Rapid identification of mycolic acid patterns of mycobacteria by high-performance liquid chromatography using pattern recognition software and a Mycobacterium library

Mycobacterium avium: an overview

Mycobacterium avium is an environmental microorganism found in soil and water sources worldwide. It is the most prevalent species of nontuberculous mycobacteria that causes infectious diseases, especially in immunocompromised individuals. This review discusses and highlights key topics about M. avium, such as epidemiology, pathogenicity, glycopeptidolipids, laboratory identification, genotyping, antimicrobial therapy and antimicrobial resistance. Additionally, the main comorbidities associated with M. avium infection are discussed.

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.

Metabolomics biomarkers for tuberculosis diagnostics: current status and future objectives

Numerous studies have contributed to our current understanding of the complex biology of pulmonary tuberculosis and subsequently provided solutions to its control or eradication. Metabolomics, a newcomer to the Omics research domain, has significantly contributed to this understanding by identifying biomarkers originating from the disease-associated metabolome adaptations of both the microbe and host. These biomarkers have shed light on previously unknown disease mechanisms, many of which have been implemented toward the development of improved diagnostic strategies. In this review, we will discuss the role that metabolomics has played in tuberculosis research to date, with a specific focus on new biomarker identification, and how these have contributed to improved disease characterization and diagnostics, and their potential clinical applications.

Extracellular Alkaline Lipase from a Novel Fungus Curvularia sp. DHE 5: Optimisation of Physicochemical Parameters, Partial Purification and Characterisation

Thirty isolated fungal strains were screened for lipase production using Phenol Red plates, containing tributyrin as lipidic substrate, and a novel fungus identified genetically as Curvularia sp. DHE 5 was found as the most prominent strain. Various agro-industrial substrates were evaluated as inert supports for lipase production in solid-state fermentation. The highest yield of lipase ((83.4±2.2) U/g on dry mass basis) was reported with wheat bran medium after seven days of fermentation at pH=7.0, temperature of 30 °C, 70% moisture content, inoculum size of 1.27·10⁷ spore/mL and 2% olive oil as an inducer. Supplementation of the medium with 0.05% KCl as an ion source further increased lipase production to (88.9±1.2) U/g on dry mass basis. The enzyme was partially purified through ammonium sulphate fractionation (40%) followed by dialysis, and its optimum pH and temperature were reported at 8.0 and 50 °C, respectively, with remarkable pH and thermal stability.

Methodological and Clinical Aspects of the Molecular Epidemiology of Mycobacterium tuberculosis and Other Mycobacteria

Molecular typing has revolutionized epidemiological studies of infectious diseases, including those of a mycobacterial etiology. With the advent of fingerprinting techniques, many traditional concepts regarding transmission, infectivity, or pathogenicity of mycobacterial bacilli have been revisited, and their conventional interpretations have been challenged. Since the mid-1990s, when the first typing methods were introduced, a plethora of other modalities have been proposed. So-called molecular epidemiology has become an essential subdiscipline of modern mycobacteriology. It serves as a resource for understanding the key issues in the epidemiology of tuberculosis and other mycobacterial diseases. Among these issues are disclosing sources of infection, quantifying recent transmission, identifying transmission links, discerning reinfection from relapse, tracking the geographic distribution and clonal expansion of specific strains, and exploring the genetic mechanisms underlying specific phenotypic traits, including virulence, organ tropism, transmissibility, or drug resistance. Since genotyping continues to unravel the biology of mycobacteria, it offers enormous promise in the fight against and prevention of the diseases caused by these pathogens. In this review, molecular typing methods for Mycobacterium tuberculosis and nontuberculous mycobacteria elaborated over the last 2 decades are summarized. The relevance of these methods to the epidemiological investigation, diagnosis, evolution, and control of mycobacterial diseases is discussed.

Direct detection of Mycobacterium tuberculosis in sputum: A validation study using solid phase extraction-gas chromatography-mass spectrometry

Tuberculosis (TB) remains a worldwide health problem, especially in developing countries. Correct identification of Mycobacterium tuberculosis (MTB) infection is extremely important for providing appropriate treatment and care to patients. Here we describe a solid phase extraction-gas chromatography-mass spectrometry method (SPE-THM-GC-MS) for the detection of five biomarkers for M. tuberculosis. The method for classification is developed and validated through the analysis of 112 sputum samples from patients suspected of having TB. Twenty of twenty-five MTB culture-positive sputum samples were correctly classified as positive by our improved SPE-THM-GC-MS method. Eighty-five of eighty-seven MTB culture-negative samples were also negative by SPE-THM-GC-MS. The overall sensitivity of the new SPE-THM-GC-MS method is 80% (20/25) and the specificity is 98% (85/87) compared with culture. The method proved to be reliable and, although complex in principle, easy to operate due to the high degree of automation.

Differential diagnostic assays for discriminating mycobacteria, especially for nontuberculous mycobacteria: what does the future hold?

