Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK® MS system

Garner, Omai B.; Mochon, A. Brian; Branda, John A.; Burnham, Carey‐Ann D.; Bythrow, Maureen; Ferraro, Mary Jane; Ginocchio, Christine C.; Jennemann, Rebecca; Manji, Ryhana; Procop, Gary W.; Richter, Sandra; Rychert, Jenna; Sercia, Linda; Westblade, Lars F.; Lewinski, Michael A.

doi:10.1111/1469-0691.12317

Cited by 87 publications

(61 citation statements)

References 16 publications

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“…Identification of A. graevenitzii as the predominant species recovered was also unique, since this species is less frequently recovered from clinical specimens than A. odontolyticus, A. turicensis, and A. radingae. (13,14) The use of 16S rRNA sequencing facilitated recognition of A. graevenitzii, since this species is not in the RapID ANA II, or MS databases, consistent with previous reports (13,15). A. odontolyticus is contained in both the Saramis RUO and Vitek MS IVD databases, facilitating its identification.…”

Section: Discussionsupporting

confidence: 82%

Pseudo-Outbreak of Actinomyces graevenitzii Associated with Bronchoscopy

et al. 2015

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Outbreaks and pseudo-outbreaks of infection related to bronchoscopy typically involve Gram-negative bacteria, Mycobacterium species or Legionella species. We report an unusual bronchoscopy-related pseudo-outbreak due to Actinomyces graevenitzii. Extensive epidemiological and microbiological investigation failed to identify a common source. Strain typing revealed that the cluster was comprised of heterogeneous strains of A. graevenitzii. A change in laboratory procedures for Actinomyces cultures was coincident with the emergence of the pseudo-outbreak, and we determined that A. graevenitzii isolates more readily adopted a white, dry, molar tooth appearance on anaerobic colistin nalidixic acid (CNA) agar which likely facilitated its detection and identification in bronchoscopic specimens. This unusual pseudo-outbreak was related to frequent requests of bronchoscopists for Actinomyces cultures combined with a change in microbiology laboratory practices. Actinomyces graevenitzii is infrequently identified in clinical specimens, and its pathogenicity is not well defined. A. graevenitzii is a component of the oropharyngeal microbiota and has been reported to cause pneumonia, lung abscesses, osteitis of the jaw, and bacteremia (1-8). In early December 2013, an increase in the recovery of A. graevenitzii from specimens from patients who underwent bronchoscopy was noted by microbiology and infection control staff. Our investigation revealed that the cluster of A. graevenitzii isolates represented a pseudo-outbreak associated with a change in laboratory practices. MATERIALS AND METHODS Setting.A 1,500-bed tertiary care university-affiliated teaching hospital was the setting for this study.Epidemiological investigation. The microbiology laboratory's computerized database was queried to obtain the number of bronchoscopy cultures performed, the number of Actinomyces cultures ordered on bronchoscopy specimens, and the number of those cultures ordered that were positive for Actinomyces from January 2011 through December 2013. Medical records of patients whose bronchoscopy specimens yielded Actinomyces were reviewed, and the following variables were recorded: date of bronchoscopy, results of bronchoscopic specimen cultures for routine respiratory pathogens and for Actinomyces, bronchoscope used, bronchoscopist, endoscopy personnel involved in the procedure, procedure room number, and medications administered during bronchoscopy procedures. Only three bronchoscopes were routinely used, and almost all bronchoscopies were performed in procedure room 3. Therefore, we focused our investigation on room 3, the three bronchoscopes, and the "wash room" in which all bronchoscopes and endoscopes undergo highlevel disinfection using one of three automated endoscope reprocessors (AERs) (DSDs Medivators, Minneapolis, MN). Findings of cytologic examination and bronchial biopsy specimens were also recorded.Environmental sources of samples collected for culture in the endoscopy suite included unopened bottles of lidocaine, atomizer, cotton ball...

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Section: Discussionsupporting

confidence: 82%

Pseudo-Outbreak of Actinomyces graevenitzii Associated with Bronchoscopy

et al. 2015

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“…11,[16][17][18][19] Overall, MALDI-TOF MS identification has been found to be highly accurate for clinically relevant bacteria, including Gram-positive, Gram-negative, and fastidious anaerobic bacteria as well as fungi detected in routine microbiology. 11,16,18,20 Herein, we confirm the power of MALDI-TOF MS in identifying bacteria and fungi, with 94.2% identification accuracy at the species level of isolates tested in a laboratory in tropical Africa (2,289 of 2,430 isolates). In the pioneering work performed in 2010 in our laboratory in Marseille, France, 84.1% of 1,660 tested isolates were accurately identified at the species level, and 11.3% of tested isolates were accurately identified at the genus level.…”

