Sequence-based identification of Mycobacterium species using the MicroSeq 500 16S rDNA bacterial identification system

The Characterisation of Lactococcus garvieae Isolated in an Outbreak of Septicaemic Disease in Farmed Sea Bass (Dicentrarchus labrax, Linnaues 1758) in Italy

In aquaculture, Lactococcus garvieae is a common fish pathogen that can cause significant economic losses in several fresh and saltwater species. Despite the extensive range of hosts, L. garvieae infection in sea bass (Dicentrarchus labrax) has rarely been reported. During the summer of 2023, an outbreak occurred in an inland farm in the Gulf of Follonica (Tuscany, Italy). Fish of various sizes were affected, showing apathy, inappetence, erratic swimming and eye lesions, while the mortality was low (2-3% per month). Anatomopathological examinations suggested a septicaemic infection characterised by melanosis, diffuse redness (skin and fins), paleness (gills and internal organs), haemorrhages and splenomegaly. Seventy swabs from the viscera of 14 subjects were collected and colonies similar to Streptococcus spp. grew from all the samples. Lactococcus garvieae was identified via the biochemical tests, API20STREP, MALDI-TOF, 16S rDNA and whole genome sequencing. Genetical characterisation revealed remarkable differences between this isolate and the strains previously isolated in Italian fish farms. Feed treatments with flumequine and erythromycin were ineffective. Considering the limited effects of antimicrobials, preventive measures, such as vaccination and biosecurity, should be implemented.

Mortality in farmed European eel (Anguilla anguilla) in Italy due to Streptococcus iniae

BACKGROUND

Streptococcal infections are one of the main causes of fish disease. During the last decade, Streptococcus iniae has become one of the most important aquatic pathogens worldwide, causing high losses in marine and freshwater finfish. Clinical signs in farmed fish include loss of appetite, lethargy and grouping at the bottom of the tank. Gross changes comprise darkening of the skin and haemorrhage at the basis of fins and opercula. To date, S. iniae has been isolated from several wild and farmed fish species but never in the European eel (Anguilla anguilla). In Europe, eel production from aquaculture is around 4500 tonnes and Italy is the third largest producer. This communication represents the first report of an outbreak of S. iniae infection in European eels.

CASE PRESENTATION

The outbreak occurred at an eel farm in northern Italy between May 2021 and September 2021. The outbreak caused about 2% mortality per month, resulting in the loss of about 10% of the farmed fish. The diseased eels showed apathy, lethargy, inactivity and inappetence. In July 2021, three eels were necropsied. Necropsy revealed skin and branchial hyperaemia, a few skin ulcers, and diffuse peritoneal congestion with a few haemorrhagic-like spot lesions. Swab samples for bacteriology were taken from the kidneys, liver, spleen, and brain. Additionally, four eels were opened and swap samples as above were taken. All the investigated eels were found dead. Bacteriological examination revealed growth of Streptococcus spp. from all samples. Identification of S. iniae was done by biochemical characterization, the API20STREP microsystem, 16S rDNA sequencing, and MALDI-TOF. Antimicrobial therapy (oxytetracycline and erythromycin) was ineffective.

CONCLUSIONS

This is the first report of S. iniae infection in the European eel. Although this may be an isolated outbreak, it is of concern due to the losses associated with this pathogen in fish worldwide and because the European eel is an endangered species. Due to the difficulties of controlling the disease with antimicrobials, it is advisable to plan other effective control measures, such as improving water quality and the environmental conditions, reducing fish density, improving biosecurity, and by using immunostimulants and, when possible, vaccines.

Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections

Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients’ samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.

Production optimization, stability and oil emulsifying potential of biosurfactants from selected bacteria isolated from oil-contaminated sites

Oil pollution is of increasing concern for environmental safety and the use of microbial surfactants in oil remediation has become inevitable for their efficacy and ecofriendly nature. In this work, biosurfactants of bacteria isolated from oil-contaminated soil have been characterized. Four potent biosurfactant-producing strains (SD4, SD11, SD12 and SD13) were selected from 27 isolates based on drop collapse assay and emulsification index, and identified as species belonging to Bacillus, Burkholderia, Providencia and Klebsiella, revealed from their 16S rRNA gene-based analysis. Detailed morphological and biochemical characteristics of each selected isolate were determined. Their growth conditions for maximum biosurfactant production were optimized and found quite similar among the four isolates with a pH of 3.0 and temperature 37°C after 6 or 7 days of growth on kerosene. The biosurfactants of SD4, SD11 and SD12 appeared to be glycolipids and that of SD13 a lipopeptide. Emulsification activity of most of the biosurfactants was stable at low and high temperatures (4-100°C), a wide range of pH (2-10) and salt concentrations (2-7% NaCl). Each biosurfactant showed antimicrobial activity against two or more pathogenic bacteria. The biosurfactants were well-capable of emulsifying kerosene, diesel and soya bean, and could efficiently degrade diesel.

