Evaluation of the Rapid ID 32A system for identification of anaerobic Gram-negative bacilli, excluding the Bacteroides fragilis group

The value of MALDI-TOF MS for the identification of clinically relevant anaerobic bacteria in routine laboratories

Between 2010 and 2011, 283 clinically relevant non-duplicate anaerobic isolates were analysed by MALDI-TOF MS and the results were compared with conventional identification. Immediately after isolation, an ethanol precipitation was carried out on isolated colonies and the stabilized samples were anonymized and sent to the laboratory of Bruker Daltonik, Bremen, Germany, where the identification was done using the standard protocol for micro-organism identification on a Microflex LT mass spectrometer equipped with the MALDI Biotyper 3.0 software. Of 283 isolates, 218 (77 %) were identified at species level [log(score) ≥2.0], 31 isolates (10.95 %) were identified at genus level [log(score) 1.7-2.0] and 34 (12 %) gave non-reliable identification [log(score) <1.7]. Out of the 31 isolates with log(score) 1.7-2.0, in the case of 24 isolates the species name given by the MALDI Biotyper was accepted if it was the same as for the classical identification. Of 218 isolates identified at species level, 40 results were discordant with phenotypic identification, and of the 31 isolates identified at genus level according to the manufacturer's score cut-off, four gave results discordant with the phenotypic method. For the 44 discordant results, 16S rRNA gene sequencing confirmed MALDI-TOF MS identification in 41 cases, leaving three isolates (0.7 %) that had been misidentified by MALDI-TOF MS.

Species identification of clinical isolates of anaerobic bacteria: a comparison of two matrix-assisted laser desorption ionization-time of flight mass spectrometry systems

We compared two matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) systems (Shimadzu/SARAMIS and Bruker) on a collection of consecutive clinically important anaerobic bacteria (n = 290). The Bruker system had more correct identifications to the species level (67.2% versus 49.0%), but also more incorrect identifications (7.9% versus 1.4%). The system databases need to be optimized to increase identification levels. However, MALDI-TOF MS in its present version seems to be a fast and inexpensive method for identification of most clinically important anaerobic bacteria.

Evaluation of the Vitek 2 ANC card for identification of clinical isolates of anaerobic bacteria

An evaluation of the Vitek 2 ANC card (bioMérieux, Marcy l'Etoile, France) was performed with 301 anaerobic isolates. Each strain was identified by 16S rRNA gene sequencing, which is considered to be the reference method. The Vitek 2 ANC card correctly identified 239 (79.4%) of the 301 clinical isolates to the genus level, including 100 species that were not represented in the database. Correct species identification was obtained for 60.1% (181/301) of the clinical isolates. For the isolates not identified to the species level, a correct genus identification was obtained for 47.0% of them (47/100), and 16 were accurately designated not identified. Although the Vitek 2 ANC card allows the rapid and acceptable identification of the most common clinically important anaerobic bacteria within 6 h, improvement is required for the identification of members of the genera Fusobacterium, Prevotella, and Actinomyces and certain Gram-positive anaerobic cocci (GPAC).

16S rRNA gene sequencing in routine identification of anaerobic bacteria isolated from blood cultures

A comparison between conventional identification and 16S rRNA gene sequencing of anaerobic bacteria isolated from blood cultures in a routine setting was performed (n = 127). With sequencing, 89% were identified to the species level, versus 52% with conventional identification. The times for identification were 1.5 days and 2.8 days, respectively.

Identification of clinically important anaerobic bacteria by an oligonucleotide array

Anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. Conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. An oligonucleotide array based on the 16S-23S rRNA intergenic spacer (ITS) sequences was developed to identify 28 species of anaerobic bacteria and Veillonella. The method consisted of PCR amplification of the ITS regions with universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of 35 oligonucleotide probes (17- to 30-mers) immobilized on a nylon membrane. The performance of the array was determined by testing 310 target strains (strains which we aimed to identify), including 122 reference strains and 188 clinical isolates. In addition, 98 nontarget strains were used for specificity testing. The sensitivity and the specificity of the array for the identification of pure cultures were 99.7 and 97.1%, respectively. The array was further assessed for its ability to detect anaerobic bacteria in 49 clinical specimens. Two species (Finegoldia magna and Bacteroides vulgatus) were detected in two specimens by the array, and the results were in accordance with those obtained by culture. The whole procedure of array hybridization took about 8 h, starting with the isolated colonies. The array can be used as an accurate alternative to conventional methods for the identification of clinically important anaerobes.

