Assessment of Chicken Carcass Microbiome Responses During Processing in the Presence of Commercial Antimicrobials Using a Next Generation Sequencing Approach

Abstract

The purpose of this study was to 1) identify microbial compositional changes on chicken carcasses during processing, 2) determine the antimicrobial efficacy of peracetic acid (PAA) and Amplon (blend of sulfuric acid and sodium sulfate) at a poultry processing pilot plant scale, and 3) compare microbial communities between chicken carcass rinsates and recovered bacteria from media. Birds were collected from each processing step and rinsates were applied to estimate aerobic plate count (APC) and Campylobacter as well as Salmonella prevalence. Microbiome sequencing was utilized to identify microbial population changes over processing and antimicrobial treatments. Only the PAA treatment exhibited significant reduction of APC at the post chilling step while both Amplon and PAA yielded detectable Campylobacter reductions at all steps. Based on microbiome sequencing, Firmicutes were the predominant bacterial group at the phyla level with over 50% frequency in all steps while the relative abundance of Proteobacteria decreased as processing progressed. Overall microbiota between rinsate and APC plate microbial populations revealed generally similar patterns at the phyla level but they were different at the genus level. Both antimicrobials appeared to be effective on reducing problematic bacteria and microbiome can be utilized to identify optimal indicator microorganisms for enhancing product quality.

Figure 1. Diagram to illustrate the first processing stage for chicken carcass, antimicrobial treatments, and the sampling points taken for microbial analyses and microbiome.

Condition of antimicrobial treatment: Amplon spray (pH 1.3); simulated on-line reprocessing (OLR) with Amplon (pH 1.4 and a 15 s dip); post-chilling with Amplon (pH 1.4 and 15 s dip); post-chilling with PAA (750 ppm and 15 s dip). Ten birds were taken from each group (total 80 birds). PAA, peracetic acid.

Figure 2

Average populations of aerobic plate counts (A) and Campylobacter (B) and Salmonella prevalence (C) on chicken carcasses (n = 10, each group) during general chicken processing steps. Values denoted by the same letter within each microbial group were not significantly different. All counts were considered significantly different at P < 0.05.

Figure 3. Bacterial reduction of aerobic plate counts on chicken carcasses (n = 10, each group) by antimicrobial treatments including Amplon spray, simulated OLR, post-chilling with Amplon, and post-chilling with PAA.

Values denoted by the same letter within each microbial group were not significantly different. All counts were considered significantly different at P < 0.05. PAA, peracetic acid.

Figure 4. Bacterial reduction of Campylobacter populations on chicken carcasses (n = 10, each group) by antimicrobial treatments including Amplon spray, simulated OLR, post-chilling with Amplon, and post-chilling with PAA.

Values denoted by the same letter within each microbial group were not significantly different. All counts were considered significantly different at P < 0.05. PAA, peracetic acid.

Figure 5. Reduction of number of Salmonella positive chicken carcasses (n = 10, each group) by antimicrobial treatments including Amplon spray, simulated OLR, post-chilling with Amplon, and post-chilling with PAA.

PAA, peracetic acid.

Figure 6

Alpha diversity analysis among groups. Rarefaction curves of (A) Observed_OTUs, (B) Chao 1, and (C) Shannon diversity. PAA, peracetic acid.

Figure 7. Beta diversity analysis among groups.

(A) Weighted and (B) unweighted UniFrac PCoA plots of individual chickens in each group. PAA, peracetic acid.

Figure 8

Relative abundance of major bacteria among different groups in chicken carcass rinsates at a phylum (A) and genus level (B). PAA, peracetic acid. f and o in parenthesis indicate family and order, respectively.

Figure 9

Relative abundance of major bacteria among different groups in APC Petrifilm at a phylum level (A) and genus level (B). PAA, peracetic acid. f in parenthesis indicate family.

Figure 10

Relative abundance of major bacteria in colonies from Campy-Cefex selective media at a phylum level (A) and genus level (B). f in parenthesis indicate family.