Comparison of the Biolog OmniLog Identification System and 16S ribosomal RNA gene sequencing for accuracy in identification of atypical bacteria of clinical origin

Morgan, Megan C.; Boyette, Marilyn; Goforth, Chris; Sperry, Katharine Volpe; Greene, Shermalyn R.

doi:10.1016/j.mimet.2009.10.005

Cited by 58 publications

(35 citation statements)

References 39 publications

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“…To validate this trend, 16S rDNA sequencings and analyses were performed. 16S rDNA is the marker of reference in bacterial classification and was used to classify nonfermenting GN bacteria (Morgan et al. 2009).…”

Section: Discussionmentioning

confidence: 99%

Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure

Pinot

Deredjian

Nazaret

et al. 2011

Journal of Applied Microbiology

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Aims: Aim of the study is to identify accurately Stenotrophomonas maltophilia isolates recovered from environmental and clinical samples. Methods and Results: Recovery of Sten. maltophilia‐like isolates from soil samples using the vancomycin, imipenem, amphotericin B (VIA) selective agar medium enabled distinction of various morphotype colonies. A set of soil and clinical isolates was tested for species identification using different methods. 16S rDNA analyses showed the dark green with a blue halo morphotype to be typical Sten. maltophilia strains. The API‐20NE, Vitek‐2 and Biolog phenotypic analyses typically used for the identification of clinical isolates did not perform well on these soil isolates. The species‐specific PCR screening targeting Sten. maltophilia 23S rDNA and the multiplex smeD/ggpS PCR, differentiating Sten. maltophilia from Stenotrophomonas rhizophila, were tested for improvement of these identification schemes. The latter multiplex PCR identified all isolates tested in this study, whatever be their origin. Conclusions: Isolation on VIA medium and confirmation of Sten. maltophilia species membership by smeD PCR is proposed to identify environmental and clinical isolates of Sten. maltophilia. Significance and Impact of the Study: The proposed approach enables isolation and identification of Sten. maltophilia from different environments in an easy and rapid way. This approach will be useful to accurately manage studies on the abundance and distribution of Sten. maltophilia in hospital and nonhospital environments.

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Section: Discussionmentioning

confidence: 99%

Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure

Pinot

Deredjian

Nazaret

et al. 2011

Journal of Applied Microbiology

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“…In a study of the molecular method on 177 difficult‐to‐identify organisms, the following was noted: 80% matched a known species; 10% represented a new species within a known genus, and another 10% represented a novel taxon . When methods such as Biolog , cellular fatty acid profiles, carbon source utilization, and conventional biochemical identification were compared, the 16S rRNA method yielded more accurate and prompt identification of coryneforms and gram‐negative bacilli .…”

Section: Discussionmentioning

confidence: 99%

Clinical impact of the use of 16S rRNA sequencing method for the identification of “difficult‐to‐identify” bacteria in immunocompromised hosts

Bharadwaj

Swaminathan

Salimnia

et al. 2011

Transplant Infectious Dis

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Molecular method of 16S rRNA sequencing is reported to be helpful in the accurate identification of organisms with ambiguous phenotypic profiles. We analyzed the use of 16S rRNA sequencing method to identify clinically significant, "difficult-to-identify" bacteria recovered from clinical specimens, and evaluated its role in patient management and consequent clinical outcome. Among the 172 "difficult-to-identify" bacteria recovered over a 4-year period, 140 were gram-positive cocci or gram-negative bacilli; identification by 16S rRNA did not play a role in the management of patients infected with these bacteria. From 32 patients, 33 "difficult-to-identify" gram-positive bacilli were identified; the organisms were mycobacteria, Nocardia, Tsukamurella, Rhodococcus, and Gordonia. In 24 patients for whom clinical data were available, results from the 16S rRNA sequencing method led to treatment change in 14 immunocompromised patients (including 7 hematopoietic stem cell recipients and 1 liver transplant recipient). Therapy was modified in 9 patients, initiated in 3 patients, and discontinued in 2 patients. Most patients' therapy was switched to oral antibiotics with discontinuation of intravascular catheters, facilitating early hospital discharge. All 14 patients were alive 30 days after infection onset. The present study demonstrates the clinical application of 16S rRNA sequencing method to identify "difficult-to-identify" mycobacteria and other gram-positive bacilli in clinical specimens, particularly in immunocompromised hosts.

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“…Other microbes, such as clinical bacteria, have been similarly successfully identified using assimilation methods (Holmes et al 1994;Morgan et al 2009), although atypical bacteria were problematic. In filamentous fungi, such as Zygomycetes, most carbon-assimilation profiles correlated with species (Schwarz et al 2007), but certain species, e.g.…”

Section: Discussionmentioning

confidence: 99%

Yeast identification: reassessment of assimilation tests as sole universal identifiers

Spencer

Rawling

Stratford

et al. 2011

Letters in Applied Microbiology

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Aims: To assess whether assimilation tests in isolation remain a valid method of identification of yeasts, when applied to a wide range of environmental and spoilage isolates. Methods and Results: Seventy‐one yeast strains were isolated from a soft drinks factory. These were identified using assimilation tests and by D1/D2 rDNA sequencing. When compared to sequencing, assimilation test identifications (MicroLog™) were 18·3% correct, a further 14·1% correct within the genus and 67·6% were incorrectly identified. The majority of the latter could be attributed to the rise in newly reported yeast species. Conclusions: Assimilation tests alone are unreliable as a universal means of yeast identification, because of numerous new species, variability of strains and increasing coincidence of assimilation profiles. Assimilation tests still have a useful role in the identification of common species, such as the majority of clinical isolates. Significance and Impact of the Study: It is probable, based on these results, that many yeast identifications reported in older literature are incorrect. This emphasizes the crucial need for accurate identification in present and future publications.

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Comparison of the Biolog OmniLog Identification System and 16S ribosomal RNA gene sequencing for accuracy in identification of atypical bacteria of clinical origin

Cited by 58 publications

References 39 publications

Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure

Identification of Stenotrophomonas maltophilia strains isolated from environmental and clinical samples: a rapid and efficient procedure

Clinical impact of the use of 16S rRNA sequencing method for the identification of “difficult‐to‐identify” bacteria in immunocompromised hosts

Yeast identification: reassessment of assimilation tests as sole universal identifiers

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