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Steyaert S, Peeters C, Wieme AD, Muyldermans A, Vandoorslaer K, Spilker T, Wybo I, Piérard D, LiPuma JJ, Vandamme P. Novel Ralstonia species from human infections: improved matrix-assisted laser desorption/ionization time-of-flight mass spectrometry-based identification and analysis of antimicrobial resistance patterns. Microbiol Spectr 2024:e0402123. [PMID: 38661349 DOI: 10.1128/spectrum.04021-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024] Open
Abstract
A collection of 161 Ralstonia isolates, including 90 isolates from persons with cystic fibrosis, 27 isolates from other human clinical samples, 8 isolates from the hospital environment, 7 isolates from industrial samples, and 19 environmental isolates, was subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) identification and yielded confident species level identification scores for only 62 (39%) of the isolates, including four that proved misidentified subsequently. Whole-genome sequence analysis of 32 representative isolates for which no confident MALDI-TOF MS species level identification was obtained revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively, and provided the basis for updating an in-house MALDI-TOF MS database. A reanalysis of all mass spectra with the updated MALDI-TOF MS database increased the percentage of isolates with confident species level identification up to 77%. The antimicrobial susceptibility of 30 isolates mainly representing novel human clinical and environmental Ralstonia species was tested toward 17 antimicrobial agents and demonstrated that the novel Ralstonia species were generally multi-resistant, yet susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline. An analysis of genomic antimicrobial resistance genes in 32 novel and publicly available genome sequences revealed broadly distributed beta-lactam resistance determinants.IMPORTANCEThe present study demonstrated that a commercial matrix-assisted laser desorption/ionization time-of-flight mass spectrometry identification database can be tailored to improve the identification of Ralstonia species. It also revealed the presence of seven novel Ralstonia species, including three and four that were isolated from cystic fibrosis or other human clinical samples, respectively. An analysis of minimum inhibitory concentration values demonstrated that the novel Ralstonia species were generally multi-resistant but susceptible to trimethoprim/sulfamethoxazole, ciprofloxacin, and tigecycline.
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Affiliation(s)
- Stephanie Steyaert
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
| | - Charlotte Peeters
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
| | - Anneleen D Wieme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- BCCM/LMG Bacteria Collection, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Astrid Muyldermans
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Theodore Spilker
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Ingrid Wybo
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - Denis Piérard
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Brussels, Belgium
| | - John J LiPuma
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Gent, Belgium
- National Reference Center for Burkholderia cepacia complex, La Plata, Belgium
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Vanstokstraeten R, Callewaert E, Blotwijk S, Rombauts E, Crombé F, Emmerechts K, Soetens O, Vandoorslaer K, De Geyter D, Allonsius C, Vander Donck L, Blockeel C, Wybo I, Piérard D, Demuyser T, Mackens S. Comparing Vaginal and Endometrial Microbiota Using Culturomics: Proof of Concept. Int J Mol Sci 2023; 24:ijms24065947. [PMID: 36983020 PMCID: PMC10055768 DOI: 10.3390/ijms24065947] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/17/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
It is generally accepted that microorganisms can colonize a non-pathological endometrium. However, in a clinical setting, endometrial samples are always collected by passing through the vaginal-cervical route. As such, the vaginal and cervical microbiomes can easily cross-contaminate endometrial samples, resulting in a biased representation of the endometrial microbiome. This makes it difficult to demonstrate that the endometrial microbiome is not merely a reflection of contamination originating from sampling. Therefore, we investigated to what extent the endometrial microbiome corresponds to that of the vagina, applying culturomics on paired vaginal and endometrial samples. Culturomics could give novel insights into the microbiome of the female genital tract, as it overcomes sequencing-related bias. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy were included. An additional vaginal swab was taken from each participant right before hysteroscopy. Both endometrial biopsies and vaginal swabs were analyzed using our previously described WASPLab-assisted culturomics protocol. In total, 101 bacterial and two fungal species were identified among these 10 patients. Fifty-six species were found in endometrial biopsies and 90 were found in vaginal swabs. On average, 28 % of species were found in both the endometrial biopsy and vaginal swab of a given patient. Of the 56 species found in the endometrial biopsies, 13 were not found in the vaginal swabs. Of the 90 species found in vaginal swabs, 47 were not found in the endometrium. Our culturomics-based approach sheds a different light on the current understanding of the endometrial microbiome. The data suggest the potential existence of a unique endometrial microbiome that is not merely a presentation of cross-contamination derived from sampling. However, we cannot exclude cross-contamination completely. In addition, we observe that the microbiome of the vagina is richer in species than that of the endometrium, which contradicts the current sequence-based literature.
