Chicken liver is a potential reservoir of bacteriophages and phage‐derived particles containing antibiotic resistance genes

Abstract

Summary Poultry meat production is one of the most important agri‐food industries in the world. The selective pressure exerted by widespread prophylactic or therapeutic use of antibiotics in intensive chicken farming favours the development of drug resistance in bacterial populations. Chicken liver, closely connected with the intestinal tract, has been directly involved in food‐borne infections and found to be contaminated with pathogenic bacteria, including Campylobacter and Salmonella. In this study, 74 chicken livers, divided into sterile and non‐sterile groups, were analysed, not only for microbial indicators but also for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Both bacteria and phages were detected in liver tissues, including those dissected under sterile conditions. The phages were able to infect Escherichia coli and showed a Siphovirus morphology. The chicken livers contained from 103 to 106 phage particles per g, which carried a range of ARGs (blaTEM, blaCTx‐M‐1, sul1, qnrA, armA and tetW) detected by qPCR. The presence of phages in chicken liver, mostly infecting E. coli, was confirmed by metagenomic analysis, although this technique was not sufficiently sensitive to identify ARGs. In addition, ARG‐carrying phages were detected in chicken faeces by qPCR in a previous study of the group. Comparison of the viromes of faeces and liver showed a strong coincidence of species, which suggests that the phages found in the liver originate in faeces. These findings suggests that phages, like bacteria, can translocate from the gut to the liver, which may therefore constitute a potential reservoir of antibiotic resistance genes.

Bacteriophage-Associated Antimicrobial Resistance Genes in Avian Pathogenic Escherichia coli Isolated from Brazilian Poultry

“…In this study, predicted resistance genes against β-lactams were found in 63.49% of the isolates harboring one or more of the following genes: blaCTX-M-1 , blaCTX-M-15 , blaCTX-M-164 , blaCTX-M-2 , blaCTX-M-55 , blaCTX-M-8 , blaSHV-12 , blaSHV-187 , blaTEM-106 , blaTEM-141 , blaTEM-1A , and blaTEM-1B . Some studies analyzed the genomes of phages obtained from different matrices—such as sewage, wastewater treatment stations, poultry meat, phages found in the environment, products, pig feces, meat, pork, beef and chicken minced meat, ham and mortadella, chicken feces, chicken liver, and compost—and have described the presence of all genes except blaCMY-2 [ 41 , 42 , 43 , 44 , 45 , 48 , 49 , 50 , 51 , 52 ].…”

“…In the present study, 78.1% of the APEC isolates harbored one or more aminoglycoside resistance genes ( aac (3)-IId , aac (3)-IVa , aac (3)-VIa , aadA12 , aadA2 , aadA5 , ant (2″)-Ia , ant (3″)-Ia , aph (3′)-Ia , aph (3″)-Ib , aph (4)-Ia , and aph (6)-Idii) . Studies analyzed the genome of phages isolated from poultry meat derivatives, pig feces, chicken feces and chicken liver and described the presence of aac (6′)-Im , aac-(Ib)-cr , aac (3)-Via , aphA1 , aadA2 , aph (3′)-IIIa , ant (6)-Ia , aph (2″)-Ig , and aph (3′)-III resistance genes [ 42 , 43 , 45 , 46 , 50 , 51 ].…”

“…The current study shows that 74.6% of the isolates carried predicted resistance genes against sulfonamides ( sul1 , sul2 , and sul3 ). Previous studies described the presence of sulfonamide resistance genes in bacteriophage isolated from pig feces, meat, pork, beef, chicken minced meat, ham and mortadella, dog urinary tract, chicken feces, chicken liver, and compost [ 43 , 44 , 45 , 50 , 51 , 52 , 55 ].…”

“…These genes have been detected in the genome of Enterobacteria phage P7 (accession number AF503408) [ 40 ]; phages from the Myoviridae , Siphoviridae , Podoviridae , and Inoviridae families [ 48 , 49 , 50 ]; and Drexlerviridae [ 51 ]. The gene qacE was identified in the prophage (uid33411_0.8) of Escherichia coli IAI39; the genes catA1 , blaTEM-1 , mph (A) , and sul1; and in prophage (uid33415_0.1) of Escherichia coli UMN026 [ 40 ].…”

Non-Canonical Aspects of Antibiotics and Antibiotic Resistance

“…However, both transformation and transduction may easily rival conjugation as a means for AR gene spread. With the millions of copies per milliliter of extracellular DNA encoding carbapenemases being dumped into wastewater [ 213 ]; the fact that fragmented (≥20 bp) and damaged DNA can be acquired by transformation [ 214 ]; that transformation can occur in unexpected places, such as the phylloplane of edible vegetables [ 215 ]; and AR genes being routinely found in phages (even towards the “last resort” antibiotic colistin [ 216 ])—from the fecal “phageome” of healthy humans [ 217 ], food samples [ 218 ] (up to the point that the liver of farm chickens can be considered as a reservoir of AR genes [ 219 ]). Furthermore, genomic islands shared by distantly related bacteria were likely mobilized between them by phages [ 220 ].…”