Rapid identification of clinically relevant Nocardia species using real-time PCR with SYBR Green and melting-curve analysis

Molecular detection of Nocardia: development and application of a real-time PCR assay in sputum and bronchoalveolar lavage fluid samples

The diagnosis of pulmonary nocardiosis remains challenging. Rapid detection of Nocardia is of primary importance for early diagnosis and precise treatment of nocardiosis. In this study, our objective was to develop and validate a new TaqMan real-time PCR (qPCR) assay for rapidly detecting Nocardia spp. in respiratory samples. Based on published sequence data, primers in a conserved region of the 16S rRNA gene and a probe within that region that was specific for Nocardia were designed. The distinction effect of the qPCR assay was assessed between Nocardia and other respiratory-associated bacteria. Furthermore, the specificity and sensitivity of the assay were evaluated in respiratory clinical samples (n = 205), compared to the results of 16S rRNA gene amplicon sequencing and clinical diagnosis. The qPCR assay exhibited high specificity, sensitivity, repeatability, and reproducibility. The limit of detection of standard plasmid DNA was 3 × 10² copies/mL. Additionally, the qPCR assay was applied to the direct detection of 205 clinical respiratory samples. The specificity and sensitivity of the qPCR were all 100% compared to 16S rRNA gene amplicon sequencing, as well as 98.4% and 100% compared to clinical diagnosis respectively. The qPCR yielded results within 3 h of sample processing, compared to several days for culture, significantly reducing turnaround time. The results suggest that the new qPCR assay developed in this study provides reliable and rapid detection of Nocardia spp. in the respiratory tracts and is expected to reduce the time required for diagnosing and treating nocardiosis.

Loop-mediated Isothermal Amplification Test for Rapid Identification of Clinical Nocardia Isolates

Background: Nocardia is a Gram-positive and partially acid-fast bacterium. The species are widely distributed in the environment and cause severe human infections. Nocardiosis is not easily identifiable due to the lack of pathognomonic clinical signs. Objectives: The present study was designed to develop and evaluate a simple and quick method based on a loop-mediated isothermal amplification (LAMP) assay for detecting Nocardia spp isolated from bronchoalveolar lavage (BAL) samples. Methods: In this cross-sectional study, 357 BAL samples were collected from two teaching hospitals. The polymerase chain reaction (PCR) was performed using a set of species-specific primers for the 16S rRNA gene. Kinyoun acid-fast staining and culture were done on the Sabouraud dextrose plate. The optimal LAMP reaction condition was set at 65°C for 45 min, with the recognition limit as 1 pg DNA/tube and 100 CFU/reaction. In addition to calcein and manganous ions, agarose gel electrophoresis was used to visualize the amplified LAMP products. Results: Out of 357 BAL samples, 0 (0.0%), 4 (1.1%), 9 (2.5%), and 10 (2.8%) Nocardia strains were identified by direct staining of partial acid-fast, streak culture plate, PCR, and LAMP methods, respectively. Conclusions: We developed a new LAMP technique for the recognition of Nocardia, which is fast, very precise, simple, and low-cost. According to our knowledge, this is the first report of the LAMP method to detect Nocardia in clinical samples.

Targeting novel genes for simultaneous detection of five fungal and bacterial agents from BAL samples using multiplex PCR assay

The main purpose of our study was to evaluate multiplex PCR assay targeting novel genes for detection of five fungal and bacterial agents in BAL samples; because many fungi and bacteria that cause respiratory infections have similar clinical symptoms, diagnosing and differentiating them are therefore essential to controlling and treating them. A total of 100 BAL specimens from a mycobacterium and mycology laboratory were collected from patients suspected of having TB or other respiratory diseases. Novel DNA targets for Aspergillus, Nocardia, Cryptococcus, and Streptomyces were found using modified comparative genomic analysis. Afterward, the primers were designed based on novel targets, and the sensitivity and specificity of the newly designed primers were evaluated. These primers, along with specific primers for M. tuberculosis (SDR), were used in a multiplex PCR assay. The results showed the culture test to be more sensitive than the PCR assay in detecting M. tuberculosis. However, in the detection of Aspergillus, the PCR assay was more sensitive than the culture test. We also found one positive culture and two positive PCR assays for Nocardiosis. Cryptococcal infections and Streptomyces associated with lung diseases were not identified by the culture test nor by the PCR assay. The multiplex PCR is one of the cheapest molecular diagnostic tests readily available for BAL samples in clinical laboratories. This assay can be used for early reports of the causative agents and for treating patients with appropriate drugs at an early stage.