Enzymatic substrates in microbiology

Enzymatic substrates are powerful tools in biochemistry. They are widely used in microbiology to study metabolic pathways, to monitor metabolism and to detect, enumerate and identify microorganisms. Synthetic enzymatic substrates have been customized for various microbial assays, to detect an expanding range of both new enzymatic activities and target microorganisms. Recent developments in synthetic enzymatic substrates with new spectral, chemical and biochemical properties allow improved detection, enumeration and identification of food-borne microorganisms, clinical pathogens and multi-resistant bacteria in various sample types. In the past 20 years, the range of synthetic enzymatic substrates used in microbiology has been markedly extended supporting the development of new multi-test systems (e.g., Microscan, Vitek 2, Phoenix) and chromogenic culture media. The use of such substrates enables an improvement in time to detection and specificity over conventional tests that employ natural substrates. In the era of intense developments in molecular biology, phenotypic tests involving enzymatic substrates remain useful to analyse both simple and complex samples. Such tests are applicable to diagnostic and research laboratories all over the world.

Evaluation of the new Vitek 2 ANC card for identification of medically relevant anaerobic bacteria

Of 261 anaerobic clinical isolates tested with the new Vitek 2 ANC card, 257 (98.5%) were correctly identified at the genus level. Among the 251 strains for which identification at the species level is possible with regard to the ANC database, 217 (86.5%) were correctly identified at the species level. Two strains (0.8%) were not identified, and eight were misidentified (3.1%). Of the 21 strains (8.1%) with low-level discrimination results, 14 were correctly identified at the species level by using the recommended additional tests. This system is a satisfactory new automated tool for the rapid identification of most anaerobic bacteria isolated in clinical laboratories.

A rare presentation of ventriculitis and brain abscess caused by Fusobacterium nucleatum

Anaerobic ventriculitis is rare, and usually seen in patients with predisposing factors such as otitis media, mastoiditis, sinusitis or recent neurosurgery. We report what we believe to be the first case of ventriculitis and brain abscess due to Fusobacterium nucleatum infection in a man with no significant predisposing factors. He was successfully treated with antibiotic therapy.

Multicenter evaluation of the Vitek 2 anaerobe and Corynebacterium identification card

The new anaerobe and Corynebacterium (ANC) identification card for Vitek 2 was compared with a 16S rRNA gene sequencing (16S) reference method for accuracy in the identification of corynebacteria and anaerobic species. Testing was performed on a Vitek 2 XL system with modified software at three clinical trial laboratories. Reproducibility was determined with nine ATCC quality control strains that were tested 20 times over a minimum of 10 days at all three sites. A challenge set of 50 well-characterized strains and 365 recent fresh and frozen clinical isolates were included in the study. The expected positive and negative biochemical well reactions were also evaluated for substrate reproducibility. All strains were tested with the ANC card, and clinical isolates were saved for 16S rRNA gene sequencing. All reproducibility tests yielded expected results within a 95% confidence interval, except for that with Corynebacterium striatum ATCC 6940, for which identification failed at one trial site. For the challenge isolates, there was 98% correct identification, 5% low discrimination, and 2% incorrect identification, and 0% were unidentified. For clinical strains, there was 95.1% correct identification, 4.9% low discrimination, and 4.6% incorrect identification, and 0.3% were unidentified. The 4.6% (17/365) of clinical isolates that were incorrectly identified consisted of 14 isolates that were correct at the genus level and three that were incorrect at the genus level. The new ANC card met all performance criteria within a 95% confidence interval compared to the identification performance by 16S rRNA gene sequencing.

Physiological alterations of a Fusobacterium nucleatum strain exposed to oxidative stress

AIM

The purpose of this study was to investigate the effect of oxidative stress on physiological and genetic characteristics of Fusobacterium nucleatum and its interference on this microbial identification methods.

METHODS AND RESULTS

Fus. nucleatum ssp. nucleatum ATCC 25586 (wt-strain) and an oxidative-stress-adapted strain derived from the wt-strain (aero-strain) were employed in the study. Cell-free crude protein extracts were obtained from both strains and differentially expressed proteins were identified by two-dimensional electrophoresis. Bacterium identification was performed by conventional biochemical tests, automated Rapid ID 32A system and specific PCR analysis. Genetic diversity between wt- and aero-strain was assessed by arbitrarily-primed (AP)-PCR. There were significant changes in the protein profile of aero-strain. The identification of the wt-strain was confirmed by all methods employed. Similar results were obtained for aero-strain when conventional biochemical tests and PCR were used. However, aero-strain was identified as Fusobacterium varium when submitted to Rapid ID 32A system. According to AP-PCR analysis, no significant genetic alteration was detected in aero-strain.