Mycobacteria infections are an important medical problem, and many are regarded as emerging and re-emerging diseases. Mycobacterium tuberculosis, the causative agent of tuberculosis, remains a leading cause of human morbidity and mortality worldwide, with approximately 8.6 million cases and 1.3 million deaths in 2012. In addition, the incidence of nontuberculous Mycobacterium infection has significantly increased, especially among developed countries. Although phenotypical appearances such as culture characteristics and/or susceptibility to anti-Mycobacterium drugs are variable between different mycobacterial species, early diagnosis is crucial in terms of patient treatment and clinical outcome. In this manuscript, we describe the development of diagnostic techniques, from the classical/conventional to the most recent advances, and provide an overview of the future direction of discrimination procedures.

IDENTIFICATION OF MYCOBACTERIUM GENAVENSE IN A DIANA MONKEY (CERCOPITHECUS DIANA) BY POLYMERASE CHAIN REACTION AND HIGH-PERFORMANCE LIQUID CHROMATOGRAPHY

A 25-yr-old Diana monkey (Cercopithecus diana) with a 1.5-yr history of chronic colitis and diarrhea was found to have disseminated granulomatous disease with intralesional acid fast bacilli. Bacilli were identified as Mycobacterium genavense by polymerase chain reaction, sequencing of the 16S-23S ribosomal RNA intergenic spacer (ITS) gene, and mycolic acid analysis by high-performance liquid chromatography. Mycobacterium genavense is a common cause of mycobacteriosis in free-ranging and captive birds. In addition, recognition of opportunistic infection in human immunodeficiency virus-positive patients is increasing. Disease manifestations of M. genavense are similar to Mycobacterium avium complex (MAC) and include fever, wasting, and diarrhea with disseminated disease. Similar clinical signs and lesions were observed in this monkey. Mycobacterium genavense should be considered as a differential for disseminated mycobacterial disease in nonhuman primates as this agent can mimic MAC and related mycobacteria.

Tsukamurella infection: a rare cause of community-acquired pneumonia

A 79-year-old Asian man was admitted with community-acquired pneumonia. Antimycobacterial therapy was initiated when sputum smears revealed acid fast bacilli. The patient was, however, diagnosed to have pneumonia secondary to Tsukamurella spp. This is an exceedingly rare cause of pneumonia, especially in immunocompetent individuals. Clinical presentation, diagnosis and treatment strategies of Tsukamurella pneumonia are discussed with a literature review.

Polymerase chain reaction-restriction fragment length polymorphism of the rpoB gene for identification of Mycobacterium avium subsp. paratuberculosis and differentiation of Mycobacterium avium subspecies

Mycobacterial speciation by polymerase chain reaction (PCR)-restriction fragment length polymorphism analysis (PRA) of the rpoB gene was evaluated for identification of Mycobacterium avium subsp. paratuberculosis (MAP) and other Mycobacterium avium complex (MAC) members to the species or subspecies level by comparison with conventional methods including hsp65 sequencing, high-performance liquid chromatography, and PCR for accepted species- or subspecies-specific genomic targets. A total of 185 type and clinical mycobacterial strains from humans, animals, and environments were tested. A 360-bp PCR product was subsequently digested with MspI, HaeIII, and SmaI restriction enzymes. The PRA using SmaI restriction showed a unique digestion pattern for MAP distinguishing it from other MAC members and other Mycobacterium spp. Moreover, HaeIII and MspI restriction of the rpoB gene enabled MAC-species and -subspecies discrimination. The rpoB-PRA using SmaI or MspI and HaeIII restriction of the rpoB gene is a simple, convenient, and reliable confirmatory assay for simultaneous identification of MAP and other MAC members.

Diagnosis and species identification of mycobacterial infections by polymerase chain reaction-restriction fragment length polymorphism analysis of sterile body fluids

BACKGROUND/AIMS

The development of effective, accurate, and rapid diagnostic methods for Mycobacterium infection and mycobacterial species identification is required. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is an easy, rapid and inexpensive technique for identifying Mycobacterium spp.

METHODS

We performed PCR-RFLP to detect and identify Mycobacterium spp. from 10 sterile body fluids, including ascites, cerebrospinal fluid, pleural fluid, synovial fluid, and peritoneal dialysis fluid. Clinical samples were collected from patients with diagnoses of definite, probable or suspected mycobacterial infection. The conserved RNA polymerase genes of Mycobacterium spp. were amplified by PCR.

RESULTS

The amplified 360-bp region of rpoB was digested with the restriction enzyme MspI or HaeIII. The PCR-RFLP results for the clinical samples were identical to those for M. tuberculosis, M. fortuitum, M. intracellulare, and M. avium. In addition, the results of the PCR-RFLP were identical to those obtained by DNA sequencing.

CONCLUSIONS

PCR-RFLP analysis of sterile body fluids may be a useful method for the diagnosis of mycobacterial infections and for the differentiation of mycobacterial species.