Medical Management of Pulmonary Nontuberculous Mycobacterial Disease

Nontuberculous mycobacterial (NTM) lung infections are increasingly recognized as a cause of chronic pulmonary disease. This article focuses on the most common NTM species known to cause human lung disease and the treatment options currently available. The diagnosis of NTM lung disease is also discussed, emphasizing the necessity for treating clinicians to have sufficient familiarity of the mycobacteria laboratory to provide optimal patient management.

Recent advances in molecular diagnostics and understanding mechanisms of drug resistance in nontuberculous mycobacterial diseases

Accumulating evidence suggests that human infections caused by nontuberculous mycobacteria (NTM) are increasing worldwide, indicating that NTM disease is no longer uncommon in many countries. As a result of an increasing emphasis on the importance of differential identification of NTM species, several molecular tools have recently been introduced in clinical and experimental settings. These advances have led to a much better understanding of the diversity of NTM species with regard to clinical aspects and the potential factors responsible for drug resistance that influence the different outcomes of NTM disease. In this paper, we review currently available molecular diagnostics for identification and differentiation of NTM species by summarizing data from recently applied methods, including commercially available assays, and their relevant strengths and weaknesses. We also highlight drug resistance-associated genes in clinically important NTM species. Understanding the basis for different treatment outcomes with different causative species and drug-resistance mechanisms will eventually improve current treatment regimens and facilitate the development of better control measures for NTM diseases.

Molecular identification and distribution of non-tuberculous mycobacteria isolated from clinical specimens by PCR-sequencing method in West of Iran

BACKGROUND AND AIMS

Infections by non-tuberculous mycobacteria (NTM) has rapidly increased in recent years, due to high infection rates related to the populations at risk like immunocompromised individuals, patients predisposed by prior pulmonary. The aim of this study was to investigate the presence of NTM in clinical samples and genetic diversity using 16S rRNA and rpoB sequence analysis.

METHODS

A cross-sectional study was conducted on 45 diverse isolates collected from sputum in 2 years 2014-2015 using standard decontamination procedure. All mycobacterial isolates were grown on LJ medium and also conventional tests for preliminary identification of mycobacteria rely on traits and then DNA extraction. PCR was performed, and sequencing of 16S rRNA and rpoB genes was applied for NTM strains identification.

RESULTS

A total of 45 isolates collected, 37 samples (83%) were evaluated as NTM. All NTM strains using molecular methods by sequencing 16S rRNA and rpoB gene were identified, by this way 12 different species have been identified which sequencing of rpoB was able to identify all species. The major species obtained were Mycobacterium simiae (22%), M. fortuitum (19%), and M. abscessus (13%).

CONCLUSIONS

The results of our study showed that the patients were infected by a wide range of atypical mycobacteria. It was concluded that 16S rRNA gene sequencing coupled with rpoB marker is a high discriminatory power in identification of NTM. The presence of various species in clinical samples in Iran emphasizes the use of molecular method like sequence analysis of genes is necessary for reliable identification.

In Vitro Comparison of Ertapenem, Meropenem, and Imipenem against Isolates of Rapidly Growing Mycobacteria and Nocardia by Use of Broth Microdilution and Etest

We compared the activities of the carbapenems ertapenem, meropenem, and imipenem against 180 isolates of rapidly growing mycobacteria (RGM) and 170 isolates of Nocardia using the Clinical and Laboratory Standards Institute (CLSI) guidelines. A subset of isolates was tested using the Etest. The rate of susceptibility to ertapenem and meropenem was limited and less than that to imipenem for the RGM. Analysis of major and minor discrepancies revealed that >90% of the isolates of Nocardia had higher MICs by the broth microdilution method than by Etest, in contrast to the lower broth microdilution MICs seen for >80% of the RGM. Imipenem remains the most active carbapenem against RGM, including Mycobacterium abscessus subsp. abscessus For Nocardia, imipenem was significantly more active only against Nocardia farcinica Although there may be utility in testing the activities of the newer carbapenems against Nocardia, their activities against the RGM should not be routinely tested. Testing by Etest is not recommended by the CLSI.

Direct identification of mycobacteria from liquid media using a triplex real-time PCR coupled with pyrosequencing method

Culture in enriched broth, as well as on a solid medium, is recommended for primary isolation of mycobacteria. With the introduction of liquid mycobacterial culture methods, a substantial workload regarding the identification of culture-recovered mycobacterial species, particularly Mycobacterium tuberculosis complex (MTC), has been imposed on our laboratory. We thus developed a triplex, real-time PCR coupled with pyrosequencing assay that can directly identify mycobacterial species from liquid media, which can reduce the workload. In this assay, real-time PCR simultaneously detects MTC and Mycobacterium xenopi, and amplifies the region of 16S rRNA gene containing hypervariable region A for pyrosequencing analysis; subsequent, pyrosequencing identifies many other nontuberculous mycobacteria. The assay was evaluated using 333 DNA samples directly prepared from liquid media, including 24 reference strains and 309 clinical isolates. Three hundred and twenty-eight (98.5%) of the 333 samples were correctly identified. The remaining five were determined as indeterminate. In conclusion, this coupled assay would be an alternative method for rapid identification of mycobacteria directly from liquid media in a clinical laboratory with a high workload in regions where tuberculosis is endemic.