CONCLUSIONS

The adaptive response of Fus. nucleatum to oxidative stress is associated with changes on its biology, which may lead to misidentification of the organism, according to the conventional identification methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

Oxidative stress may act as a cause of adaptive response in Fus. nucleatum with consequences to its biology, such as alterations on biochemical and physiological profile.

Rapid identification of Fusobacterium nucleatum and Fusobacterium necrophorum by fluorescence in situ hybridization

Identification of clinically relevant Fusobacterium spp. is hampered by their slow growth, their frequent occurrence in polymicrobial culture, and the low reliability of biochemical differentiation methods. A newly developed fluorescence in situ hybridization (FISH) assay allowed reliable and rapid identification of Fusobacterium necrophorum and Fusobacterium nucleatum from culture. Preliminary results show that the method offers the perspective for direct detection of these pathogens in blood cultures and abscess aspirates.

Microarrays complement culture methods for identification of bacteria in endodontic infections

The aim of this study was to investigate the microbial composition of necrotic root canals using culture methods and microarray technology. Twenty uniradicular teeth with radiographic evidence of periapical bone loss and with no previous endodontic treatment were selected for this study. For molecular diagnosis a DNA chip with 20 different species-specific, 16S-rDNA-directed catcher probes was used. The microorganisms most frequently detected by the DNA chip were: Micromonas micros, Fusobacterium nucleatum ssp., Tannerella forsythia, Treponema denticola, Veillonella parvula, Eubacterium nodatum, Porphyromonas gingivalis, Actinomyces odontolyticus, and Streptococcus constellatus. As expected, additional important bacterial taxa were found by culture analysis, but microorganisms such as T. forsythia and T. denticola could not be identified. In conclusion, microarrays may provide significant additional information regarding the endodontic microbiota by detecting bacterial species that are otherwise difficult or impossible to culture.

Antimicrobial susceptibility of non-Bacteroides fragilis group anaerobic Gram-negative bacilli in Europe

OBJECTIVE: To investigate the in vitro activity of a range of anti-anaerobe antimicrobials against non-Bacteroides fragilis group anaerobic Gram-negative bacilli isolated in Europe. METHODS: Isolates from 15 laboratories in 13 countries were identified by conventional methods. The MICs of 20 antibiotics were determined by an agar dilution method. RESULTS: There were 488 Prevotella spp., 174 fusobacteria, 69 Porphyromonas spp., 33 Bacteroides spp., 28 Bilophila wadsworthia and 16 Campylobacter spp. isolates, one Sutterella wadsworthensis isolate and four unidentified isolates. Penicillin resistance (and diminished susceptibility to piperacillin) was most common in Prevotella spp. and Bilophila wadsworthia but was also seen in many other species. All isolates, except three of Bilophila wadsworthia, were susceptible to amoxycillin/clavulanate. Most isolates were susceptible to cefoxitin (except Bilophila wadsworthia) and all were susceptible to the carbapenems. Clinafloxacin was the most active quinolone, followed by trovafloxacin and then sparfloxacin. Most fusobacteria were inherently resistant to the macrolides, as expected, but resistance to macrolides and a ketolide in other species was uncommon. Most Fusobacterium varium isolates were resistant to clindamycin, but resistance to clindamycin in all other species was rare. Tetracycline resistance was common but this did not affect the glycylcyclines. There was one isolate of Bacteroides putredinis resistant to chloramphenicol, and three isolates, a Bacteroides ureolyticus isolate, the Sutterella wadsworthensis isolate and one of the unnamed isolates, were metronidazole resistant. Rifampicin was active against most Prevotella and Porphyromonas spp., but not against many other genera. CONCLUSIONS: Penicillin resistance has increased in Europe among non-Bacteroides fragilis anaerobic Gram-negative bacilli, much of it due to beta-lactamase. Acquired resistance to other beta-lactams, macrolides and rifampicin has not significantly increased, and chloramphenicol and metronidazole are unaffected. However, resistance to tetracycline is common. The new compounds, a ketolide (HMR 3647), the glycylcyclines and clinafloxacin, are highly active.