Rapid mycobacterial liquid culture-screening method for Mycobacterium avium complex based on secreted antigen-capture enzyme-linked immunosorbent assay

Sensors in automated liquid culture systems for mycobacteria, such as MGIT, BacT/Alert 3D, and Trek ESP II, flag growth of any type of bacteria; a positive signal does not mean that the target mycobacteria are present. All signal-positive cultures thus require additional and often laborious testing. An immunoassay was developed to screen liquid mycobacterial cultures for evidence of Mycobacterium avium complex (MAC). The method, called the MAC-enzyme-linked immunosorbent assay (ELISA), relies on detection of MAC-specific secreted antigens in liquid culture. Secreted MAC antigens were captured by the MAC-ELISA with polyclonal anti- Mycobacterium avium subsp. paratuberculosis chicken immunoglobulin Y (IgY), detected using rabbit anti-MAC IgG, and then revealed using horseradish peroxidase-conjugated goat anti-rabbit IgG. When the MAC-ELISA was evaluated using pure cultures of known mycobacterial (n = 75) and nonmycobacterial (n = 17) organisms, no false-positive or false-negative MAC-ELISA results were found. By receiver operator characteristic (ROC) analysis of 1,275 previously identified clinical isolates, at the assay optimal cutoff the diagnostic sensitivity and specificity of the MAC-ELISA were 92.6% (95% confidence interval [95% CI], 90.3 to 94.5) and 99.9% (95% CI, 99.2 to 100), respectively, with an area under the ROC curve of 0.992. Prospective evaluation of the MAC-ELISA with an additional 652 clinical samples inoculated into MGIT ParaTB medium and signaling positive per the manufacturer's instructions found that the MAC-ELISA was effective in determining those cultures that actually contained MAC species and warranting the resources required to identify the organism by PCR. Of these 652 MGIT-positive cultures, the MAC-ELISA correctly identified 96.8% (of 219 MAC-ELISA-positive cultures) as truly containing MAC mycobacteria, based on PCR or high-performance liquid chromatography (HPLC) as reference tests. Only 6 of 433 MGIT signal-positive cultures (1.4%) were MAC-ELISA false negative, and only 7 of 219 MGIT signal-negative cultures (3.2%) were false positive. The MAC-ELISA is a low-cost, rapid, sensitive, and specific test for MAC in liquid cultures. It could be used in conjunction with or independent of automated culture reading instrumentation. For maximal accuracy and subspecies-specific identification, use of a confirmatory multiplex MAC PCR is recommended.

Nontuberculous mycobacterial infections

CONTEXT

Nontuberculous mycobacteria include numerous acid-fast bacilli species, many of which have only recently been recognized as pathogenic. The diagnosis of mycobacterial disease is based on a combination of clinical features, microbiologic data, radiographic findings, and histopathologic studies.

OBJECTIVE

To provide an overview of the clinical and pathologic aspects of nontuberculous mycobacteria infection, including diagnostic laboratory methods, classification, epidemiology, clinical presentation, and treatment.

DATA SOURCES

Review of the pertinent literature and published methodologies.

CONCLUSIONS

Nontuberculous mycobacteria include numerous acid-fast bacilli species, many of which are potentially pathogenic, and are classified according to the Runyon system based on growth rates and pigment production. Their slow growth hinders cultures, which require special medium and prolonged incubation. Although such methods are still used, newer nucleic acid-based technologies (polymerase chain reaction and hybridization assays) can rapidly detect and speciate some mycobacteria--most notably, distinguishing Mycobacterium tuberculosis from other species. Infections caused by these organisms can present as a variety of clinical syndromes, not only in immunocompromised patients but also in immunocompetent hosts. Most common among these are chronic pulmonary infections, superficial lymphadenitis, soft tissue and osteoarticular infections, and disseminated disease. Treatment of nontuberculous mycobacterial infections is difficult, requiring extended courses of multidrug therapy with or without adjunctive surgical intervention.

Mycobacterium avium in the postgenomic era

The past several years have witnessed an upsurge of genomic data pertaining to the Mycobacterium avium complex (MAC). Despite clear advances, problems with the detection of MAC persist, spanning the tests that can be used, samples required for their validation, and the use of appropriate nomenclature. Additionally, the amount of genomic variability documented to date greatly outstrips the functional understanding of epidemiologically different subsets of the organism. In this review, we discuss how postgenomic insights into the MAC have helped to clarify the relationships between MAC organisms, highlighting the distinction between environmental and pathogenic subsets of M. avium. We discuss the availability of various genetic targets for accurate classification of organisms and how these results provide a framework for future studies of MAC variability. The results of postgenomic M. avium study provide optimism that a functional understanding of these organisms will soon emerge, with genomically defined subsets that are epidemiologically distinct and possess different survival mechanisms for their various niches. Although the status quo has largely been to study different M. avium subsets in isolation, it is expected that attention to the similarities and differences between M. avium organisms will provide greater insight into their fundamental differences, including their propensity to cause disease.

