Genome Sequencing of Pathogenic Rhodococcus spp.

Genome Sequencing of Pathogenic Rhodococcus spp. To the Editor: Infections caused by non-equi Rhodococcus spp. are uncommon but can cause severe pneumonia and bloodstream infections with sepsis (1–4). Increasing prevalence of immune-compromising illnesses and use of immunosuppres-sive agents might contribute to re-emergence of these pathogens (5,6). Rhodococci infections may go undi-agnosed or misclassifi ed because of diffi culties in laboratory identifi ca-tion, nomenclatural instability, and similarity of signs and symptoms to Mycobacterium tuberculosis infection (e.g., increasing cough, dyspnea, hemoptysis, and weight loss; failure to respond to broad-spectrum antimicro-bial drugs; progressive cavitary lesion on repeated chest imaging). A 73-year-old immunocompetent man with chronic obstructive pulmonary disease who lived on a ranch in the southwestern United States was evaluated for possible malignancy of the left lung. Computed tomography showed expansion of an upper lobe cavitary lesion, and he underwent a partial lobectomy. Rhodococcus spp. infection was suspected on the basis of the fi nding of the progressive le-sion, salmon-pink colony growth on chocolate agar, and gram-positive coccobacilli on Gram stain. The isolate , R1101, could not be further iden-tifi ed by using commercial automated systems in the laboratory and so was subjected to genome study. Alignment of 16S rRNA gene sequences showed that R1101 was most closely related to R. rhodochrous, with identities of 98.78%, 99.32%, and 99.86% to the 16S rRNA gene for type strains R. rhodochrous DSM43271, R. pyridinivorans PDB9, and R. gordo-nae W4937 (7), respectively. In contrast , sequence identity with R. equi type strain DSM20307 was 95.57%. Phylogenetic analysis with Rhodo-coccus 16S rRNA genes suggested that R1101 was a member of R. rho-dochrous and evolutionarily separate from R. equi (Figure, panel A). A query against the National Center for Biotechnology Information nonredun-dant DNA database (http://blast.ncbi. nlm.nih.gov/Blast.cgi) found 60 rho-dococcal 16S rRNA sequences that are 99%–100% identical to R1101, which demonstrates worldwide distribution of these closely related strains in diverse environments. Optical genome mapping (8) of R1101 generated a consensus full-length map showing a circular chromosome map of »4.32 Mb (± 5%) in length. The whole-genome restriction map for R1101 was compared with in silico NcoI restriction maps of 33 complete genome sequences from the family Nocardiaceae, retrieved from GenBank; these sequences included R. equi. No substantial similarity (alignment scores >15%) was detected between R1101 and these genomes. Thus, we determined that R1101 was not an R. equi isolate. Pyrosequencing of the R1101 genome yielded an average coverage depth …