Nocardia Real-time PCR

Standard laboratory techniques for the diagnosis of nocardiosis include culture and anti-microbial sensitivity testing for species with clinical significance, as many of the organisms are resistant to antibiotics. Nocardiosis diagnosis is often overlooked due to the length of time the isolates take to grow. Identification of Nocardia species by PCR will allow for a more rapid turnaround time enabling physicians to know to treat specifically for Nocardia rather than another bacteria.

About Nocardia

Nocardia is a gram positive bacterium that is mainly found in the soil. There are over 87 species in the genus, 48 of which are medically impactful. Found all over the United States, the pathogen can cause chronic and progressive infections. It is not often the first pathogen thought of and cultures can take weeks to grow. Treatment for the organism is different than that of other bacterial pathogens, therefore a late diagnosis can result in mortality of up to 40% in some studies. Most species are susceptible to linezolid and many to Trimethoprim/sulfamethoxazole (TMP – SMX).

Typically presenting as pneumonia, nocardiosis can also present as neurological disease and, in less severe cases, cutaneously. It causes the most severe disease in immunocompromised patients – such as solid organ transplants, and HIV positive patients. The most common clinical presentation of pulmonary nocardiosis is necrotizing pneumonia which is progressive and life threatening. Disseminated nocardiosis presents late as brain and skin lesions with the primary pulmonary cause going undiagnosed.

Extraction of Nocardia DNA from specimen followed by amplification and detection using real-time, qualitative PCR. A full-process internal control is added to each clinical specimen in order to ensure the extraction was performed correctly and the PCR reaction was not inhibited. This test has not been cleared or approved for diagnostic use by the U.S. Food and Drug Administration.

The Nocardia species assay design includes pathogen sequence information from 11 Nocardia species described in the literature as causing human illness (Brown-Elliot BA et al., 2012). The target species belong to the Nocardia genus (N. cyriacigeorgica, N. asteroides complex, N. nova complex, N. transvalensis, N. wallacei, N. brasiliensis, N. pseudobrasiliensis, N. africana, N. abscessus, N. otitidiscaviarum, and N. farcinica).

The assays were tested for cross reactivity against 30 bacterial targets including common causes of respiratory pneumonia. Cross-reactivity has been observed with Rhodococcus equi and Crossiella cryophila. Micromonospora saelicesensis, Streptomyces gardneri, Streptomyces platensis and Saccharothrix genus members showed cross reactivity in silico (none of these have been reported to cause human infections but observed only in reports of environmental sampling).