16S rRNA Gene Sequencing in Routine Identification of Anaerobic Bacteria Isolated from Blood Cultures

Justesen, Ulrik Stenz; Skov, Marianne Nielsine; Knudsen, Elisa; Holt, Hanne Marie; Søgaard, Per; Justesen, T.

doi:10.1128/jcm.02075-09

Cited by 53 publications

(38 citation statements)

References 14 publications

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“…Since November 2007, 16S rRNA gene sequencing (MicroSeq 500 system; Perkin-Elmer, Applied Biosystems Division, Foster City, CA) has been applied to pure culture material (originating from blood cultures) from solid media as soon as anaerobic bacteria, including Lactobacillus spp. and Actinomyces spp., were suspected (8). From November 2008, this strategy has also included pure culture material from other sterile body sites (e.g., the central nervous system, pleura, bones, and joints) and suspected Fusobacterium spp.…”

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confidence: 99%

“…Identification by 16S rRNA gene sequencing was chosen as the "gold standard" in this study, as it has been shown to be an excellent method for the identification of anaerobic bacteria (8). All isolates identified to the species level with a Ն99% match by 16S rRNA gene sequencing, according to CLSI guideline MM18-A (6), from the period November 2007 to October 2010, were included in the study (only one isolate of the same species per patient).…”

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Species Identification of Clinical Isolates of Anaerobic Bacteria: a Comparison of Two Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems

et al. 2011

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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.Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a fast and inexpensive technology for identification of bacteria. The technique has in a short time been widely adopted and is integrated into many clinical microbiology laboratories. Several papers have reported the advantages and performance of MALDI-TOF MS versus conventional systems (1, 14-16). Although MALDI-TOF MS has revolutionized bacterial identification, there are still some limitations (e.g., the viridans group streptococci), and moreover, there are groups of bacteria which have not been evaluated on a larger scale or in a clinical setting (2). This is partly the case for the anaerobic bacteria. The Bacteroides fragilis group has been evaluated by Nagy et al. as part of an antibiotic resistance surveillance study (13). Veloo et al. have evaluated the Gram-positive anaerobic cocci and also compared two MALDI-TOF MS systems on a collection (n ϭ 79) of clinically relevant anaerobic bacteria (17,18). The existing data from these studies were recently reviewed by Veloo et al., the application of MALDI-TOF MS in routine identification of anaerobic bacteria was discussed, and it was concluded that the existing databases need optimizing for routine identification of anaerobic bacteria (19). However, databases are continuously updated, and MALDI-TOF MS represents a fast and inexpensive technology for species identification. Species identification of anaerobic bacteria from serious infections (e.g., blood cultures) is important because information about virulence, potential resistance to certain antimicrobial agents, and primary site of infection can be obtained (5). MALDI-TOF MS can be applied as a first-line identification system without delaying the final identification result. To our knowledge, an evaluation of MALDI-TOF MS in a clinical setting with consecutive clinical isolates, regardless of whether the species included are present in the system databases, has not been performed before.To evaluate the performance of the Bruker system (Bruker Daltonik, Bremen, Germany) and the Shimadzu/SARAMIS system

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Species Identification of Clinical Isolates of Anaerobic Bacteria: a Comparison of Two Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems

et al. 2011

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“…The reasons for this are probably multifactorial. First, regular use of 16S rRNA partial gene sequencing significantly expands the number of anaerobic organisms that can be accurately identified (10,16). It is also well recognized that Leptotrichia are not reliably identified by a commonly used phenotypic identification system (RapID ANA II; Remel, Lenexa, KS) (12,14).…”