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Affiliation(s)
- Robin Vanstokstraeten
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ellen Callewaert
- Department of Pharmaceutical Sciences, Entity of In Vitro Toxicology, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Susanne Blotwijk
- Biostatistics and Medical Informatics Research Group (BISI), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Eleni Rombauts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Florence Crombé
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Kristof Emmerechts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Deborah De Geyter
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Camille Allonsius
- Department of Bioscience Engineering, University of Antwerp (UA), 2020 Antwerp, Belgium
| | - Leonore Vander Donck
- Department of Bioscience Engineering, University of Antwerp (UA), 2020 Antwerp, Belgium
| | - Christophe Blockeel
- Brussels IVF, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
- AIMS Lab, Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Shari Mackens
- Brussels IVF, Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
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Vanstokstraeten R, Mackens S, Callewaert E, Blotwijk S, Emmerechts K, Crombé F, Soetens O, Wybo I, Vandoorslaer K, Mostert L, De Geyter D, Muyldermans A, Blockeel C, Piérard D, Demuyser T. Culturomics to Investigate the Endometrial Microbiome: Proof-of-Concept. Int J Mol Sci 2022; 23:12212. [PMID: 36293066 PMCID: PMC9602868 DOI: 10.3390/ijms232012212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/03/2022] [Accepted: 10/09/2022] [Indexed: 08/29/2023] Open
Abstract
The microbiome of the reproductive tract has been associated with (sub)fertility and it has been suggested that dysbiosis reduces success rates and pregnancy outcomes. The endometrial microbiome is of particular interest given the potential impact on the embryo implantation. To date, all endometrial microbiome studies have applied a metagenomics approach. A sequencing-based technique, however, has its limitations, more specifically in adequately exploring low-biomass settings, such as intra-uterine/endometrial samples. In this proof-of-concept study, we demonstrate the applicability of culturomics, a high-throughput culturing approach, to investigate the endometrial microbiome. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy, as part of their routine work-up at Brussels IVF, were included after their informed consent. Biopsies were used to culture microbiota for up to 30 days in multiple aerobic and anaerobic conditions. Subsequent WASPLab®-assisted culturomics enabled a standardized methodology. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA sequencing was applied to identify all of bacterial and fungal isolates. Eighty-three bacterial and two fungal species were identified. The detected species were in concordance with previously published metagenomics-based endometrial microbiota analyses as 77 (91%) of them belonged to previously described genera. Nevertheless, highlighting the added value of culturomics to identify most isolates at the species level, 53 (62.4%) of the identified species were described in the endometrial microbiota for the first time. This study shows the applicability and added value of WASPLab®-assisted culturomics to investigate the low biomass endometrial microbiome at a species level.
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Affiliation(s)
- Robin Vanstokstraeten
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Shari Mackens
- Brussels IVF, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ellen Callewaert
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Susanne Blotwijk
- Biostatistics and Medical Informatics Research Group (BISI), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
| | - Kristof Emmerechts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Florence Crombé
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Laurence Mostert
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Deborah De Geyter
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Astrid Muyldermans
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Christophe Blockeel
- Brussels IVF, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
| | - Thomas Demuyser
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), 1090 Brussels, Belgium
- Center for Neurosciences, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, 1090 Brussels, Belgium
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Herroelen PH, Heestermans R, Emmerechts K, Vandoorslaer K, Wybo I, Piérard D, Muyldermans A. Correction to: Validation of Rapid Antimicrobial Susceptibility Testing directly from blood cultures using WASPLab®, including Colibrí™ and Radian® in-Line Carousel. Eur J Clin Microbiol Infect Dis 2022; 41:1001. [PMID: 35511407 DOI: 10.1007/s10096-022-04451-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Pauline Hilda Herroelen
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B‑1090, Brussels, Belgium
| | - Robbe Heestermans
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B‑1090, Brussels, Belgium
| | - Kristof Emmerechts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B‑1090, Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B‑1090, Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B‑1090, Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B‑1090, Brussels, Belgium
| | - Astrid Muyldermans
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B‑1090, Brussels, Belgium.