Development and evaluation of a rapid multiplex-PCR based system for Mycobacterium tuberculosis diagnosis using sputum samples

Global tuberculosis (TB) control and eradication is hampered by the unavailability of simple, rapid and affordable diagnostic tests deployable at low infrastructure microscopy centers. We have developed and evaluated the performance of a nucleic acid amplification test for detection of Mycobacterium tuberculosis (MTB), the NWU-TB test, in clinical sputum specimens from 306 patients with suspected pulmonary tuberculosis. The test involves sputum sample processing using a Lyser device within 7 min, followed by rapid multiplex-PCR on a fast thermal cycler within 25 min, and amplicon resolution on agarose gel electrophoresis. Samples were also examined for presence of MTB using smear microscopy, GeneXpert and MGIT culture. Results were assessed in comparison to a MGIT culture as gold standard. Of the 306 patients, 174 had a previous TB history or already on treatment, and 132 were TB naïve cases. The NWU-TB system was found to have an overall sensitivity and specificity of 80.8% (95% CI: 75-85.7) and 75.6% (95% CI: 64.9-84.4) respectively, in comparison to 85.3% (95% CI: 79.9-89.6) and 73.2% (95% CI: 62.2-82.4) respectively for GeneXpert; and 62.1% (95% CI: 55.3-68.4) and 56.1% (95% CI: 44.7-67) respectively for smear microscopy. The study has shown that the NWU-TB system allows detection of TB in less than two hours and can be utilized at low infrastructure sites to provide quick and accurate diagnosis at a very low cost.

Evaluation of a low-density hydrogel microarray technique for mycobacterial species identification

In addition to the obligatory pathogenic species of the Mycobacterium tuberculosis complex and Mycobacterium leprae, the genus Mycobacterium also includes conditionally pathogenic species that in rare cases can lead to the development of nontuberculous mycobacterial diseases. Because tuberculosis and mycobacteriosis have similar clinical signs, the accurate identification of the causative agent in a clinical microbiology laboratory is important for diagnostic verification and appropriate treatment. This report describes a low-density hydrogel-based microarray containing oligonucleotide probes based on the species-specific sequences of the gyrB gene fragment for mycobacterial species identification. The procedure included the amplification of a 352-nucleotide fragment of the gene and its hybridization on a microarray. The triple-species-specific probe design and the algorithm for hybridization profile recognition based on the calculation of Pearson correlation coefficients, followed by the construction of a profile database, allowed for the reliable and accurate identification of mycobacterial species, including mixed-DNA samples. The assay was used to evaluate 543 clinical isolates from two regions of Russia, demonstrating its ability to detect 35 mycobacterial species, with 99.8% sensitivity and 100% specificity when using gyrB, 16S, and internal transcribed spacer (ITS) fragment sequencing as the standard. The testing of clinical samples showed that the sensitivity of the assay was 89% to 95% for smear-positive samples and 36% for smear-negative samples. The large number of identified species, the high level of sensitivity, the ability to detect mycobacteria in clinical samples, and the up-to-date profile database make the assay suitable for use in routine laboratory practice.

Localized cutaneous infections in immunocompetent individuals due to rapidly growing mycobacteria

Rapidly growing mycobacteria (RGM) cause skin infections that are refractory to standard antibiotic regimens. Although typically associated with disseminated cutaneous or other systemic infections in immunocompromised patients, RGM sometimes cause localized cutaneous infections in immunocompetent hosts. These infections are almost always associated with precedent skin trauma and inoculation, and therefore have been implicated in outbreaks involving contaminated tattoo ink and inadequately sterilized acupuncture needles. Histologic features often include suppurative granulomatous inflammation, and microorganisms are rarely visualized with stains for acid-fast bacilli. The differential diagnosis includes granulomatous fungal and non-RGM bacterial infections as well as noninfectious suppurative or sarcoidlike conditions. Because no pathognomonic histologic features exist for cutaneous RGM infections, clinical suspicion and appropriate workup are essential to reach an accurate and timely diagnosis. Most localized cutaneous RGM infections in immunocompetent individuals respond well to either clarithromycin or amikacin, in combination with surgical debridement.

Evaluation of performance of the Real-Q NTM-ID kit for rapid identification of eight nontuberculous mycobacterial species

We evaluated a multiplex real-time PCR and melting curve analysis assay (Real-Q NTM-ID kit; Biosewoom, Seoul, South Korea) for the identification of eight common nontuberculous mycobacterial species, using 30 type strains and 230 consecutive clinical isolates. The concordance rate of this assay with multigene sequence-based typing was 97.0% (223/230 isolates).

Heterogeneity of Iranian clinical isolates of Mycobacterium fortuitum

BACKGROUND AND OBJECTIVES

The increase of infections caused by nontuberculous mycobacteria (NTM) is receiving increasing attention worldwide. Mycobacterium fortuitum is encountered with increasing frequency in clinical laboratories of Iran.

MATERIALS AND METHODS

Sequence variation of 48 M. fortuitum clinical isolates, were investigated by sequence analysis of the 16S-23S Internal Transcribed Spacer.

