Abstract
Antibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown. In this study, we aimed to investigate the presence of horizontally acquired antibiotic resistance genes among chicken gut microbiota members in 259 isolates with known whole genomic sequences. Altogether 124 isolates contained at least one gene coding for antibiotic resistance. Genes coding for the resistance to tetracyclines (detected in 101 isolates), macrolide-lincosamide-streptogramin B antibiotics (28 isolates) and aminoglycosides (25 isolates) were the most common. The most frequent tetracycline resistance genes were tet(W), tet(32), tet(O) and tet(Q). Lachnospiraceae and Ruminococcaceae frequently encoded tet(W). Lachnospiraceae commonly coded also for tet(32) and tet(O). The tet(44) gene was associated with Erysipelotrichaceae and tet(Q) was detected in the genomes of Bacteroidaceae and Porphyromonadaceae. Without any bias we have shown that antibiotic resistance is quite common in gut commensals. However, a comparison of codon usage showed that the above-mentioned families represent the most common current reservoirs but probably not the original host of the detected resistances.
Highlights
Antibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown
Due to increasing resistance to antibiotics in pathogens like Klebsiella, Staphylococcus, Pseudomonas or Salmonella[1,2], diseases caused by these pathogens, possible to control when caused by antibiotic-sensitive strains, become serious threats when caused by antibiotic-resistant clones
The resistant commensals may later act as reservoirs of antibiotic resistance genes, quite extensive reservoirs, since microbiota of distal parts of intestinal tract consists of approx. one thousand different species with a population density of around 1010 bacterial cells per gram of digesta
Summary
Antibiotic resistance in bacterial pathogens or several indicator bacteria is commonly studied but the extent of antibiotic resistance in bacterial commensals colonising the intestinal tract is essentially unknown. We aimed to investigate the presence of horizontally acquired antibiotic resistance genes among chicken gut microbiota members in 259 isolates with known whole genomic sequences. Studies on the distribution of antibiotic resistance among gut microbiota are limited due to their specific culture requirements. One of the most frequently used protocols includes shotgun sequencing of DNA purified from faecal material or intestinal digesta Those performed in chickens demonstrated that chicken gut microbiota represents an important source of antibiotic resistance genes with the most abundant genes encoding different drug efflux pumps, resistances to fluoroquinolones and tetracyclines[6,7,8].
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