Rapid species and strain differentiation of non-tubercoulous mycobacteria by Fourier-Transform Infrared microspectroscopy

Rapid identification of non-tuberculous mycobacteria (NTM) species is important in clinical laboratories to stipulate the appropriate therapy and to offer a comprehensive infection control. We applied Fourier-Transform Infrared microspectroscopy to evaluate, whether the most frequent species of NTM can be rapidly and uniformly identified by this method using microcolonies of NTM growing on solid nutrient agar plates. To establish a standardized protocol, the heterogeneity of cell growth within the microcolonies and the reproducibility of measuring the IR spectra from whole mycobacterial microcolonies were first studied. Hierarchical cluster analysis applied to spectra obtained by linear mapping across microcolony imprints from fast- and slow-growing NTM revealed only little spectral variance between the various microcolony zones. In parallel, when repetitive measurements were performed on independently grown whole single microcolonies with diameters of 80 and 140 mum, excellent reproducibility could be achieved, verifying that mycobacterial microcolonies are well suited for FT-IR-based identification. Twenty-eight different and well-defined strains, comprising the most frequent species of NTM isolated in clinical laboratories, were used to create a classification system based on FT-IR spectra from single microcolonies. Hierarchical cluster analysis allowed the assignment of all isolates measured in replicates to their correct species-specific clusters. Additionally, a clear separation of all strains into strain-specific sub-clusters was observed. These results demonstrate the potential of FT-IR microspectroscopy to rapidly differentiate NTM at the species and strain level. The data so far obtained suggest that an extended spectral database, containing more NTM strains and covering a broader biological variance, may provide a practical solution to rapidly identify unknown NTM isolates in routine clinical-microbiological laboratories with the additional possibility to type these microorganisms at the sub-species level.

Volatile biomarkers of pulmonary tuberculosis in the breath

Pulmonary tuberculosis may alter volatile organic compounds (VOCs) in breath because Mycobacteria and oxidative stress resulting from Mycobacterial infection both generate distinctive VOCs. The objective of this study was to determine if breath VOCs contain biomarkers of active pulmonary tuberculosis. Head space VOCs from cultured Mycobacterium tuberculosis were captured on sorbent traps and assayed by gas chromatography/mass spectroscopy (GC/MS). One hundred and thirty different VOCs were consistently detected. The most abundant were naphthalene, 1-methyl-, 3-heptanone, methylcyclododecane, heptane, 2,2,4,6,6-pentamethyl-, benzene, 1-methyl-4-(1-methylethyl)-, and cyclohexane, 1,4-dimethyl-. Breath VOCs were assayed by GC/MS in 42 patients hospitalized for suspicion of pulmonary tuberculosis and in 59 healthy controls. Sputum cultures were positive for Mycobacteria in 23/42 and negative in19/42 patients. Breath markers of oxidative stress were increased in all hospitalized patients (p<0.04). Pattern recognition analysis and fuzzy logic analysis of breath VOCs independently distinguished healthy controls from hospitalized patients with 100% sensitivity and 100% specificity. Fuzzy logic analysis identified patients with positive sputum cultures with 100% sensitivity and 100% specificity (95.7% sensitivity and 78.9% specificity on leave-one-out cross-validation); breath VOC markers were similar to those observed in vitro, including naphthalene, 1-methyl- and cyclohexane, 1,4-dimethyl-. Pattern recognition analysis identified patients with positive sputum cultures with 82.6% sensitivity (19/23) and 100% specificity (18/18), employing 12 principal components from 134 breath VOCs. We conclude that volatile biomarkers in breath were sensitive and specific for pulmonary tuberculosis: the breath test distinguished between "sick versus well" i.e. between normal controls and patients hospitalized for suspicion of pulmonary tuberculosis, and between infected versus non-infected patients i.e. between those whose sputum cultures were positive or negative for Mycobacteria.

[New methods for mycobacteria identification]

Currently, the genus Mycobacterium comprises more than 100 different species, many of which cause significant clinical infections with high morbidity and mortality. Mycobacteria identification by conventional methods (rate and optimal temperature of growth, pigment production, colony morphology, and biochemical characteristics) has been the standard in most clinical microbiology laboratories. However, this phenotypic approach has considerable limitations, since numerous species cannot be differentiated. Moreover, because of the slow growth of these microorganisms, the results may not be available until 2-4 weeks after the initial isolation. Therefore, one of the most important challenges for clinical mycobacteriology laboratories is rapid and accurate identification of this variety of microorganism. This review aims to briefly describe several alternative procedures for mycobacterial identification. Although analysis of cell wall lipids (mycolic acids) by high-performance liquid chromatography is an interesting and well-known option, the most promising innovation for mycobacteria identification is the use of rapid molecular methods such as nucleic acid probes and, especially, genomic amplification methods.

Mycobacterium parascrofulaceum sp. nov., novel slowly growing, scotochromogenic clinical isolates related to Mycobacterium simiae

A group of pigmented, slowly growing mycobacteria identified by 16S rRNA gene sequencing as ‘MCRO 33’ (GenBank accession no. AF152559) have been isolated from several clinical specimens in various laboratories across Canada. Genotypically, the organism is most closely related to Mycobacterium simiae. However, it presents with a similar phenotypic profile to Mycobacterium scrofulaceum. Several reference strains obtained from ATCC and TMC culture collections, previously identified as M. scrofulaceum or M. simiae, have also been found to possess the MCRO 33 16S rRNA gene sequence. Biochemical testing, susceptibility testing, HPLC, hsp65 gene and 16S–23S spacer (ITS1) sequencing were performed on clinical and reference strains to characterize further this unique species. Of the clinical strains, one was isolated from a cervix biopsy whereas all other clinical isolates were obtained from respiratory samples. In one patient, symptoms, imaging and repeat clinical specimens positive on culture for this organism were suggestive of active clinical disease. The description of this species, for which the name Mycobacterium parascrofulaceum sp. nov. is proposed, follows the present trend of a large number of novel Mycobacterium species identified due in great part to sequence-based methods. The type strain is HSC68T (=ATCC BAA-614T=DSM 44648T).