RESULTS

Twelve different sequence types (sequevar) were identified by sequence analysis of ITS region. Seven previously described sequevar including MfoA, MfoB, MfoC, MfoD, MfoE, MfoF and MfoG identified. Five novel sequevar namely MfoH, MfoI, MfoJ, MfoK and MfoL that were distinctly different from the previously described sequevar were detected among different clinical strains of M. fortuitum, from Iran.

CONCLUSION

This study showed that the ITS region possesses high discriminatory power between the clinical isolates up to the clonal level. The results also suggest the possibility of the existence of predominant clone of M. fortuitum in affected patients in Iran. The data also point to the conclusion that a large variety of M. fortuitum clone can produce disease although certain clones seem to be predominant.

Isolation and Identification of Mycobacteria from Soils at an Illegal Dumping Site and Landfills in Japan

In order to study the diversity and community of genus Mycobacterium in polluted soils, we tried to isolate mycobacteria from 11 soil samples collected from an illegal dumping site and 3 landfills in Japan. Using culture methods with or without Acanthamoeba culbertsoni, a total of 19 isolates of mycobacteria were obtained from 5 soil samples and 3 of them were isolated only by the co-culture method with the amoeba. Conventional biochemical tests and sequencing of the hsp65, rpoB, and 16S rRNA genes were performed for species identification of 17 of the 19 isolates. Among the 17 isolates, there was one isolate each of Mycobacterium vanbaalenii, Mycobacterium mageritense, Mycobacterium frederiksbergense, M. vanbaalenii or Mycobacterium austroafricanum, and Mycobacterium chubuense or Mycobacterium chlorophenolicum. The remaining 12 isolates could not be precisely identified at the species level. A phylogenic tree based on the hsp65 sequences indicated that 2 of the 12 isolates were novel species. In addition, 4 isolates were phylogenically close to species that degrade polycyclic aromatic hydrocarbons, which induce some cancers in humans. These results demonstrated that there were many hitherto-unreported mycobacteria in the polluted soils, and suggested that some mycobacteria might play roles in the natural attenuation and engineered bioremediation of contaminated sites with other microorganisms.

Evaluation of 16SpathDB 2.0, an automated 16S rRNA gene sequence database, using 689 complete bacterial genomes

Interpretation of 16S rRNA sequences is a difficult problem faced by clinical microbiologists and technicians. In this study, we evaluated the updated 16SpathDB 2.0 database, using 689 16S rRNA sequences from 689 complete genomes of medically important bacteria. Among these 689 16S rRNA sequences, none was wrongly identified, with 35.8% reported as a single bacterial species having >98% identity with the query sequence (category 1), 63.9% reported as more than 1 bacterial species having >98% identity with the query sequence (category 2), 0.3% reported to the genus level (category 3), and none reported as no match (category 4). For the 16S rRNA sequences of non-duplicated bacterial species reported as category 1 or 2, the percentage of bacterial species reported as category 1 was significantly higher for anaerobic Gram-positive/Gram-negative bacteria than aerobic/facultative anaerobic Gram-positive/Gram-negative bacteria. 16SpathDB 2.0 is a user-friendly and accurate database for 16S rRNA sequence interpretation in clinical laboratories.

Left thigh phlegmon caused by Nocardia farcinica identified by 16S rRNA sequencing in a patient with leprosy: a case report

BACKGROUND

In recent years, Nocardia farcinica has been reported to be an increasingly frequent cause of localized and disseminated infections in the immunocompromised patient. However, recent literature is limited. We report a case of left thigh phlegmon caused by N. farcinica that occurred in a patient with leprosy undergoing treatment with prednisone for leprosy reaction.

CASE PRESENTATION

We describe the case of left thigh phlegmon caused by Nocardia farcinica in a 54-year-old Italian man affected by multi-bacillary leprosy. The patient had worked in South America for 11 years. Seven months after his return to Italy, he was diagnosed with leprosy and started multi-drug antibiotic therapy plus thalidomide and steroids. Then, during therapy with rifampicin monthly, minocycline 100 mg daily, moxifloxacin 400 mg daily, and prednisone (the latter to treat type 2 leprosy reaction), the patient complained of high fever associated with erythema, swelling, and pain in the left thigh. Therefore, he was admitted to our hospital with the clinical suspicion of cellulitis. Ultrasound examination and Magnetic Resonance Imaging showed left thigh phlegmon. He was treated with drainage and antibiotic therapy (meropenem and vancomycin replaced by daptomycin). The responsible organism, Nocardia farcinica, was identified by 16S rRNA sequencing in the purulent fluid taken out by aspiration. The patient continued treatment with intravenous trimethoprim/sulfamethoxazole and imipenem followed by oral trimethoprim/sulfamethoxazole and moxifloxacin. A whole-body computed tomography did not reveal dissemination to other organs like the lung or brain.The patient was discharged after complete remission. Oral therapy with trimethoprim/sulfamethoxazole, moxifloxacin, rifampicin monthly, clofazimine and thalidomide was prescribed to be taken at home. One month after discharge from the hospital the patient is in good clinical condition with complete resolution of the phlegmon.