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Herroelen PH, Heestermans R, Emmerechts K, Vandoorslaer K, Wybo I, Piérard D, Muyldermans A. Validation of Rapid Antimicrobial Susceptibility Testing directly from blood cultures using WASPLab ®, including Colibrí ™ and Radian ® in-Line Carousel. Eur J Clin Microbiol Infect Dis 2022; 41:733-739. [PMID: 35217936 PMCID: PMC9042988 DOI: 10.1007/s10096-022-04421-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Abstract
With the increase in antimicrobial resistance, fast reporting of antimicrobial susceptibility testing (AST) results is becoming increasingly important. EUCAST developed a method for rapid AST (RAST) directly from the broth of positive blood cultures (BC). Inhibition zones are read after 4, 6, and 8 h, with specific breakpoints per time point. We evaluated the RAST method based on EUCAST disk diffusion methodology with inoculation of BC broth using WASPLab® (inclusive Colibrí™ and Radian®). Forty-nine non-duplicate strains were tested: Escherichia coli n = 17, Klebsiella pneumoniae n = 7, Pseudomonas aeruginosa n = 4, Acinetobacter baumannii n = 2, Staphylococcus aureus n = 10, Enterococcus faecalis n = 6, and Enterococcus faecium n = 3. Results were compared to direct AST and standardized AST. Good categorical agreement was obtained at all time points for all groups, except P. aeruginosa. RAST cut-offs for extended-spectrum β-lactamase (ESBL)-producing Enterobacterales enabled the detection of all included ESBL isolates (n = 5) at all time points, except for 1 E. coli ESBL after 4 h. RAST cut-offs for carbapenemase-producing Enterobacterales enabled the detection of only one carbapenemase after 6 h. However, all carbapenemases (n = 3) were correctly detected after 8 h. Two methicillin-resistant S. aureus were included; both were correctly categorized as cefoxitin-resistant at 6 and 8 h. At 4 h, there was insufficient growth for inhibition zone interpretation. EUCAST RAST is a fast supplementary tool for direct AST of positive BC. WASPLab® provides a significant advantage as pictures are made automatically implicating that we are not strictly bound to the time points for inhibition zone interpretation.
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Affiliation(s)
- Pauline Hilda Herroelen
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - Robbe Heestermans
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - Kristof Emmerechts
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B-1090, Brussels, Belgium
| | - Astrid Muyldermans
- Department of Microbiology and Infection Control, Vrije Universiteit Brussel (VUB), Universitair Ziekenhuis Brussel (UZ Brussel), Laarbeeklaan 101, B-1090, Brussels, Belgium.
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Demuyser T, De Geyter D, Van Dorpe D, Vandoorslaer K, Wybo I. Extensive evaluation of fastidious anaerobic bacteria recovery from the Copan eSwab® transport system. J Microbiol Methods 2018; 144:73-78. [DOI: 10.1016/j.mimet.2017.11.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 11/09/2017] [Accepted: 11/12/2017] [Indexed: 11/16/2022]
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De Keukeleire S, Wybo I, Naessens A, Echahidi F, Van der Beken M, Vandoorslaer K, Vermeulen S, Piérard D. Anaerobic bacteraemia: a 10-year retrospective epidemiological survey. Anaerobe 2016; 39:54-9. [PMID: 26923749 DOI: 10.1016/j.anaerobe.2016.02.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Revised: 02/17/2016] [Accepted: 02/22/2016] [Indexed: 10/22/2022]
Abstract
In order to identify current trends in anaerobic bacteraemia, a 10-year retrospective study was performed in the University Hospital Brussel, Belgium. All clinically relevant bacteraemia detected from 2004 until 2013 were included. Medical records were reviewed in an attempt to define clinical parameters that might be associated with the occurrence of anaerobic bacteraemia. 437 of the isolated organisms causing anaerobic bacteraemia were thawed, subcultured and reanalyzed using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF). There were an average of 33 cases of anaerobic bacteraemia per year during 2004-2008 compared to an average of 27 cases per year during 2009-2013 (P = 0.017), corresponding to a decrease by 19% between the first and the latter period. Also, the total number of cases of anaerobic bacteraemia per 100,000 patient days decreased from 17.3 in the period from 2004 to 2008 to 13.7 in the period 2009 to 2013 (P = 0.023). Additionally, the mean incidence of anaerobic bacteraemia decreased during the study period (1.27/1000 patients in 2004 vs. 0.94/1000 patients in 2013; P = 0.008). In contrast, the proportion of isolated anaerobic bacteraemia compared to the number of all bacteraemia remained stable at 5%. Bacteroides spp. and Parabacteroides spp. accounted for 47.1% of the anaerobes, followed by 14.4% Clostridium spp., 12.6% non-spore-forming Gram-positive rods, 10.5% anaerobic cocci, 8.2% Prevotella spp. and other Gram-negative rods and 7.1% Fusobacterium spp. The lower gastrointestinal tract (47%) and wound infections (10%) were the two most frequent sources for bacteraemia, with the origin remaining unknown in 62 cases (21%). The overall mortality rate was 14%. Further studies focusing on the antimicrobial susceptibility and demographic background of patients are needed to further objectify the currently observed trends.
