Revista da Sociedade Brasileira de Medicina Tropical 46(4):447-452, Jul-Aug, 2013 http://dx.doi.org/10.1590/0037-8682-0097-2013 MCaseajor ReportArticle Rapid detection and differentiation of mycobacterial species using a multiplex PCR system Andrea Santos Lima[1], Rafael Silva Duarte[2], Lílian Maria Lapa Montenegro[1] and Haiana Charifker Schindler[1] [1]. Departamento de Imunologia, Centro de Pesquisas Aggeu Magalhães, Fundação Oswaldo Cruz, Recife, PE. [2]. Instituto de Microbiologia, Universidade Federal do Rio Janeiro, Rio de Janeiro, RJ. ABSTRACT Introduction: The early diagnosis of mycobacterial infections is a critical step for initiating treatment and curing the patient. Molecular analytical methods have led to considerable improvements in the speed and accuracy of mycobacteria detection. Methods: The purpose of this study was to evaluate a multiplex polymerase chain reaction system using mycobacterial strains as an auxiliary tool in the differential diagnosis of tuberculosis and diseases caused by nontuberculous mycobacteria (NTM) Results: Forty mycobacterial strains isolated from pulmonary and extrapulmonary origin specimens from 37 patients diagnosed with tuberculosis were processed. Using phenotypic and biochemical characteristics of the 40 mycobacteria isolated in LJ medium, 57.5% (n=23) were characterized as the Mycobacterium tuberculosis complex (MTBC) and 20% (n=8) as nontuberculous mycobacteria (NTM), with 22.5% (n=9) of the results being inconclusive. When the results of the phenotypic and biochemical tests in 30 strains of mycobacteria were compared with the results of the multiplex PCR, there was 100% concordance in the identifi cation of the MTBC and NTM species, respectively. A total of 32.5% (n=13) of the samples in multiplex PCR exhibited a molecular pattern consistent with NTM, thus disagreeing with the fi nal diagnosis from the attending physician. Conclusions: Multiplex PCR can be used as a differential method for determining TB infections caused by NTM a valuable tool in reducing the time necessary to make clinical diagnoses and begin treatment. It is also useful for identifying species that were previously not identifi able using conventional biochemical and phenotypic techniques. Keywords: Mycobacterium tuberculosis complex. Nontuberculous mycobacteria. Diagnosis. Polymerase chain reaction. Multiplex. guided by video, where the instruments are subjected to INTRODUCTION high levels of sterilization in glutaraldehyde solution. From 1998 to 2009, there were 2,520 reported cases of post- The ability of nontuberculous mycobacteria (NTM) to cause surgical infections related to rapidly growing mycobacteria, disease is clearly described in the literature, and its importance is including Mycobacterium fortuitum, Mycobacterium chelonae, increasing progressively, with an increasing amount of various M. abscessus and Mycobacterium massiliense, which were species being cultured and isolated in laboratories1-3. distributed predominantly in private hospitals throughout In Brazil, the NTM species most frequently associated with the country. Cases have been reported in 23 states of Brazil, 6 lung disease are Mycobacterium kasasii and Mycobacterium with 97.8% of the cases concentrated within 10 states . The avium. Other species, such as Mycobacterium xenopi, diseases caused by NTMs are not compulsorily notifi able, Mycobacterium malmoense, Mycobacterium lentiflavum, except where the infection occurred during surgical procedures; Mycobacterium abscessus and Mycobacterium szulgai, have however, several studies in Brazil have noted isolated strains of occasionally been isolated in cultures4.5. In 2011 the National nontuberculous mycobacteria in pulmonary and extrapulmonary 4,7,8. Agency for Sanitary Surveillance (ANVISA) published the clinical samples from patients with suspected tuberculosis number of cases of infections by rapidly growing mycobacteria The differential diagnosis between tuberculosis (TB) and (RGMs) obtained in the last eleven years in Brazil. diseases caused by NTMs is of great importance because Data also suggest that this disease occurs in subjects the epidemiology, treatment and prognosis are different. undergoing invasive procedures, mostly surgical cases Conventional diagnostics present numerous diffi culties as clinical symptoms are generally similar and non-specifi c smear testing has limited sensitivity and cannot differentiate the species of mycobacteria. a o Address to: Dr Andrea Santos Lima. Dept de Imunologia/CPqAM/FIOCRUZ. For many years, the identifi cation of mycobacteria was Av. Moraes Rego s/n, Cidade Universitária, 50670-420 Recife, PE, Brasil. undertaken by gathering phenotypic results and biochemical Phone: 55 81 2101-2569; Fax: 55 81 3453-1911 9,10 e-mail: [email