Disseminated nocardiosis caused by Nocardia elegans: a case report and review of the literature

BACKGROUND

Disseminated nocardiosis is a rare disease mostly occurring in immunocompromised patients.

METHODS

We report a case of disseminated nocardiosis in a diabetic patient with both pulmonary and cutaneous involvement. Nocardia elegans was isolated and identified using the 16s ribosomal RNA gene sequence data.

RESULTS

Clinical improvement was observed within 3 months after initiation of antimicrobial treatment with oral doxycycline, trimethoprim-sulfamethoxazole and intravenous penicillin, but the patient died 5 months later after arbitrary discontinuation of the treatment.

CONCLUSIONS

This is the first case report of disseminated nocardiosis caused by Nocardia elegans in China.

The use of PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) to detect bacterial and fungal colonization in healthy military service members

Background

The role of microbial colonization in disease is complex. Novel molecular tools to detect colonization offer theoretical improvements over traditional methods. We evaluated PCR/Electrospray Ionization-Time-of-Flight-Mass Spectrometry (PCR/ESI-TOF-MS) as a screening tool to study colonization of healthy military service members.

Methods

We assessed 101 healthy Soldiers using PCR/ESI-TOF-MS on nares, oropharynx, and groin specimens for the presence of gram-positive and gram-negative bacteria (GNB), fungi, and antibiotic resistance genes. A second set of swabs was processed by traditional culture, followed by identification using the BD Phoenix automated system; comparison between PCR/ESI-TOF-MS and culture was carried out only for GNB.

Results

Using PCR/ESI-TOF-MS, at least one colonizing organism was found on each individual: mean (SD) number of organisms per subject of 11.8(2.8). The mean number of organisms in the nares, groin and oropharynx was 3.8(1.3), 3.8(1.4) and 4.2(2), respectively. The most commonly detected organisms were aerobic gram-positive bacteria: primarily coagulase-negative Staphylococcus (101 subjects: 341 organisms), Streptococcus pneumoniae (54 subjects: 57 organisms), Staphylococcus aureus (58 subjects: 80 organisms) and Nocardia asteroides (45 subjects: 50 organisms). The mecA gene was found in 96 subjects. The most commonly found GNB was Haemophilus influenzae (20 subjects: 21 organisms) and the most common anaerobe was Propionibacterium acnes (59 subjects). Saccharomyces species (30 subjects) were the most common fungi detected. Only one GNB (nares E. coli) was identified in the same subject by both diagnostic systems.

Conclusion

PCR/ESI-TOF-MS detected common colonizing organisms and identified more typically-virulent bacteria in asymptomatic, healthy adults. PCR/ESI-TOF-MS appears to be a useful method for detecting bacterial and fungal organisms, but further clinical correlation and validation studies are needed.

The potential of high resolution melting analysis (hrma) to streamline, facilitate and enrich routine diagnostics in medical microbiology

BACKGROUND

Routine medical microbiology diagnostics relies on conventional cultivation followed by phenotypic techniques for identification of pathogenic bacteria and fungi. This is not only due to tradition and economy but also because it provides pure culture needed for antibiotic susceptibility testing. This review focuses on the potential of High Resolution Melting Analysis (HRMA) of double-stranded DNA for future routine medical microbiology.

METHODS AND RESULTS

Search of MEDLINE database for publications showing the advantages of HRMA in routine medical microbiology for identification, strain typing and further characterization of pathogenic bacteria and fungi in particular. The results show increasing numbers of newly-developed and more tailor-made assays in this field. For microbiologists unfamiliar with technical aspects of HRMA, we also provide insight into the technique from the perspective of microbial characterization.