Section: Discussionsupporting

confidence: 65%

The Ongoing Revolution of MALDI-TOF Mass Spectrometry for Microbiology Reaches Tropical Africa

Fall¹,

Lo²,

Samb-Ba³

et al. 2015

The American Society of Tropical Medicine and Hygiene

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Abstract. Matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) represents a revolution in routine pathogen identification in clinical microbiology laboratories. A MALDI-TOF MS was introduced to tropical Africa in the clinical microbiology laboratory of the Hô pital Principal de Dakar (Senegal) and used for routine pathogen identification. Using MS, 2,429 bacteria and fungi isolated from patients were directly assayed, leading to the identification of 2,082 bacteria (85.7%) and 206 fungi (8.5%) at the species level, 109 bacteria (4.5%) at the genus level, and 16 bacteria (0.75%) at the family level. Sixteen isolates remained unidentified (0.75%). Escherichia coli was the most prevalent species (25.8%) followed by Klebsiella pneumoniae (14.8%), Streptococcus agalactiae (6.2%), Acinetobacter baumannii (6.1%), Pseudomonas aeruginosa (5.9%), and Staphylococcus aureus (5.9%). MALDI-TOF MS has also enabled the detection of rare bacteria and fungi. MALDI-TOF MS is a powerful tool for the identification of bacterial and fungal species involved in infectious diseases in tropical Africa.

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“…Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been utilized in the clinical microbiology laboratory for rapid and accurate identification of bacteria, mycobacteria, and yeasts (2)(3)(4)(5)(6)(7)(8)(9). For filamentous fungi, databases have been limited, and unlike bacteria, filamentous fungi require additional processing steps to disrupt the cell wall, extract proteins, and inactivate the isolate (10).…”

mentioning

confidence: 99%

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi

et al. 2016

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bInvasive fungal infections have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. With the increasing incidence of invasive disease attributed to filamentous fungi, rapid and accurate species-level identification of these pathogens is necessary. Traditional methods for identification of filamentous fungi can be slow and may lack resolution. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has emerged as a rapid and accurate method for identification of bacteria and yeasts, but a paucity of data exists on the performance characteristics of this method for identification of filamentous fungi. The objective of our study was to evaluate the accuracy of the Vitek MS for mold identification. A total of 319 mold isolates representing 43 genera recovered from clinical specimens were evaluated. Of these isolates, 213 (66.8%) were correctly identified using the Vitek MS Knowledge Base, version 3.0 database. When a modified SARAMIS (Spectral Archive and Microbial Identification System) database was used to augment the version 3.0 Knowledge Base, 245 (76.8%) isolates were correctly identified. Unidentified isolates were subcultured for repeat testing; 71/ 319 (22.3%) remained unidentified. Of the unidentified isolates, 69 were not in the database. Only 3 (0.9%) isolates were misidentified by MALDI-TOF MS (including Aspergillus amoenus [n ‫؍‬ 2] and Aspergillus calidoustus [n ‫؍‬ 1]) although 10 (3.1%) of the original phenotypic identifications were not correct. In addition, this methodology was able to accurately identify 133/144 (93.6%) Aspergillus sp. isolates to the species level. MALDI-TOF MS has the potential to expedite mold identification, and misidentifications are rare. Filamentous fungi are ubiquitous environmental microorganisms that have become increasingly important pathogens, especially in immunocompromised patients. Invasive fungal diseases have a high rate of morbidity and mortality, and accurate identification is necessary to guide appropriate antifungal therapy. Traditionally, the identification of filamentous fungi has required the use of different phenotypic methods in conjunction with macro-and microscopic assessment of the organism (1). This process requires highly trained mycologists, and, in some cases, turnaround time may be prolonged due to a requirement for extended incubation periods, potentially delaying appropriate therapy. Molecular methods, which can provide accurate identification to the species level, can be expensive, require specialized equipment or expertise, and are not commonly available in clinical laboratories.Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been utilized in the clinical microbiology laboratory for rapid and accurate identification of bacteria, mycobacteria, and yeasts (2-9). For filamentous fungi, databases have been limited, and unlike bacteria, filamentous fungi require additional processing steps to dis...

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Multi-centre evaluation of mass spectrometric identification of anaerobic bacteria using the VITEK® MS system

Cited by 87 publications

References 16 publications

Pseudo-Outbreak of Actinomyces graevenitzii Associated with Bronchoscopy

Pseudo-Outbreak of Actinomyces graevenitzii Associated with Bronchoscopy

The Ongoing Revolution of MALDI-TOF Mass Spectrometry for Microbiology Reaches Tropical Africa

Evaluation of the Vitek MS Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry System for Identification of Clinically Relevant Filamentous Fungi

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