. Department of Agriculture/Food Safety and Inspection Service (USDA/FSIS) enrichment conditions and the FDA Bacteriological Analytical Manual (BAM) isolation and confirmation techniques. A total of 14 collaborators participated. Raw and cooked ground beef were inoculated with E. coli O157:H7 at 2 different levels: a high level where predominantly positive results were expected, and a low level where fractional recovery was anticipated. Collaborators tested 378 test portions and controls by both the 8 h EIA and the USDA/FSIS enrichment methods, for a total of 756 test portions. Of the 378 paired test portions, 75 were positive and 212 were negative by both methods. Thirteen test portions were presumptively positive by EIA and could not be confirmed culturally; 30 were negative by EIA, but confirmed positive by culture; and 65 were negative by the culture method, but confirmed positive by the EIA method. There was no statistical difference between results obtained with the Assurance EIA for EHEC 8 h method and the culture method for raw ground beef. The Assurance EIA had a significantly higher recovery for cooked beef.

Two methods (the American Public Health Association (APHA) method and the elevated temperature method) for recovery of Vibrio cholerae from oysters were compared in a collaborative study. Oysters were inoculated with high (about 150 cells/g) and low (about 20 cells/ g) levels of V. cholerae. The elevated temperature method gave a significantly higher (P < 0.05) recovery rate and showed greater specificity (P < 0.01), as determined by the confirmation rate of suspect colonies. The elevated temperature method required only 25% of the labor and materials necessary for the APHA method. The elevated temperature method has been adopted official first action.