CONCLUSION

N. farcinica is a rare infectious agent that mainly affects immunocompromised patients. Presentation of phlegmon only without disseminated infection is unusual, even in these kinds of patients. In any case, a higher index of suspicion is needed, as diagnosis can easily be missed due to the absence of characteristic symptoms and the several difficulties usually encountered in identifying the pathogen.

Clinical and laboratory aspects of the diagnosis and management of cutaneous and subcutaneous infections caused by rapidly growing mycobacteria

Rapidly growing mycobacteria (RGM) are known to cause pulmonary, extra-pulmonary, systemic/disseminated, and cutaneous and subcutaneous infections. The erroneous detection of RGM that is based solely on microscopy, solid and liquid cultures, Bactec systems, and species-specific polymerase chain reaction (PCR) may produce misleading results. Thus, inappropriate therapeutic measures may be used in dermatologic settings, leading to increased numbers of skin deformity cases or recurrent infections. Molecular tools such as the sequence analyses of 16S rRNA, rpoB and hsp65 or PCR restriction enzyme analyses, and the alternate gene sequencing of the superoxide dismutase (SOD) gene, dnaJ, the 16S-23S rRNA internal transcribed spacers (ITS), secA, recA1, dnaK, and the 32-kDa protein gene have shown promising results in the detection of RGM species. PCR restriction enzyme analyses (PRA) work better than conventional methods at identifying species that are closely related. Recently introduced molecular tools such as matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), pyrosequencing, DNA chip technology, and Beacon probes-combined PCR probes have shown comparable results in the detection of various species of RGM. Closely related RGM species (e.g., Mycobacterium fortuitum, M. chelonae, and M. abscessus) must be clearly differentiated using accurate molecular techniques because their therapeutic responses are species-specific. Hence, this paper reviews the following aspects of RGM: (i) its sources, predisposing factors, clinical manifestations, and concomitant fungal infections; (ii) the risks of misdiagnoses in the management of RGM infections in dermatological settings; (iii) the diagnoses and outcomes of treatment responses in common and uncommon infections in immunocompromised and immunocompetent patients; (iv) conventional versus current molecular methods for the detection of RGM; (v) the basic principles of a promising MALDI-TOF MS, sampling protocol for cutaneous or subcutaneous lesions and its potential for the precise differentiation of M. fortuitum, M. chelonae, and M. abscessus; and (vi) improvements in RGM infection management as described in the recent 2011 Clinical and Laboratory Standards Institute (CLSI) guidelines, including interpretation criteria of molecular methods and antimicrobial drug panels and their break points [minimum inhibitory concentrations (MICs)], which have been highlighted for the initiation of antimicrobial therapy.

Antimicrobial susceptibility of nontuberculous mycobacteria from eye infections

PURPOSE

To characterize formerly designated atypical or nontuberculous mycobacteria (NTM) associated with eye infections.

METHODS

All clinical NTM eye isolates (112 isolates from 100 patients) submitted to a single national NTM reference laboratory between 1982 and 2009 were identified using polymerase chain reaction and restriction fragment length polymorphism of the hsp65 gene. Isolates were tested against 10 antimicrobials, including besifloxacin, a new 8-chloro-fluoroquinolone. Assessments included species of NTM recovered, year of isolation, type of eye infection, geographic location, and drug susceptibilities.

RESULTS

In the 1980s, the major pathogen isolated was Mycobacterium abscessus. In the 1990 s, Mycobacterium chelonae emerged as the major pathogen. By 2000, it was responsible for more than 50% of all cases. The majority of M. abscessus and Mycobacterium fortuitum were from southern coastal states and Texas, whereas M. chelonae isolates were more widespread geographically. The most active antimicrobials were amikacin and clarithromycin/azithromycin for M. abscessus and clarithromycin/azithromycin, amikacin, and tobramycin, and the quinolones for M. chelonae.

CONCLUSIONS

This is the largest study of NTM ophthalmic isolates to date and is the first to include susceptibilities and molecular identification for all isolates studied. This series establishes M. chelonae (44%) and M. abscessus (37%) as the NTM species most frequently associated with ophthalmic infections. Topical ophthalmic fluoroquinolones may have a role in the management of ocular infections involving M. chelonae and M. fortuitum.

Molecular Identification of Rare Clinical Mycobacteria by Application of 16S-23S Spacer Region Sequencing

OBJECTIVES

In addition to several molecular methods and in particular 16S rDNA analysis, the application of a more discriminatory genetic marker, i.e., 16S-23S internal transcribed spacer gene sequence has had a great impact on identification and classification of mycobacteria. In the current study we aimed to apply this sequencing power to conclusive identification of some Iranian clinical strains of mycobacteria.

MATERIALS AND METHODS

The test strains consisted of nineteen mycobacterial isolates which were initially identified by the use of conventional phenotypic techniques and molecular methods and subjected to further definitive identification using the 16S-23S internal transcribed spacer gene sequencing.

RESULTS

Out of 19 studied strains, 7 isolates were found to be rapidly growing and 12 isolates as slowly growing mycobacteria. With the exception of one isolate, i.e., the isolate HNTM87, which yielded a distinct ITS sequence incomparable with all previously identified mycobacteria, the remaining isolates produced the sequences similar to the established mycobacteria and were clearly identified and differentiated from closely related taxa. A phylogenetic tree based on maximum parsimony analysis of 16S-23S internal transcribed spacer gene sequences constructed showing the relatedness of Iranian clinical isolates with the closely related type species of mycobacteria.

