Critical control points in rendering plants with regard to high level contamination, bioaerosol production and the risk for the environment involve unloading of the raw material and wastewater treatment. In the unloading section of the rendering plant, the raw material is dumped from collecting containers of the transport vehicles to destructors. This is associated with potential aerosolisation of liquids, such as blood, intestinal contents and similar.

Very similar drugs (beta lactams, penicillin, ampicillin, cloxacillin, tetracyclines, sulphonamides and potentiated sulphonamides, cephalosporins, and fluoroquinolones) have been used in both human medicine and agriculture production29.

Antimicrobials used in poultry production have the potential to accumulate in poultry feathers and during the rendering process are not completely destroyed. Poultry feathers can be recycled to a feather meal and used as a fertilizer and animal feed, thereby providing a potential pathway for re-entry of drugs into the human food supply30.

Hofacre et al.31 found that a high percentage of feed samples for poultry containing meat and bone meal from rendering plant were contaminated by bacteria resistant to amoxicillin, ampicillin, cephalothin or clavulanic acid. Some samples contained bacteria resistant to kanamycin, trimethoprim/sulfamethoxazole or ciprofloxacin. The presence of mobile genetic elements mediate multi-drug resistance was proved in many of the isolated bacteria.

Higher than 30% prevalence among the 3rd-generation cephalosporin-resistant E. coli was detected mostly in poultry production32.

In our study we observed the highest incidence of beta-lactams resistance to ampicillin (68%), followed by cephalosporins—veterinary ceftiofur (36%), cefquinom (15.9%) and ceftriaxone (12.5%) while the beta-lactam resistance to ceftazidime was detected only in 4.5% of all strains.

ESBLs and AmpC beta-lactamases are usually responsible for the mediation of resistance to 3rd-generation cephalosporins in E. coli33.

Similar ESBL phenotypes with high level fluoroquinolones resistance in animal E. coli isolated from a Slovak poultry slaughterhouse was described by Gregova et al.10. Aggregated European Community data for E. coli isolates from broilers showed that over 50% of isolates were resistant to ciprofloxacin34. Moreover, the fluoroquinolones-resistant E. coli typically exhibited clinically significant elevations in MIC values35. E. coli isolates resistant to fluoroquinolones are often resistant to other antibiotic groups and genes of virulence36.

The CMY-2-producing E. coli O25b-ST131 represent a clonal lineage that differs from the CTX-M-15-producing ST131-O25b cluster. ST131-O25b strains with the presence of ESBL-type CTX-M-15 and resistance to fluoroquinolones have been reported worldwide. They are frequently a cause of infections, particularly of the urinary tract of humans. In human patients in Europe, approximately 1% of the 3rd generation cephalosporin-resistant E. coli produce CMY-2. However, recent studies in Asia showed higher rates and an increasing trend among the 3rd-generation cephalosporin-resistant E. coli isolates has been reported33.

Recently, ten multi-resistant strains of E. coli that harboured CMY-2 were observed with increasing tendency in the European livestock production. However, ST131 isolates with CMY-2 production have been reported rarely37,38.

We also detected multidrug-resistant clones O25b-ST131 with CMY-2 and enrofloxacin resistance with Int1, Tn 3, cvaC and iutA.

CMY-2-producing E. coli isolates were also detected in products from meat, livestock animals and human patients. The predominant way of transmission of blaCMY-2 genes between animals and humans is the horizontal transfer of temporarily stable blaCMY-2-carrying IncK2 and IncI1 plasmids33. This suggests a zoonotic potential of the blaCMY-2 genes and their transmission by horizontal transfer and clonal spread along the food production chain33,37.

We also detected resistant strains (CTR, TTC, STM, FLO, COT) with genes, such as blaCTX-M-1, blaCMY-2 together with virulence factors cvaC, iutA and mobile elements (Int1, Tn3).

Extraintestinal virulence genes encoding adhesins, iron capture systems, toxins, and protectins have been correlated with successful colonization of gut in humans and animals39,40.

Our study of E. coli strains from wastewater showed that virulence genes cvaC, iutA, iss, papC were the most frequently detected in them. In some E. coli samples, we detected genes kps, tsh, papC, ibeA.

Similarly, examination of meat from healthy broilers from Slovakia conducted by Drugdova et al.41 showed presence of antimicrobial-resistant E. coli strains with virulence factors (most frequently iutA, iss, cvaC, tsh and papC) related to avian pathogenic or human uropathogenic E. coli.

The study conducted in Canada42 revealed high prevalence of many virulence genes (ompT, traT, uidA, vat, hemF, iss and cvaC), including the genes responsible for adhesion, fimH and kpsMT KII, in ExPEC isolates from frozen poultry meat.

Chicken meat and eggshells also harbour E. coli strains containing genes of virulence papA, papC, sfa, foc, afa, dra, kpsM II and iutA43.

Bok et al.44 observed that virulence genes (fimH, papAH, iutA, iroN, ompT, traT, and iss) were more frequently identified in isolates from piglets than from sows. E. coli from piglets constituted a substantial reservoir of extraintestinal virulence genes and could increase the potential risk of extraintestinal infections. According this study44 the mobile genetic elements transmitted via horizontal gene transfer play an important role in the evolution of E. coli resistance. Most ExPEC virulence genes are clustered together on mobile genetic elements, usually on pathogenicity islands (PAI) or virulence plasmids, exhibiting a unique organization.

Cunha et al.45 characterized APEC strains from different poultry farms in Brazil, that harboured a number of virulence factors such as sfa, usp (100% each), pap (85%), kpsMTII (66%), hlyA (52%), cnf1 (22%), ibeA (4%), iss (37%), tsh, ompT, and hlyF (8% each), and cvi/cva (0%).

Ten out of 13 tetracycline resistant strains carried the Int1 gene, and 6 of them the iutA gene. Five from among 8 streptomycin-resistant strains carried iutA and Int1 genes, which indicate a horizontal transfer of resistant genes between bacteria. The high number of isolates resistant to streptomycin, tetracycline and cotrimoxazol can be spread by same mobile genetic elements.