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confidence: 99%

Leptotrichia Bacteremia in Patients Receiving High-Dose Chemotherapy

et al. 2012

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Leptotrichia spp. are anaerobic, pencil-shaped, Gram-negative rods that are part of the normal oral and intestinal human flora. Although not typically considered pathogenic, invasive Leptotrichia infections have been reported in immunosuppressed patients. A perceived rise in the identification of Leptotrichia spp. at our institution prompted a retrospective evaluation of these infections. Laboratory and clinical records were reviewed to identify Leptotrichia culture-positive patients. Over a 5-year period, 68 Leptotrichia-positive specimens were identified. Of these, 21% (14/68) were identified in original samples submitted from 13 different patients at our institution, and the remainder (79% [54/68]) were unknown isolates referred from outside hospitals for molecular identification. All in-house Leptotrichia were identified from blood cultures. Only 64% (9/14) of these grew on solid media, and 5 were a part of polymicrobial bacteremias containing other enteric pathogens. All local patients were receiving chemotherapy and a majority received hematopoietic stem cell transplant (HSCT) (11/13). All had neutropenic fever with symptoms of mucositis and/or enteritis. Most of the HSCT patients (73% [8/11]) were autologous recipients hospitalized after recent highdose chemotherapy for multiple myeloma. L. hongkongensis, a novel species, was found in the majority of myeloma cases (63% [5/8]). In conclusion, we suggest that Leptotrichia spp. may be an underappreciated cause of bacteremia, particularly in multiple myeloma patients receiving cytotoxic chemotherapy for autologous HSCT. In our cohort, these infections were associated with neutropenic fever from an enteric source, and most isolates remained sensitive to standard antibiotics. H igh-dose chemotherapy followed by hematopoietic stem-cell transplantation (HSCT), is a well-established treatment modality for a variety of hematologic malignancies; however, infectious complications remain a major barrier to the overall success of this procedure. HSCT recipients are at particularly high risk for the development of invasive bacterial infections as a result of regimen-related neutropenia and cytotoxic damage to the oral and gastrointestinal mucosa. Mucositis severity, specifically, is an independent predictor of anaerobic bloodstream infection (BSI) following HSCT (11).Leptotrichia spp. are fastidious anaerobic, pencil-shaped, Gram-negative rods that reside in the mouths, intestines, and female genital tracts of humans (20). Traditionally considered to be nonpathogenic, Leptotrichia species have occasionally been reported to cause invasive disease in HSCT patients and other immunocompromised hosts (6, 14, 18). The overall incidence of Leptotrichia infections in at-risk patient populations, however, may be underestimated. These organisms are notoriously difficult to recover from blood culture and may retain crystal violet, which can lead to their misidentification as Gram-positive rods. Commercially available phenotypic identification systems also have problems classifying...

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“…A previously described 16S rRNA gene PCR targeting an 817-base-pair fragment was used [12][13][14]. Sequencing results were interpreted using the CLSI (Clinical and Laboratory Standards Institute) guideline MM18-A "Interpretive Criteria for Identifi cation of Bacteria and Fungi by DNA Target Sequencing; Approved Guideline" [15] as detailed [16]. MALDI-TOF-MS analysis was performed using a Shimadzu/Kratos "AXIMA Assurance" MALDI-TOF mass spectrometer (Shimadzu Germany Ltd., Duisburg, Germany) as described [14] with a minor modifi cation.…”

Section: Assessment Of Isolated Strainsmentioning

confidence: 99%

Identification of nasal colonization with β-lactamase-producing enterobacteriaceae in patients, health care workers and students in Madagascar

Micheel¹,

Hogan²,

Rakotoarivelo³

et al. 2015

European Journal of Microbiology and Immunology

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This study assesses the nasal occurrence of β-lactamase-producing Enterobacteriaceae both in patients in a hospital department of infectious diseases at admission and in healthy Madagascan students and health care workers.Nasal swabs from 681 students, 824 health care workers, and 169 patients were obtained in Antananarivo, Madagascar, and transferred to Germany. Screening for β-lactamase (ESBL, ampC) producing Enterobacteriaceae was performed by cultural and molecular approaches, comprising Brilliance ESBL agar, E-testing, ABCD-testing, and commercial hyplex ESBL and SuperBug ID PCR.Regarding ESBL-positive strains and strains with resistance against at least three out of the four tested bactericidal antibiotic drugs, 0.3% (five out of 1541) of the students and health care workers group showed nasal colonization, whereas colonization was observed in 7.1% (12 out of 169) of the hospitalized patients at admission. No appreciably reduced detection rates after sample storage and intercontinental transport were observed.A considerable proportion of nasal colonization with cephalosporin-resistant Enterobacteriaceae was demonstrated in Madagascan hospital patients at admission, posing a risk of developing future endogenous infections. The nasal colonization of healthy individuals was negligible. Good storage and transport stability of Enterobacteriaceae will allow for future studies even in areas difficult to access.

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16S rRNA Gene Sequencing in Routine Identification of Anaerobic Bacteria Isolated from Blood Cultures

Cited by 53 publications

References 14 publications

Species Identification of Clinical Isolates of Anaerobic Bacteria: a Comparison of Two Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems

Species Identification of Clinical Isolates of Anaerobic Bacteria: a Comparison of Two Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry Systems

Leptotrichia Bacteremia in Patients Receiving High-Dose Chemotherapy

Identification of nasal colonization with β-lactamase-producing enterobacteriaceae in patients, health care workers and students in Madagascar

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