CONCLUSION

This study showed that the 16S-23S internal transcribed spacer gene of the genus Mycobacterium exhibits a high variation which is of value for discriminating closely related taxa and could be used independently or in combination with 16S rDNA sequencing to delineate the true identity of rare mycobacterial species.

Multi-centre evaluation of the speed-oligo Mycobacteria assay for differentiation of Mycobacterium spp. in clinical isolates

BACKGROUND

A new DNA line probe assay (Speed-oligo Mycobacteria, Vircell) has been launched for rapid differentiation of Mycobacterium spp. from cultures. Compared to other line-probe assays, Speed-oligo Mycobacteria covers a relatively limited spectrum of species but uses a simpler and faster dip-stick technique. The present multi-centre, multi-country study aimed at evaluating the utility and usability of Speed-oligo Mycobacteria in routine mycobacteriology diagnostics. Results from Speed-oligo Myobacteria were compared to those from Genotype CM (HAIN lifescience, Nehren, Germany), another line-probe assay.

METHODS

Speed-oligo Mycobacteria assay was performed in three main steps: 1) DNA extraction from cultured material 2) PCR amplification of the target gene and an internal control and 3) hybridization of the PCR products to specific probes by means of a dip-stick.

RESULTS

Two hundred forty-two clinical isolates were recovered from consecutive positive mycobacterial cultures at two German (IML Gauting, Bioscientia Ingelheim), one Czech (KLINLAB Prague), and at a Sudanese (Khartoum) laboratory. All Mycobacterium species covered by the assay were reliably recognized. The rate of false positive results was 1.2% and concerned only the species M. marinum and M. peregrinum. The identification rate, i.e. the proportion of isolates which was correctly differentiated to the level of species or complex by the assay, differed significantly among laboratories being 94.9%, 90.7%, and 75.0% at the study sites IML Gauting, KLINLAB Prague and Bioscientia Ingelheim, respectively. This difference was caused by different spectra of NTM species encountered by the laboratory centres in daily routine diagnostics.

CONCLUSIONS

Speed-oligo Mycobacteria assay was proved a rapid and easy-to-perform alternative to conventional line-probe assays. The assay showed excellent sensitivity with regard to identification of genus Mycobacterium and species/complexes covered by the test. However, due to its relatively limited spectrum of taxa, a varying proportion of NTM may not be identified by the assay in daily diagnostics demanding further analyses. The only significant shortcoming in terms of specificity was the misidentification of the clinically relevant species M. marinum.

Five-year outbreak of community- and hospital-acquired Mycobacterium porcinum infections related to public water supplies

Mycobacterium porcinum is a rarely encountered rapidly growing Mycobacterium (RGM). We identified M. porcinum from 24 patients at a Galveston university hospital (University of Texas Medical Branch) over a 5-year period. M. porcinum was considered a pathogen in 11 (46%) of 24 infected patients, including 4 patients with community-acquired disease. Retrospective patient data were collected, and water samples were cultured. Molecular analysis of water isolates, clustered clinical isolates, and 15 unrelated control strains of M. porcinum was performed. Among samples of hospital ice and tap water, 63% were positive for RGM, 50% of which were M. porcinum. Among samples of water from the city of Galveston, four of five households (80%) were positive for M. porcinum. By pulsed-field gel electrophoresis (PFGE), 8 of 10 environmental M. porcinum were determined to belong to two closely related clones. A total of 26 of 29 clinical isolates subjected to PFGE (including isolates from all positive patients) were clonal with the water patterns, including patients with community-acquired disease. Fifteen control strains of M. porcinum had unique profiles. Sequencing of hsp65, recA, and rpoB revealed the PFGE outbreak clones to have identical sequences, while unrelated strains exhibited multiple sequence variants. M. porcinum from 22 (92%) of 24 patients were clonal, matched hospital- and household water-acquired isolates, and differed from epidemiologically unrelated strains. M. porcinum can be a drinking water contaminant, serve as a long-term reservoir (years) for patient contamination (especially sputum), and be a source of clinical disease. This study expands concern about public health issues regarding nontuberculous mycobacteria. Multilocus gene sequencing helped define clonal populations.

An appraisal of PCR-based technology in the detection of Mycobacterium tuberculosis

Tuberculosis is an under-recognized yet catastrophic health problem, particularly in developing countries. The HIV pandemic has served to increase the number of susceptible individuals, and multidrug-resistance and poor socioeconomic conditions also augment the prevalence and the consequences of the disease. To control the disease and its spread, it is vital that tuberculosis diagnostics are accurate and rapid. Whereas microscopy and culture have several limitations (low sensitivity is a problem for the former, while the latter has a delayed turnaround time), PCR-based techniques targeting regions of the Mycobacterium tuberculosis genome such as IS6110 have proved to be useful. The purpose of this review is to assess the use of PCR-RFLP, nested PCR and real-time PCR protocols and the choice of target regions for the detection of M. tuberculosis. Real-time PCR for the detection of M. tuberculosis target genes in clinical specimens has contributed to improving diagnosis and epidemiologic surveillance in the past decade. However, targeting one genome sequence such as IS6110 may not by itself be sufficiently sensitive to reach 100% diagnosis, especially in the case of pulmonary tuberculosis. Additional testing for target genome sequences such as hsp65 seems encouraging. An interesting approach would be a multiplex real-time PCR targeting both IS6110 and hsp65 to achieve comprehensive and specific molecular diagnosis. This technology needs development and adequate field testing before it becomes the acceptable gold standard for diagnosis.