Characterization of a novel group of mycobacteria and proposal of Mycobacterium sherrisii sp. nov

We describe here the characterization of five isolates of Mycobacterium simiae-like organisms representing a novel group based on whole-cell fatty acid analysis and genotypic evaluation. Two of the five isolates in this study, W55 and W58, were previously considered to belong to M. simiae serotype 2. Analysis of cellular fatty acids by gas-liquid chromatography indicated a close clustering of this group, which was well differentiated from the other M. simiae-like species. Molecular characterization was performed by nucleic acid sequencing of the small subunit rRNA gene and the gene encoding the 65-kDa heat shock protein and genomic DNA hybridization. Sequence analysis of the entire 16S rRNA gene showed a unique sequence most closely related to those of M. triplex and M. simiae. The hsp65 partial gene sequence was identical for the five isolates, with 97% identity to the M. simiae type strain. However, qualitative whole genomic DNA hybridization analysis confirmed that this group is genetically distinct from M. simiae and M. triplex. Antimicrobial susceptibilities for this group resemble those of M. simiae and M. lentiflavum. We conclude that this group represents a unique Mycobacterium species for which we propose the name Mycobacterium sherrisii sp. nov.

The HPLC-double-cluster pattern of some Mycobacterium gordonae strains is due to their dicarboxy-mycolate content

The mycolic acids of several strains of Mycobacterium gordonae were examined by chromatographic and spectroscopic techniques. Both HPLC and TLC revealed two patterns of mycolates among the M. gordonae strains studied. As determined by TLC, one pattern was composed of alpha-, methoxy- and keto-mycolates; the other was composed of these mycolates plus an additional component, which was identified as dicarboxy-mycolates. The dicarboxy-mycolates were only found in those M. gordonae strains that displayed a so-called HPLC-double-cluster pattern. Detailed structural analyses of the dicarboxy-mycolates indicated that these compounds contained predominantly 61-65 carbon atoms (C(63) was the major component) and a trans-1,2-disubstituted cyclopropane ring. Thus, the dicarboxy-mycolate content of strains of M. gordonae determines their HPLC pattern. In spite of the differences in their HPLC patterns, and although they belonged to different PCR-restriction length polymorphism clusters, all of the M. gordonae strains examined in this study were closely related on the basis of the structural features of their alpha-, keto- and methoxy-mycolates; the predominant alpha-mycolates contained two cis-1,2-disubstituted cyclopropane rings, the major keto-mycolates contained a trans-1,2-disubstituted cyclopropane ring and the methoxy-mycolates contained one cis- or one trans-1,2-disubstituted cyclopropane ring. It is noteworthy that the strains containing dicarboxy-mycolates also displayed significant amounts of alpha-mycolates that contained one cis-1,2-disubstituted cyclopropane ring and one cis double bond. The results obtained in this study demonstrate heterogeneity among M. gordonae strains.

Central venous catheter-related bacteremia due to Tsukamurella species in the immunocompromised host: a case series and review of the literature

We report 6 cases of bacteremia due to Tsukamurella species, all of which were in immunosuppressed patients with indwelling central venous catheters (CVCs). Fewer than 20 cases of serious illness due to these gram-positive bacilli have been reported in the medical literature; these cases have mostly been ascribed to the species Tsukamurella paurometabola. Tsukamurella species are frequently misidentified as Rhodococcus or Corynebacterium species. We used high-performance liquid chromatography to identify these organisms to the genus level and 16S ribosomal RNA gene sequencing and DNA-DNA dot blots for species identification. Three of our isolates were identified as Tsukamurella pulmonis, 1 was identified as Tsukamurella tyrosinosolvans, and 1 was identified as a unique species. One isolate was not maintained long enough for species identification. All patients were successfully treated with antimicrobial therapy and CVC removal. Infection with this organism should be considered in the immunosuppressed patient with an indwelling CVC and gram-positive bacilli in the blood.

