Deciphering Resistome and Virulome Diversity in a Porcine Slaughterhouse and Pork Products Through Its Production Chain.

Guillermo Campos Calero,Beatriz Pérez Montoro,Hikmate Abriouel,Nabil Benomar,Natacha Caballero Gómez,Antonio Gálvez,Charles W Knapp

doi:10.3389/fmicb.2018.02099

Guillermo Campos Calero, Beatriz Pérez Montoro + Show 5 more

Open Access

https://doi.org/10.3389/fmicb.2018.02099

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Abstract

We aimed to better understand resistome and virulome patterns on animal and process-area surfaces through a pig slaughterhouse to track possible contamination within the food production chain. Culture-dependent methods revealed high levels of microbial contamination, corresponding to mesophilic and pathogenic bacteria on both the animal and process-area surfaces mainly in the anesthesia (AA and AS) zone followed by “scorching and whip” (FA and FS) zone and also in the end products. To evaluate the potential risk of antibiotic resistance and virulence determinants, shotgun metagenomic DNA-sequencing of isolates from selected areas/products uncovered a high diversity and richness of antibiotic resistance genes (ARGs): 55–62 genes in the anesthesia area (AA and AS) and 35–40 in “animal-arrival zone” (MA and MS). The “scorching and whip” (FA and FS) area, however, exhibited lowered abundance of ARGs (1–6), indicating that the scalding and depilating process (an intermediate zone between “anesthesia” and “scorching and whip”) significantly decreased bacterial load by 1–3 log10 but also diminished the resistome. The high prevalence of antibiotic-inactivating enzyme genes in the “animal-arrival zone” (60–65%) and “anesthesia” area (56%) were mainly represented by those for aminoglycoside (46–51%) and lincosamide (14–19%) resistance, which did not reflect selective pressures by antibiotics most commonly used in pig therapy—tetracyclines and beta-lactams. Contrary to ARGs, greater number of virulence resistance genes were detected after evisceration in some products such as kidney, which reflected the poor hygienic practices. More than 19 general virulence features—mainly adherence, secretion system, chemotaxis and motility, invasion and motility were detected in some products. However, immune evasion determinants were detected in almost all samples analyzed from the beginning of the process, with highest amounts found from the anesthesia area. We conclude that there are two main sources of contamination in a pig slaughterhouse: the microorganisms carried on the animals’ hide, and those from the evisceration step. As such, focussing control measures, e.g., enhanced disinfection procedures, on these contamination-source areas may reduce risks to food safety and consumer health, since the antibiotic and virulence determinants may spread to end products and the environment; further, ARG and virulence traits can exacerbate pathogen treatments.

Highlights

Antibiotic resistance is a natural phenomenon, ancient, highly diverse and globally distributed (Hecker et al, 2003; Davies and Davies, 2010; Pawlowski et al, 2016), which has become elevated during the antibiotic era
The presence of various groups of bacteria throughout meat production chain were determined from animal and slaughterhouse surfaces: total aerobic mesophilic bacteria, Staphylococcus aureus, Listeria monocytogenes, Escherichia coli, Salmonella sp., pseudomonads and lactic acid bacteria (LAB) (Lavilla Lerma et al, 2013)
Culture dependent-methods revealed many populations from several bacterial groups recovered from animal and environmental surfaces of a pig slaughterhouse and meat processing plant in Jaén (Figure 1 and Table 1)

Summary

Introduction

Antibiotic resistance is a natural phenomenon, ancient, highly diverse and globally distributed (Hecker et al, 2003; Davies and Davies, 2010; Pawlowski et al, 2016), which has become elevated during the antibiotic era. The use, misuse and abuse of antibiotics in veterinary, agriculture and clinical therapy for decades have increased the prevalence of resistance genes (ARGs), especially the acquired resistance elements by horizontal gene transfer into the human and animal microbiomes (Laxminarayan, 2014). These resistance determinants present on mobile genetic elements have increased the risk of their transfer between different ecosystems. ARB and ARGs can spread to humans throughout the food-supply chain (e.g., Antibiotic Resistance from the Farm to the Table, 2014) by exposure via contaminated animals, meat products, or natural environment (i.e., air, water, and soil) (Founou et al, 2016)

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