CONCLUSIONS

We can anticipate that the routine availability of HRMA in medical microbiology laboratories will provide a strong stimulus to this field. This is already envisioned by the growing number of medical microbiology applications published recently. The speed, power, convenience and cost effectiveness of this technology virtually predestine that it will advance genetic characterization of microbes and streamline, facilitate and enrich diagnostics in routine medical microbiology without interfering with the proven advantages of conventional cultivation.

Cutaneous nocardiosis: report of two cases and review of the literature

BACKGROUND

Cutaneous nocardiosis is an uncommon infectious disease that presents as a primary cutaneous infection or as a disseminated disease. It is often misdiagnosed because of its rarity and nonspecific clinical picture.

METHODS

We report a case of each type. The first case is an immunocompetent patient who was infected by Nocardia while gardening and developed a superficial skin infection--one of the three clinical manifestations of primary cutaneous nocardiosis. The second case is an immunocompromised patient with pulmonary nocardiosis that extended to the skin as part of a disseminated disease.

RESULTS

The immunocompetent patient with primary cutaneous nocardiosis had the classical features of a superficial skin infection. He had a nodular–pustular lesion on the right arm, which appeared 7 days after gardening with bare hands. Nocardia was identified in a skin culture taken from a pustule, unfortunately not to the species level. Treatment with minocycline for 3 months resulted in full remission of the lesion. The immunocompromised patient with disseminated nocardiosis had high fever, productive cough, hemoptysis, and erythematous nodules and pustules on the extremities. N. brasiliensis was isolated from bronchial samples and skin. Treatment with a high dose of trimethoprim and sulfamethoxazole for five months resulted in full recovery from cutaneous and pulmonary complaints. No relapse of the infection was found on follow-up in either patient.

CONCLUSION

These cases demonstrate the need for a high degree of suspicion, focused clinical search, and appropriate laboratory procedures in the diagnosis and management of cutaneous nocardiosis.

Nocardiosis: updated clinical review and experience at a tertiary center

Nocardiosis is a rare opportunistic disease that affects mainly patients with deficient cell-mediated immunity, such as those with acquired immunodeficiency syndrome (AIDS) or transplant recipients. Pulmonary disease is the most common presentation in immunosuppressed patients and approximately one-third have a disseminated disease. Primary cutaneous nocardiosis is more frequently observed in immunocompetent patients with direct inoculation of the organism through professional exposure. The diagnosis can be challenging, as signs and symptoms are not specific and a high index of clinical of suspicion is necessary. Although gram stain, modified acid-fast stain, and cultures remain as the standard diagnostic tools, novel molecular techniques have changed the taxonomy of these organisms and, in some instances, have facilitated their identification. The disease has a marked tendency to recur and a high morbidity and mortality rate in immunosuppressed patients. Treatment is usually prolonged and an associated antibiotic treatment is preferred for severe disease. Although sulfonamides in combination with other antibiotics are still the treatment of choice, other associations such as imipenem plus amikacin are preferred in some centers. Linezolid is a useful alternative therapeutic agent due to its oral availability and activity against most of the isolates studied. Twenty-eight cases of nocardiosis were diagnosed at our center between January 1989 and April 2009. We report the epidemiologic characteristics of Nocardia spp. observed in our institution and discuss the risk factors, clinical features, diagnosis, and management of the disease.

Reverse line blot hybridization and DNA sequencing studies of the 16S-23S rRNA gene intergenic spacer regions of five emerging pathogenic Nocardia species

The objective of this study was to examine DNA sequence polymorphisms in the 16S-23S rRNA gene intergenic spacer (ITS) regions of five emerging pathogenic Nocardia species: Nocardia beijingensis, Nocardia blacklockiae, Nocardia thailandica, Nocardia elegans and Nocardia vinacea. A set of six isolates belonging to the species of interest and 135 isolates belonging to other Nocardia species was studied. A PCR-based reverse line blot (RLB) hybridization assay incorporating species- or intraspecies ITS rRNA gene operon-specific probes was then developed for species identification. Substantial intraspecies sequence variation among different ITS operons was identified. Four sequence types of N. thailandica, eight sequence types of N. beijingensis (four types for each of two strains) and five sequence types of N. blacklockiae, N. elegans and N. vinacea were found. The results represent the first evidence of ITS sequence heterogeneity in emerging species of Nocardia. By incorporating species/operon-specific probes into a RLB assay, unique RLB patterns were identified for each of the species and every sequence type. The PCR/RLB assay demonstrated high specificity and showed promise in both the identification and genotyping of Nocardia species. More detailed studies of the polymorphism within the ITS locus may further advance our capacity to reliably identify and subtype medically important Nocardia species.

