Prophage elements function as reservoir for antibiotic resistance and virulence genes in nosocomial pathogens

Prophages are often involved in host survival strategies and contribute toward increasing the genetic diversity of the host genome. Prophages also drive horizontal propagation of various genes as vehicles. However, there are few retrospective studies contributing to the propagation of antimicrobial resistance (AMR) and virulence factor (VF) genes by prophage. In this study, we extracted complete genome sequences of seven pathogens, including ESKAPE bacteria and Escherichia coli deposited in a public database, and examined the distribution of both AMR and VF genes in certain genomic regions of prophage, including prophage-like element. We found that the ratios of AMR and VF genes greatly varied among the seven species. More than 55% of Enterobacter cloacae strains had VF genes, but only 0.8% of Klebsiella pneumoniae strains had VF genes from prophages. The prophage types carrying AMR genes were detected in a broad range of hosts, whereas prophages containing VF genes were conserved in only one or two species, suggesting that distribution patterns of prophages were different between prophages encoding AMR or VF genes. We also found that the prophage containing class 1 integrase possessed a significantly higher number of AMR genes than prophages with no class 1 integrase. Moreover, AMR genes in the prophage were located near transposase and integrase. The results of this study reveal a comprehensive picture of AMR and VF genes present in prophage elements and provide new insights into the horizontal transfer of genes associated with antimicrobial resistance and pathogenicity.ImportanceAlthough we believe phages play an important role in horizontal gene transfer in exchanging genetic material, we do not know the distribution of the antimicrobial resistance and/or virulence genes in prophages. We collected different prophage elements from the complete genome sequence of seven species – Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae, as well as Escherichia coli –, and characterized the distribution of antimicrobial resistance and virulence genes encoded in the prophage region. While virulence genes in prophage were found to be species-specific, antimicrobial resistance genes in prophages were highly conserved in various species. Integron structure was detected within prophage regions in almost all of the genera. Maximum of 11 antimicrobial resistance genes were found in a single prophage region, suggesting that prophages act as a reservoir for antimicrobial resistance genes. Our results highlight new insights on prophages as horizontal gene carriers.

Population Heterogeneity in Corynebacterium glutamicum ATCC 13032 Caused by Prophage CGP3

ABSTRACT The genome of Corynebacterium glutamicum type strain ATCC 13032 (accession number BX927147) contains three prophages, CGP1, CGP2, and CGP3. We recently observed that many genes within the CGP3 prophage region have increased mRNA levels in a dtxR deletion mutant that lacks the master regulator of iron homeostasis (J. Wennerhold and M. Bott, J. Bacteriol. 188:2907-2918, 2006). Here, we provide evidence that this effect is due to the increased induction of the prophage CGP3 in the dtxR mutant, possibly triggered by DNA damage caused by elevated intracellular iron concentrations. Upon induction, the CGP3 prophage region is excised from the genome and forms a circular double-stranded DNA molecule. Using quantitative real-time PCR, an average copy number of about 0.1 per chromosome was determined for circular CGP3 DNA in wild-type C. glutamicum. This copy number increased about 15-fold in the dtxR mutant. In order to visualize the CGP3 DNA within single cells, a derivative of the wild type was constructed that contained an array of tet operators integrated within the CGP3 region and a plasmid-encoded YFP-TetR fusion protein. As expected, one to two fluorescent foci that represented the chromosomally integrated CGP3 prophage were detected in the majority of cells. However, in a small fraction (2 to 4%) of the population, 4 to 10 CGP3 DNA molecules could be observed in a single cell. Interestingly, the presence of many CGP3 copies in a cell often was accompanied by an efflux of chromosomal DNA, indicating the lysis of the corresponding cell. However, evidence for the formation of functional infective CGP3 phage particles could not be obtained.