The purpose of the study was to examine the prevalence of Escherichia coli in shrimps and mussels, and to determine the distribution of β-lactam, aminoglycoside, quinolone, and multi-drug resistance phenotypically and genotypically in E. coli isolates obtained from mussels and shrimps in Istanbul. Faecal samples were collected from mussels (n = 96) and shrimps (n = 96) from the Marmara Sea coastline and fish markets in Istanbul. For the detection of antibiotic susceptibilities, seven antibiotic groups were used. β-lactamase, aminoglycoside, and quinolone genes were also determined. A total of 34 (17.7%, 15 shrimps, and 19 mussels) E. coli were isolated, and 17 (50%) were found to be resistant to one or more antimicrobials. The highest resistance was seen against aminoglycosides with 11 isolates (32.35%), followed by quinolones with 10 isolates (29.41%) and extended-spectrum β-lactamase (ESBL) with 4 isolates (11.76%). Multi-drug resistance was detected in 5 isolates (14.7%) from 3 shrimp and 2 mussel samples. The prevalence of ESBL genes was demonstrated at 3.84% in mussels and shrimp samples. There were no AmpC and carbapenemase-producing genes. These samples harbored blaCTX-M-1 (n = 3) and blaTEM (n = 4). Ten isolates were resistant to aminoglycosides genotypically. Resistance genes detected were strB in 2 isolates, aadA in 5, strB and aadA together in 3, ANT('')-Ia, aphA1 and aphA2 simultaneously in 3, aphA1 in 1, aac(3)-IIa in 1 isolate. aac(6')-Ib-cr gene was detected in only one of 10 phenotypically resistant isolates to quinolones.

• Keywords
• E. coli, ESBL, aquatic animals, multiple drug resistance,
• Publication type
• Journal Article MeSH

One of the recent trends in animal production is the revival of interest in organic farming. The increased consumer interest in organic animal farming is mainly due to concerns about animal welfare and the use of antibiotics in conventional farming. On the other hand, providing animals with a more natural lifestyle implies their increased exposure to environmental sources of different microorganisms including pathogens. To address these concerns, we determined the abundance of antibiotic resistance and diversity within fecal microbiota in pigs kept under conventional and organic farming systems in Sweden, Denmark, France and Italy. The abundance of sul1, sul2, strA, tet(A), tet(B) and cat antibiotic resistance genes was determined in 468 samples by real-time PCR and the fecal microbiota diversity was characterized in 48 selected samples by pyrosequencing of V3/V4 regions of 16S rRNA. Contrary to our expectations, there were no extensive differences between the abundance of tested antibiotic resistance genes in microbiota originating from organic or conventionally housed pigs within individual countries. There were also no differences in the microbiota composition of organic and conventional pigs. The only significant difference was the difference in the abundance of antibiotic resistance genes in the samples from different countries. Fecal microbiota in the samples originating from southern European countries (Italy, France) exhibited significantly higher antibiotic resistance gene abundance than those from northern parts of Europe (Denmark, Sweden). Therefore, the geographical location of the herd influenced the antibiotic resistance in the fecal microbiota more than farm's status as organic or conventional.

• MeSH
• Genes, Bacterial genetics   MeSH
• Drug Resistance, Bacterial genetics   MeSH
• Organic Agriculture * MeSH
• Animal Husbandry * MeSH
• European Union MeSH
• Feces microbiology   MeSH
• Microbiota genetics   MeSH
• Swine microbiology   MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Animals MeSH
• Check Tag
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Names of Substances
• RNA, Ribosomal, 16S MeSH

Poultry meat is the most common protein source of animal origin for humans. However, intensive breeding of animals in confined spaces has led to poultry colonisation by microbiota with a zoonotic potential or encoding antibiotic resistances. In this study we were therefore interested in the prevalence of selected antibiotic resistance genes and microbiota composition in feces of egg laying hens and broilers originating from 4 different Central European countries determined by real-time PCR and 16S rRNA gene pyrosequencing, respectively. strA gene was present in 1 out of 10,000 bacteria. The prevalence of sul1, sul2 and tet(B) in poultry microbiota was approx. 6 times lower than that of the strA gene. tet(A) and cat were the least prevalent being present in around 3 out of 10,000,000 bacteria forming fecal microbiome. The core chicken fecal microbiota was formed by 26 different families. Rather unexpectedly, representatives of Desulfovibrionaceae and Campylobacteraceae, both capable of hydrogen utilisation in complex microbial communities, belonged among core microbiota families. Understanding the roles of individual population members in the total metabolism of the complex community may allow for interventions which might result in the replacement of Campylobacteraceae with Desulfovibrionaceae and a reduction of Campylobacter colonisation in broilers, carcasses, and consequently poultry meat products.

• MeSH
• Anti-Bacterial Agents pharmacology   MeSH
• Drug Resistance, Bacterial genetics   MeSH
• Feces microbiology   MeSH
• Oviposition * MeSH
• Chickens microbiology   physiology   MeSH
• Microbiota * MeSH
• RNA, Ribosomal, 16S genetics   MeSH
• Sequence Analysis, RNA MeSH
• Animals MeSH
• Check Tag
• Female MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH
• Croatia MeSH
• Hungary MeSH
• Slovenia MeSH
• Names of Substances
• Anti-Bacterial Agents MeSH
• RNA, Ribosomal, 16S MeSH