Identification of pathogenic Nocardia species by reverse line blot hybridization targeting the 16S rRNA and 16S-23S rRNA gene spacer regions

Although 16S rRNA gene sequence analysis is employed most often for the definitive identification of Nocardia species, alternate molecular methods and polymorphisms in other gene targets have also enabled species determinations. We evaluated a combined Nocardia PCR-based reverse line blot (RLB) hybridization assay based on 16S and 16S-23S rRNA gene spacer region polymorphisms to identify 12 American Type Culture Collection and 123 clinical Nocardia isolates representing 14 species; results were compared with results from 16S rRNA gene sequencing. Thirteen 16S rRNA gene-based (two group-specific and 11 species-specific) and five 16S-23S spacer-targeted (two taxon-specific and three species-specific) probes were utilized. 16S rRNA gene-based probes correctly identified 124 of 135 isolates (sensitivity, 92%) but were unable to identify Nocardia paucivorans strains (n = 10 strains) and a Nocardia asteroides isolate with a novel 16S rRNA gene sequence. Nocardia farcinica and Nocardia cyriacigeorgica strains were identified by the sequential use of an N. farcinica-"negative" probe and a combined N. farcinica/N. cyriacigeorgica probe. The assay specificity was high (99%) except for weak cross-reactivity between the Nocardia brasiliensis probe with the Nocardia thailandica DNA product; however, cross-hybridization with closely related nontarget species may occur. The incorporation of 16S-23S rRNA gene spacer-based probes enabled the identification of all N. paucivorans strains. The overall sensitivity using both probe sets was >99%. Both N. farcinica-specific 16S-23S rRNA gene spacer-directed probes were required to identify all N. farcinica stains by using this probe set. The study demonstrates the utility of a combined PCR/RLB assay for the identification of clinically relevant Nocardia species and its potential for studying subtypes of N. farcinica. Where species assignment is ambiguous or not possible, 16S rRNA gene sequencing is recommended.

Pulmonary nocardiosis: risk factors, clinical features, diagnosis and prognosis

PURPOSE OF REVIEW

Pulmonary infection by Nocardia spp. has been recognized for the past 100 years. The number of cases of pulmonary nocardiosis reported in the literature is increasing, and in some cases, a diagnosis is reached even postmortem. This increase is partly due to the growing number of patients with depressed cellular immunity. The diagnosis of this infection, which has a high rate of mortality, is usually delayed, due to a nonspecific clinical-radiological presentation and the difficulties in cultivating the bacteria. This review analyzes the current situation, in order to better understand this infection and enhance awareness and clinical suspicion that would lead to further specific microbiological studies and treatment.

RECENT FINDINGS

The number of case series in the literature is increasing. This development may be due to an absolute increase in the number of immunocompromised patients, but also to improvements in laboratory techniques and molecular methods to detect nocardiosis.

SUMMARY

It is important to keep in mind, and suspect the presence of pulmonary nocardiosis in the immunodepressed patients with clinical pulmonary infection. Furthermore, the laboratory should be notified when Nocardia is suspected in a clinical specimen so that measures can be taken to optimize recognition and recovery of the organism.

Identification of Nocardia farcinica by a PCR primer amplifying a specific DNA band for the bacterium

A PCR primer specific to Nocardia farcinica was prepared based on sequence information of random amplified polymorphic DNA (RAPD) analysis. The PCR primer amplifies N. farcinica species only; no amplification was observed in 25 other Nocardia strains that we tested. Specificity of the primer for N. farcinica was also confirmed using other fungal and bacterial strains that are frequently isolated from clinical samples such as sputa and broncho alveolar lavage (VAL).