Nontuberculous mycobacteria in the environment

It is likely that the incidence of infection by environmental opportunistic mycobacteria will continue to rise. Part of the rise will be caused by the increased awareness of these microbes as human pathogens and improvements in methods of detection and culture. Clinicians and microbiologists will continue to be challenged by the introduction of new species to the already long list of mycobacterial opportunists (see Table 3). The incidence of infection will also rise because an increasing proportion of the population is aging or subject to some type of immunosuppression. A second reason for an increase in the incidence of environmental mycobacterial infection is that these microbes are everywhere. They are present in water, biofilms, soil, and aerosols. They are natural inhabitants of the human environment, especially drinking water distribution systems. Thus, it is likely that everyone is exposed on a daily basis. It is likely that certain human activities can lead to selection of mycobacteria. Important lessons have been taught by study of cases of hypersensitivity pneumonitis associated with exposure to metalworking fluid. First, the implicated metalworking fluids contained water, the likely source of the mycobacteria. Second, the metalworking fluids contain hydrocarbons (e.g., pine oils) and biocides (e.g., morpholine) both of which are substrates for the growth of mycobacteria [53,193]. Third, outbreak of disease followed disinfection of the metalworking fluid [136,137]. Although the metalworking fluid was contaminated with microorganisms, it was only after disinfection that symptoms developed in the workers. Because mycobacteria are resistant to disinfectants, it is likely that the recovery of the mycobacteria from the metalworking fluid [137] was caused by their selection. Disinfection may also contribute, in part, to the persistence of M avium and M intracellulare in drinking water distribution systems [33,89,240]. M avium and M intracellulare are many times more resistant to chlorine, chloramine, chlorine dioxide, and ozone than are other water-borne microorganisms [141,236]. Consequently, disinfection of drinking water results in selection of mycobacteria. In the absence of competitors, even the slowly growing mycobacteria can grow in the distribution system [33]. It is likely that hypersensitivity pneumonitis in lifeguards and therapy pool attendants [139] is caused by a similar scenario.

GenoType mycobacterium assay for identification of mycobacterial species isolated from human clinical samples by using liquid medium

The GenoType Mycobacterium assay was used to identify 98 mycobacteria isolates by using liquid cultures from positive BACTEC, MGIT, and ESP bottles. This system identifies 16 mycobacteria. There was complete agreement between the GenoType results and the laboratory identifications for Mycobacterium tuberculosis complex and other Mycobacterium spp. GenoType also identified mixed mycobacterial infections.

Comparison of methods for Identification of Mycobacterium abscessus and M. chelonae isolates

Mycobacterium abscessus and Mycobacterium chelonae are two closely related species that are often not distinguished by clinical laboratories despite the fact they cause diseases requiring different treatment regimens. Multilocus enzyme electrophoresis, PCR-restriction fragment length polymorphism analysis of the 65-kDa heat shock protein gene, biochemical tests, and high-performance liquid chromatography of mycolic acids were used to identify 75 isolates as either M. abscessus or M. chelonae that were originally submitted for drug susceptibility testing. Only 36 of these isolates were submitted with an identification at the species level. Using the above methods, 46 of the isolates were found to be M. abscessus and 29 were identified as M. chelonae. Eight isolates originally submitted as M. chelonae were identified as M. abscessus, and one isolate submitted as M. abscessus was found to be M. chelonae. The four identification methods were in agreement in identifying 74 of the 75 isolates. In drug susceptibility testing, all isolates of M. abscessus exhibited resistance to tobramycin (MIC of 8 to > or =16 microg/ml), while all isolates of M. chelonae were susceptible to this drug (MIC of < or = 4 microg/ml). The results suggest that once an identification method is selected, clinical laboratories should be able to easily identify isolates of M. abscessus and M. chelonae.

Simple and rational approach to the identification of Mycobacterium tuberculosis, Mycobacterium avium complex species, and other commonly isolated mycobacteria

A novel PCR-restriction fragment length polymorphism analysis of the hsp65 gene was developed. The restriction patterns for Mycobacterium tuberculosis and Mycobacterium avium complex (MAC) species were designed to be highly distinct, and the overall number of restriction patterns was designed to be limited. Four hundred specimens (17 reference strains and 383 clinical isolates) were tested, of which 98 were M. tuberculosis and 132 were MAC species. The assay was virtually 100% sensitive and specific for M. tuberculosis and MAC species. Moreover, it gave highly concordant results for other mycobacterial species other than M. terrae complex species. This assay can be completed in one day and is user-friendly and robust. Therefore, it is highly suitable for large-scale use in a clinical laboratory.

Mycolic acid analysis by high-performance liquid chromatography for identification of Mycobacterium species

Mycobacterium tuberculosis is the etiologic agent of tuberculosis and can be accurately detected by laboratories using commercial genetic tests. Nontuberculosis mycobacteria (NTM) causing other mycobacterioses can be difficult to identify. The identification processes are confounded by an increasing diversity of newly characterized NTM species. The ubiquitous nature of NTM, combined with their potential to be opportunistic pathogens in immunocompromised as well as nonimmunodeficient patients, further complicates the problem of their identification. Since clinical case management varies depending on the etiologic agent, laboratories must identify the species in a timely manner. However, only a few identification methods can detect the species diversity within the Mycobacterium genus. Over the last decade, high-performance liquid chromatography analysis of the mycolic acids has become an accepted method for identification of mycobacteria. In this review, we assess its development and usefulness as an identification technique for Mycobacterium species.