Laboratory diagnosis of tuberculosis in resource-poor countries: challenges and opportunities

With an estimated 9.4 million new cases globally, tuberculosis (TB) continues to be a major public health concern. Eighty percent of all cases worldwide occur in 22 high-burden, mainly resource-poor settings. This devastating impact of tuberculosis on vulnerable populations is also driven by its deadly synergy with HIV. Therefore, building capacity and enhancing universal access to rapid and accurate laboratory diagnostics are necessary to control TB and HIV-TB coinfections in resource-limited countries. The present review describes several new and established methods as well as the issues and challenges associated with implementing quality tuberculosis laboratory services in such countries. Recently, the WHO has endorsed some of these novel methods, and they have been made available at discounted prices for procurement by the public health sector of high-burden countries. In addition, international and national laboratory partners and donors are currently evaluating other new diagnostics that will allow further and more rapid testing in point-of-care settings. While some techniques are simple, others have complex requirements, and therefore, it is important to carefully determine how to link these new tests and incorporate them within a country's national diagnostic algorithm. Finally, the successful implementation of these methods is dependent on key partnerships in the international laboratory community and ensuring that adequate quality assurance programs are inherent in each country's laboratory network.

Mycobacterium fortuitum infections associated with laparoscopic gastric banding

Mycobacterium fortuitum, a rapidly growing atypical mycobacteria, is commonly found in soil and water. This organism is most often known to cause skin, bone, and soft tissue infections associated with local trauma, surgical procedures, and in patients with immunodeficiency. Nosocomial infections associated with a variety of contaminated devices and equipment have also been widely documented. This report presents the first cases of M. fortuitum infection following laparoscopic gastric banding procedures. Both patients had complicated clinical courses necessitating removal of their banding devices and long-term antibiotic therapy.

Automated identification of medically important bacteria by 16S rRNA gene sequencing using a novel comprehensive database, 16SpathDB

Despite the increasing use of 16S rRNA gene sequencing, interpretation of 16S rRNA gene sequence results is one of the most difficult problems faced by clinical microbiologists and technicians. To overcome the problems we encountered in the existing databases during 16S rRNA gene sequence interpretation, we built a comprehensive database, 16SpathDB (http://147.8.74.24/16SpathDB) based on the 16S rRNA gene sequences of all medically important bacteria listed in the Manual of Clinical Microbiology and evaluated its use for automated identification of these bacteria. Among 91 nonduplicated bacterial isolates collected in our clinical microbiology laboratory, 71 (78%) were reported by 16SpathDB as a single bacterial species having >98.0% nucleotide identity with the query sequence, 19 (20.9%) were reported as more than one bacterial species having >98.0% nucleotide identity with the query sequence, and 1 (1.1%) was reported as no match. For the 71 bacterial isolates reported as a single bacterial species, all results were identical to their true identities as determined by a polyphasic approach. For the 19 bacterial isolates reported as more than one bacterial species, all results contained their true identities as determined by a polyphasic approach and all of them had their true identities as the "best match in 16SpathDB." For the isolate (Gordonibacter pamelaeae) reported as no match, the bacterium has never been reported to be associated with human disease and was not included in the Manual of Clinical Microbiology. 16SpathDB is an automated, user-friendly, efficient, accurate, and regularly updated database for 16S rRNA gene sequence interpretation in clinical microbiology laboratories.

Characterization of Bradyrhizobium Strains Isolated from Different Varieties of Soybean with 16SrDNA RFLP from Agricultural Land of Madhya Pradesh, India

Madhya Pradesh is the major soybean contributor in India. The taxonomy of nitrogen fixing bacteria forming symbiotic associations with leguminous plants has been deeply changed in recent years. The use of very sensitive and accurate molecular methods has enabled the detection of large rhizobial diversity. Molecular biotyping and characterization the Bradyrhizobium, isolates from eleven varieties of soybean from agricultural field of Sehore district of Madhya Pradesh is done using 16S rDNA typing. Bradyrhizobia were identified genetically by determining the %Guanine plus Cytosine content of the whole genome, followed by 16S rDNA-RFLP analysis % Guanine plus Cytosine content of all the Bradyrhizobium isolates reflects similarity at generic level among all Bradyrhizobial isolates. Restriction Fragment Length Polymorphism (RFLP) further showed a considerable level of genetic diversity among the Bradyrhizobial isolates. PCR-RFLP of 16S rDNA supported existence of two divergent groups among indigenous Bradyrhizobial isolates, at similarity level of 66, and 75 and 74% of similarity within the group. The technique used was helpful in characterizing Bradyrhizobium isolates to be used as inoculants for improving productivity of agricultural land of Madhya Pradesh (India).

