Molecular identification and antibiotic resistance pattern of actinomycetes isolates among immunocompromised patients in Iran, emerging of new infections

Abstract

Recent advancements in DNA-based approaches have led to the identification of uncommon and rare bacterial pathogens. In this study, by utilizing a DNA-based approach, a total of 1043 clinical specimens were processed for the identification of actinobacteria targeting the 16S rRNA and gyrB genes. Drug susceptibility testing was also conducted using micro-broth dilution and PCR. Two isolates of Nocardia flavorosea and Rhodococcus erythropolis were reported for the first time in Iran. Also, Nocardiopsis dassonvillei, Streptomyces olivaceus, and Streptomyces griseus were reported for the first time in Asia. Infections caused by Nocardia caishijiensis and Prauserella muralis have also been reported in this study. The first Asian case of pulmonary infection caused by Nocardia ignorata and the first global case of brain abscess caused by Nocardia ninae and Nocardia neocaledoniensis have been reported in this study. Overall 30 isolates belonging to 6 genera (Nocardia, Streptomyces, Rodoccoccus, Nocardiopsis, Rothia, and Prauserella) were detected in 30 patients. All 30 isolates were susceptible to amikacin and linezolid. Three isolates including Nocardia otitidiscaviarum (n = 2) and Nocardia flavorosea (n = 1) were resistant to trimethoprim-sulfamethoxazole which were the first trimethoprim-sulfamethoxazole resistant clinical actinomycetes in Iran. Isolation of rare species of actinomycetes particularly Nocardia spp. requires urgent action before they spread clinically particularly among immunocompromised patients.

Figure 1

Gel electrophoresis of dfrA gene (panel A, PC: Staphylococcus epidermidis ATCC 12228), sulf2 gene (panel B, PC: Escherichia coli strain AMR 130), sulf1 gene (panel C, PC: Escherichia coli strain AMR 130, 1: Nocardia otitidiscaviarum, 2: Nocardia flavorosea), int1 gene (panel D, PC: Vibrio cholerae O1 strain SK-10, 1: Nocardia otitidiscaviarum, 2: Nocardia flavorosea, 3: Nocardia otitidiscaviarum), int2 gene (panel E, PC: E. coli strain having a R483), and int3 gene (panel F, PC: E. coli strain having a pSMB731) PCR products. M Marker, PC positive control, NC negative control.

Figure 2

Pure colonies of isolated species (A) Nocardia cyriacigeorgica, (B) Nocardia kruczakiae, (C) Nocardia flavorosea, (D) Nocardia asteroides, (E) Streptomyces griseus, (F) Nocardia cerradoensis, (G) Nocardia caishijiensis, (H) Prauserella muralis.

Figure 3

Pure colonies of isolated species (A) Nocrdia otitidiscaviarum, (B) Nocardiopsis dassonvillei (C) Nocardia cyriacigeorgica, (D) Nocardia ninae, (E) Nocardia.brasiliensis, (F) Rhodococcus erythropolis.