Modern laboratory diagnosis of mycobacterial infections

This review summarises recent advances made in microscopic techniques (fluorescence and peptide nucleic acids) and culture techniques (solid, liquid, radiometric, and non-radiometric systems) and in the development of rapid methods for the identification of mycobacterial cultures (high performance liquid chromatography, thin layer chromatography, RNA sequencing, and polymerase chain reaction restriction enzyme assays). The role of molecular amplification systems in identifying Mycobacterium tuberculosis is described. Most methods record high specificity and sensitivity for smear positive sputum but have variable sensitivity for sputum smear negative and extrapulmonary specimens. Specimen quality will affect the performance of these assays and organisational delays, such as the batching of specimens, can reduce the time saved. In house assays can be as effective as commercial systems as long as appropriate controls are used.

Evaluation of the LiPA MYCOBACTERIA assay for identification of mycobacterial species from BACTEC 12B bottles

The LiPA MYCOBACTERIA (Innogenetics NV, Ghent, Belgium) assay was used to identify mycobacterial isolates using culture fluid from positive BACTEC 12B bottles. The LiPA method involves reverse hybridization of a biotinylated mycobacterial PCR fragment, a 16 to 23S rRNA spacer region, to oligonucleotide probes arranged in lines on a membrane strip, with detection via biotin-streptavidin coupling by a colorimetric system. This system identifies Mycobacterium species and differentiates M. tuberculosis complex, M. avium-M. intracellulare complex, and the following mycobacterial species: M. avium, M. intracellulare, M. kansasii, M. chelonae group, M. gordonae, M. xenopi, and M. scrofulaceum. The mycobacteria were identified in the laboratory by a series of tests, including the Roche AMPLICOR Mycobacterium tuberculosis (MTB) test, the Gen-Probe ACCUPROBE, and a PCR-restriction fragment length polymorphism (PCR-RFLP) analysis of the 65-kDa heat shock protein gene. The LiPA MYCOBACTERIA assay detected 60 mycobacterium isolates from 59 patients. There was complete agreement between LiPA and the laboratory identification tests for 26 M. tuberculosis complex, 9 M. avium, 3 M. intracellulare complex, 3 M. kansasii, 4 M. gordonae, and 5 M. chelonae group (all were M. abscessus) isolates. Three patient samples were LiPA positive for M. avium-M. intracellulare complex, and all were identified as M. intracellulare by the PCR-RFLP analysis. Seven additional mycobacterial species were LiPA positive for Mycobacterium spp. (six were M. fortuitum, and one was M. szulgai). The LiPA MYCOBACTERIA assay was easy to perform, and the interpretation of the positive bands was clear-cut. Following PCR amplification and gel electrophoresis, the LiPA assay was completed within 3 h.

Differentiation of Mycobacterium tuberculosis complex and nontuberculous mycobacterial liquid cultures by using peptide nucleic acid-fluorescence In situ hybridization probes

A blinded comparison of peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) with routine identification methods was performed on 74 consecutively positive mycobacterial liquid cultures. All Mycobacterium tuberculosis cultures (48 of 48) and 22 of 27 (81. 5%) nontuberculous cultures were correctly identified (including one mixed culture). Five isolates yielded no reaction with either probe and were identified as Mycobacterium xenopi, Mycobacterium fortuitum, or Mycobacterium flavescens.

Use of PCR-restriction fragment length polymorphism analysis of the hsp65 gene for rapid identification of mycobacteria in Brazil

Polymerase chain reaction amplification of part of the gene coding for the heat shock protein hsp65 followed by restriction enzyme analysis (PRA) is a recently described tool for rapid identification of mycobacteria. In this study, the speed and simplicity of PRA for identification of isolates of mycobacteria from patients with clinical symptoms of tuberculosis was evaluated and compared with identification results obtained by commercially available methods. Established PRA patterns were observed for nineteen isolates of Mycobacterium tuberculosis, eleven belonging to the complex M. avium-intracellulare, four of M. kansasii, one of M. fortuitum, one of M. abscessus, three of M. gordonae and one of the recently described species M. lentiflavum, as identified by commercially available methods. Two isolates of M. fortuitum and one of M. gordonae had unique and so far undescribed PRA patterns, suggesting geographically-related intra-species variation within the hsp65 sequence. We propose the inclusion of these new patterns in the PRA identification algorithm and have defined more accurately the molecular weight values of the restriction fragments. This is the first report on the isolation of M. lentiflavum in Brazil suggesting that identification by means of PRA could be useful for detection of mycobacterial species that are usually unnoticed. Where the use of several commercial techniques in combination was necessary for correct identification, PRA demonstrated to be a simple technique with good cost-benefit for characterization of all mycobacterial isolates in this study.

HPLC does not differentiate Mycobacterium paratuberculosis from Mycobacterium avium

HPLC, which is gaining its place as identification tool in mycobacteriology laboratories, has been proposed to distinguish Mycobacterium paratuberculosis from Mycobacterium avium. We had reported no significant difference between M. avium and M. paratuberculosis reference strain ATCC 19698. Because of the advantages offered by such a method, we enlarged our observations to include more isolates of M. paratuberculosis. Within the double cluster of peaks obtained by both M. avium and M. paratuberculosis, we could not find a consistent difference typical of M. paratuberculosis. Therefore, the present study confirmed that M. avium and M. paratuberculosis could not be distinguished by HPLC, raising doubts of a straightforward use of HPLC to identify M. paratuberculosis.

