Characterization of phages derived from strains of Rhodococcus australis and R. equii

Current taxonomy of Rhodococcus species and their role in infections

Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.

Isolation and characterization of soilborne virulent bacteriophages infecting the pathogen Rhodococcus equi

AIMS

To isolate and characterize a diversity of bacteriophages (phages) that infect the soilborne pathogen Rhodococcus equi.

METHODS AND RESULTS

Twenty-seven phages were isolated from soil samples from geographically distinct locations using a range of R. equi bacterial strains, including clinical isolates. On the basis of host range, genomic DNA restriction profiles and virion protein profiles, the diversity of these phages was extensive, with phages being divided into 16 groupings.

CONCLUSIONS

Based on a range of criteria, these phages could be divided into 16 distinct groupings. The majority of the phages recovered from soil were Siphoviridae, adding to the limited number of Siphoviridae described to date for R. equi. One grouping consisted of phages belonging to the Myoviridae.

SIGNIFICANCE AND IMPACT OF THE STUDY

This represents the first study looking at the diversity of phages infecting the pathogen R. equi, including the first Myoviridae to be isolated and characterized for the genus Rhodococcus and for the nonmycobacterial actinomycetes. Given their diverse host range, including clinical isolates, this collection of phages offers the potential for the development of phage cocktails for use as a therapeutic or alternatively in the biocontrol of this pathogen in reservoirs of infection relating to animal husbandry.

Characterization and whole genome sequences of the Rhodococcus bacteriophages RGL3 and RER2

We report here the isolation and genome sequences of two novel phages, lytic for Rhodococcus and Nocardia species. Named RER2 and RGL3, both are members of the family Siphoviridae, and each possesses a novel genome of 46,586 bp and 48,072 bp, respectively. RER2 and RGL3 phages share a modular genome organization, as seen in other sequenced Siphoviridae phage genomes, and appear to share a common evolutionary origin. The genomes of these phages share no similarity with other Rhodococcus or Nocardia phages but are related to Mycobacterium phages. The data presented here extend our understanding of Rhodococcus phage genomics.

Genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiPoco6, ReqiPine5, and ReqiDocB7

The isolation and results of genomic and functional analyses of Rhodococcus equi phages ReqiPepy6, ReqiDocB7, ReqiPine5, and ReqiPoco6 (hereafter referred to as Pepy6, DocB7, Pine5, and Poco6, respectively) are reported. Two phages, Pepy6 and Poco6, more than 75% identical, exhibited genome organization and protein sequence likeness to Lactococcus lactis phage 1706 and clostridial prophage elements. An unusually high fraction, 27%, of Pepy6 and Poco6 proteins were predicted to possess at least one transmembrane domain, a value much higher than the average of 8.5% transmembrane domain-containing proteins determined from a data set of 36,324 phage protein entries. Genome organization and protein sequence comparisons place phage Pine5 as the first nonmycobacteriophage member of the large Rosebush cluster. DocB7, which had the broadest host range among the four isolates, was not closely related to any phage or prophage in the database, and only 23 of 105 predicted encoded proteins could be assigned a functional annotation. Because of the relationship of Rhodococcus to Mycobacterium, it was anticipated that these phages should exhibit some of the features characteristic of mycobacteriophages. Traits that were identified as shared by the Rhodococcus phages and mycobacteriophages include the prevalent long-tailed morphology and the presence of genes encoding LysB-like mycolate-hydrolyzing lysis proteins. Application of DocB7 lysates to soils amended with a host strain of R. equi reduced recoverable bacterial CFU, suggesting that phage may be useful in limiting R. equi load in the environment while foals are susceptible to infection.

Correlation between antibiotic resistance, phage-like particle presence, and virulence in Rhodococcus equi human isolates

Rhodococcus equi is a gram-positive coccobacillus that appears to be emerging as a pulmonary pathogen in AIDS patients. In four human clinical isolates, two antibiotic resistance phenotypes were found to coexist: one beta-lactam resistant and the other beta-lactam susceptible. In vitro, beta-lactam-resistant mutants were obtained at a frequency of 1 x 10(-5) to 5 x 10(-5) from beta-lactam-susceptible strains on cephalothin-containing plates. Neither beta-lactamase nor plasmid DNA was detected in beta-lactam-resistant or -susceptible strains. The penicillin-binding protein patterns for the two types of strains were identical. Electron microscopy revealed that the beta-lactam-resistant strains possessed cell-surface-associated appendages and produced phage-like particles. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of total cell protein showed at least three additional bands of 42, 39, and 30 kDa found only in the beta-lactam-resistant strains. Testing for virulence in Swiss mice revealed that (i) phage-like-particle-producing strains had lower 50% lethal doses when injected intravenously in euthymic and nude mice than the non-phage-like-particle-producing strains did and (ii) intravenous inoculation of a sublethal dose (5 x 10(6) CFU) in nude mice led to chronic infection by the phage-like-particle-producing bacteria only. Finally, in vitro growth curves indicated that the phage-like-particle-producing strains possessed an ecological selection advantage. These results suggest that, among R. equi human isolates, the antibiotic resistance phenotype is associated with virulence and may be phage mediated.