protected] test results of isolated species in culture medium . In the last Received 6 May 2013 20 or 30 years, with the increasing need to identify a greater Accepted 22 July 2013 number of species and also for early diagnosis, new methods 447 Lima AS et al - Differentiation of mycobacterial species have been developed to enable rapid and accurate identifi cation from skin lesion aspiration, 3 (7.5%) from pleural fl uid (PL), of mycobacterial species10-12. In Brazil, the PRA-hsp65 1 (2.5%) from a node biopsy and 1 (2.5%) from a bone biopsy. technique proposed by Telenti et al.13, and Devallois et al.14 Clinical specimens were analyzed by bacilloscopy, culture, has enabled the identifi cation of several species of NTM, the multiplex PCR and polymerase chain reaction restriction results of which correlated well with those from biochemical enzyme analysis (PRA-hsp65) to identify and differentiate identification13-17. Beyond the molecular techniques, the mycobacterial species as described below. sequencing of the specifi c genes rpoB and hsp65 has become Smear microscopy the gold standard for identifying mycobacteria18,19. Because of its high discriminatory power, this tool has been used by The presence of acid fast bacilli in different clinical several groups in epidemiological studies to identify the species specimens was determined by Ziehl-Neelsen staining (Stewart, involved in human diseases and in outbreaks, and also for 1953) in the Public Health Laboratory of Recife (Unifi ed taxonomic reclassifi cation20,21. Health System - SUS), in accordance with the guidelines of Multiplex polymerase chain reaction (PCR) is a fast tool the Brazilian Ministry of Health29. that allows the simultaneous amplifi cation of more than one Specimen processing sequence of target deoxyribonucleic acid (DNA) in a single reaction, saving time and reagents22-24. This system, which In total, of 1-5 ml of various clinical specimens (except for amplifies two or three different targets, can differentiate the sterile samples collected) was processed using the modifi ed M. tuberculosis from the NTMs25,26. This molecular approach Petroff method in 4% NaOH29,30. is used in identifying and differentiating microbes because it is Culture able to supply a simple fi ngerprint of certain bacterial groups when compared to the standard profi les of referent strains. The Cultures were performed in a Lowenstein-Jensen medium29,31 correct choice of target sequences in the genome is one of the and mycobacterium species were identifi ed using the following key criteria for detecting and identifying mycobacteria by PCR27. biochemical tests: selective inhibition by para-nitrobenzoic Faced with the need to differentiate tuberculosis from other (PNB) acid and thiophene-2-carboxylic hydrazide (TCH) 29 mycobacteria, the aim of this study was to evaluate a system acid, niacin accumulation and heat-stable catalase at 68°C . based on multiplex PCR, already optimized by Poroca et al.26, The cultures analyzed using the biochemical tests in this study for identifying mycobacterial species isolated from different were considered as references for comparison with the results clinical samples from patients diagnosed with pulmonary and obtained by multiplex PCR and PRA-hsp65. extrapulmonary tuberculosis. This test, in addition to contributing DNA extraction to a rapid and accurate differential diagnosis between tuberculosis and other mycobacteria, will certainly assist in the early and DNA was extracted and purifi ed from reference strains of appropriate therapeutic management of the patient. Mycobacterium tuberculosis (H37Rv). In all, 40 species of mycobacteria were isolated on a Lowenstein-Jensen medium from clinical samples obtained from 37 patients diagnosed METHODS with pulmonary and extrapulmonary tuberculosis using the conventional method described by Sambrook et al. using a Study population mixture of solvents and phenol chloroform32. Thirty-seven male and female patients over the age of Polymerase chain reaction and restriction 12 years with pulmonary and extrapulmonary tuberculosis enzyme analysis diagnoses, who were referred to public clinics in the The polymerase chain reaction and restriction enzyme metropolitan region of Recife of northeastern Brazil between analysis (PRA-hsp65) were performed using the techniques March 2008 and December 2009, were chosen for this study. described in Telenti et al.13 The identifi cation was determined The types of biological samples collected were chosen based by comparing the sizes of the fragments with the algorithm on the different clinical forms of the disease. The diagnosis of described in the PRASITE site (http://app.chuv.ch/prasite/ tuberculosis was made by the attending physician in accordance index.html)17. with the standards