Identification of acid-fast bacilli using pyrosequencing analysis

Pyrosequence identification of 117 isolates of acid-fast bacilli (AFB) was compared to both routine phenotypic methods and Sanger sequencing. Two (2) vendor-provided pyrosequencing primers specific for AFB were used for the study. Pyrosequence analysis correctly identified 114 (98%) of the tested 117 AFB isolates. Among the test Mycobacterium spp., 18 of 20 Mycobacterium spp. were identified correctly to the species level. All rapidly growing mycobacteria were correctly identified to species by pyrosequencing. Other slowly growing mycobacteria such as Mycobacterium tuberculosis, Mycobacterium kansasii, Mycobacterium avium-intracellulare, and others were easily identified by pyrosequencing. Only Mycobacterium simiae and Mycobacterium scrofulaceum were not identifiable by the pyrosequence method. Among the 25 Nocardia isolates, all were correctly identified to the genus level. Identification of AFB by pyrosequence analysis provides both a rapid and accurate method for this group of organisms.

DNA barcoding and traditional taxonomy unified through Integrative Taxonomy: a view that challenges the debate questioning both methodologies

The taxonomic crisis, emphasized in recent years, is marked by the lack of popularity (lack of interest in taxonomy) and financial incentives to study biodiversity. This situation, coupled with the issues involved with the necessity of knowing many yet undiscovered species, has meant that new technologies, including the use of DNA, have emerged to revitalize taxonomy. Part of the scientific community, however, has rejected the use of these innovative ideas. DNA barcoding has especially been the target of numerous criticisms regarding its application, as opposed to the use of morphology. This paper aims to highlight the inconsistency of the debate involving DNA versus morphology, since there is a proposal for the integration of traditional taxonomy and DNA barcoding - the integrative taxonomy. The positive and negative points of this proposal will be discussed, as well as its validity and application. From it, the importance of morphology is recognized and the revitalization of traditional taxonomy is achieved by the addition of technologies to overcome the taxonomic impediment.

Guidelines for interpretation of 16S rRNA gene sequence-based results for identification of medically important aerobic Gram-positive bacteria

This study is believed to be the first to provide guidelines for facilitating interpretation of results based on full and 527 bp 16S rRNA gene sequencing and MicroSeq databases used for identifying medically important aerobic Gram-positive bacteria. Overall, full and 527 bp 16S rRNA gene sequencing can identify 24 and 40 % of medically important Gram-positive cocci (GPC), and 21 and 34 % of medically important Gram-positive rods (GPR) confidently to the species level, whereas the full-MicroSeq and 500-MicroSeq databases can identify 15 and 34 % of medically important GPC and 14 and 25 % of medically important GPR confidently to the species level. Among staphylococci, streptococci, enterococci, mycobacteria, corynebacteria, nocardia and members of Bacillus and related taxa (Paenibacillus, Brevibacillus, Geobacillus and Virgibacillus), the methods and databases are least useful for identification of staphylococci and nocardia. Only 0–2 and 2–13 % of staphylococci, and 0 and 0–10 % of nocardia, can be confidently and doubtfully identified, respectively. However, these methods and databases are most useful for identification of Bacillus and related taxa, with 36–56 and 11–14 % of Bacillus and related taxa confidently and doubtfully identified, respectively. A total of 15 medically important GPC and 18 medically important GPR that should be confidently identified by full 16S rRNA gene sequencing are not included in the full-MicroSeq database. A total of 9 medically important GPC and 21 medically important GPR that should be confidently identified by 527 bp 16S rRNA gene sequencing are not included in the 500-MicroSeq database. 16S rRNA gene sequence results of Gram-positive bacteria should be interpreted with basic phenotypic tests results. Additional biochemical tests or sequencing of additional gene loci are often required for definitive identification. To improve the usefulness of the MicroSeq databases, bacterial species that can be confidently identified by 16S rRNA gene sequencing but are not found in the MicroSeq databases should be included.

Comparison of the MicroScan, VITEK 2, and Crystal GP with 16S rRNA sequencing and MicroSeq 500 v2.0 analysis for coagulase-negative Staphylococci

Background

Three phenotypic identification systems (MicroScan, VITEK 2, and Crystal GP) were evaluated for their accuracy to identify coagulase-negative staphylococci (CNS). A total of 120 clinical isolates confirmed to be CNS via 16S rRNA sequencing and analysis with the MicroSeq 500 v2.0 database were assessed.

Results

The MicroScan, VITEK 2, and Crystal GP systems correctly identified 82.5%, 87.5%, and 67.5% of the isolates, respectively. Misidentification was the main problem in MicroScan (10.8%) and Crystal GP (23.3%) systems, whereas the main problem of VITEK 2 was low-level discrimination (7.5%).

Conclusion

None of the 3 phenotypic systems tested could accurately and reliably identify CNS at the species level. Further verifications such as biochemical testing or 16S rRNA sequencing together with analysis using a comparable database might be helpful in this regard.