Mycobacterium szulgai osteomyelitis in an AIDS patient

Mycobacterium szulgai is a scotochromogen mycobacterium that accounts for < 1% of all human isolates of non-tuberculous mycobacteria. We report the first case of osteomyelitis caused by Mycobacterium szulgai in an AIDS patient. Culture from tissue was needed for isolation and identification of the organism, which was initially misidentified as Mycobacterium gordonae. Susceptibility testing to a fluoroquinolone was carried out and is also reported here for the first time. This case demonstrates the pathogenic potential of M. szulgai in this setting, and illustrates the need to obtain tissue specimens for culture in infected immunosuppressed patients to make a specific microbiological diagnosis and institute appropriate therapy.

Routine use of PCR-reverse cross-blot hybridization assay for rapid identification of Mycobacterium species growing in liquid media

A PCR-reverse cross-blot hybridization assay procedure that is able to rapidly identify 13 species of clinically relevant mycobacteria was evaluated for routine use in the identification of acid-fast isolates growing in BACTEC 460 TB (12B and 13A) and BACTEC 9000 MB (Myco/F) liquid media. Eight of the probes used were already described by Kox et al. (L. F. F. Kox et al., J. Clin. Microbiol. 33:3225-3233, 1995). In addition, we used six other probes specific for M. chelonae, M. malmoense or M. szulgai, M. genavense, M. gordonae, M. terrae, and M. marinum/M. ulcerans that we designed ourselves. This procedure allowed us to identify 459 mycobacterial species directly from broth cultures of 5,466 clinical samples collected over 1 year and processed with the radiometric or nonradiometric BACTEC system. Our results were in agreement with those obtained by conventional identification methods and also with those obtained by mycolic acid analysis by high-performance liquid chromatography. This assay seems to be a reliable procedure for the routine identification of mycobacteria, providing an accurate identification of mycobacterial isolates more rapidly than conventional tests, with remarkable implications for an efficacious specific antimycobacterial therapy.

Analysis of lipids reveals differences between 'Mycobacterium habana' and Mycobacterium simiae

Fatty and mycolic acids and the pattern of glycolipids were studied in a collection of 34 strains of 'Mycobacterium habana' and in two strains of Mycobacterium simiae. Major glycolipids of these micro-organisms were assigned to the glycopeptidolipid (GPL) structural type, but both mycobacteria differed in the patterns obtained by TLC. The strains of 'M. habana' were separated into four groups (A-D), taking into account the presence or absence of several polar GPLs: group A contained GPL-I, GPL-II and GPL-III; group B contained GPL-I, GPL-II', GPL-II and GPL-III; group C contained GPL-II', GPL-II and GPL-III; group D did not contain any of these compounds. Fatty acids of both bacteria were similar, and ranged from 14 to 26 carbon atoms, hexadecanoic, octadecenoic and tuberculostearic acids being predominant. Mycolic acids were also similar by TLC and HPLC, and consisted of alpha-, alpha'- and ketomycolates. Partial structural analysis by MS carried out in strains 'M. habana' TMC 5135 and M. simiae ATCC 25275T revealed that alpha- and ketomycolates ranged, in general, from 79 to 87 carbon atoms, and alpha'-mycolates from 58 to 67 carbon atoms. The alpha- and ketomycolates belonged to several structural series, and minor variations were found between the two strain examined. The data obtained justified the synonymy between 'M. habana' and M. simiae but indicated, in turn, that the former can be distinguished on the basis of GPL analysis. Most strains of 'M. habana' can be defined by the presence of GPL-II and GPL-III, a finding that could be useful in the quality control of potential vaccine strains.

Phenotypic and molecular characterization of three clinical isolates of Mycobacterium interjectum

Introduction of molecular biology-based technology into an Australian mycobacterial reference laboratory has resulted in the identification of three isolates of Mycobacterium interjectum in the past 12 months. Conventional phenotypic methods failed to identify the species of these isolates, and high-performance liquid chromatography found that only one of the three isolates had a mycolic acid pattern similar to that of the type strain. In contrast, all three isolates were rapidly identified as M. interjectum by 16S rRNA gene sequence analysis. Two isolates were recovered from the lymph nodes of children with cervical lymphadenitis, confirming the pathogenicity of this organism. However, the third isolate was obtained from the sputum of an elderly male with chronic lung disease without evidence of clinical or radiological progression, suggesting that isolation of M. interjectum should not imply disease. With the increasing use of molecular biology-based technology in mycobacterial laboratories, M. interjectum may be recognized more frequently as a pathogen or commensal organism.

Mycobacteriology laboratory

This review summarizes the most important features of different mycobacterial species, and addresses the issues of specimen collection and shipment, bacteriological diagnosis of tuberculosis and other mycobacterial infections, and drug susceptibility testing of different mycobacteria. Special emphasis is placed on the expected turnaround time for the various laboratory reports from different methods. The potential of new methods of today and tomorrow to expedite laboratory results are discussed.