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Affiliation(s)
- Steven De Keukeleire
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium.
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Anne Naessens
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Fedoua Echahidi
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Mieke Van der Beken
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Stefan Vermeulen
- Department of Biomedical Sciences, Faculty of Education, Health & Social Work, University College Ghent, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Wybo I, Van den Bossche D, Soetens O, Vekens E, Vandoorslaer K, Claeys G, Glupczynski Y, Ieven M, Melin P, Nonhoff C, Rodriguez-Villalobos H, Verhaegen J, Piérard D. Fourth Belgian multicentre survey of antibiotic susceptibility of anaerobic bacteria. J Antimicrob Chemother 2013; 69:155-61. [PMID: 24008826 PMCID: PMC3861333 DOI: 10.1093/jac/dkt344] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Objectives To collect recent data on the susceptibility of anaerobes to antimicrobial agents with known activity against anaerobes, and to compare them with results from previous Belgian multicentre studies. Methods Four hundred and three strict anaerobic clinical isolates were prospectively collected from February 2011 to April 2012 in eight Belgian university hospitals. MICs were determined by one central laboratory for 11 antimicrobial agents using Etest methodology. Results According to EUCAST breakpoints, >90% of isolates were susceptible to amoxicillin/clavulanate (94%), piperacillin/tazobactam (91%), meropenem (96%), metronidazole (92%) and chloramphenicol (98%), but only 70% and 40% to clindamycin and penicillin, respectively. At CLSI recommended breakpoints, only 71% were susceptible to moxifloxacin and 79% to cefoxitin. MIC50/MIC90 values for linezolid and for tigecycline were 1/4 and 0.5/4 mg/L, respectively. When compared with survey data from 2004, no major differences in susceptibility profiles were noticed. However, the susceptibility of Prevotella spp. and other Gram-negative bacilli to clindamycin decreased from 91% in 1993–94 and 82% in 2004 to 69% in this survey. Furthermore, the susceptibility of clostridia to moxifloxacin decreased from 88% in 2004 to 66% in 2011–12 and that of fusobacteria from 90% to 71%. Conclusions Compared with previous surveys, little evolution was seen in susceptibility, except a decline in activity of clindamycin against Prevotella spp. and other Gram-negative bacteria, and of moxifloxacin against clostridia. Since resistance was detected to all antibiotics, susceptibility testing of anaerobic isolates is indicated in severe infections to confirm appropriateness of antimicrobial therapy.
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Affiliation(s)
- Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
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De Bel A, Van Hoorde K, Wybo I, Vandoorslaer K, Echahidi F, De Brandt E, Schumann P, Ieven M, Soetens O, Piérard D, Vandamme P. Staphylococcus
jettensis sp. nov., a coagulase-negative staphylococcal species isolated from human clinical specimens. Int J Syst Evol Microbiol 2013; 63:3250-3256. [DOI: 10.1099/ijs.0.044438-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Eight coagulase-negative, novobiocin-susceptible staphylococcal strains were isolated from human clinical specimens at two different Belgian medical facilities. All strains were non-motile, Gram-stain-positive, catalase-positive cocci. DNA G+C content, peptidoglycan type, menaquinone pattern, the presence of teichoic acid and cellular fatty acid composition were in agreement with the characteristics of species of the genus
Staphylococcus
. Sequencing of the 16S rRNA gene and four housekeeping genes (dnaJ, tuf, gap and rpoB) demonstrated that these strains constitute a separate taxon within the genus
Staphylococcus
. Less than 41 % DNA–DNA hybridization with the most closely related species of the genus
Staphylococcus
(
Staphylococcus haemolyticus
,
Staphylococcus hominis
and
Staphlococcus lugdunensis
) was observed. Key biochemical characteristics that allowed these bacteria to be distinguished from their nearest phylogenetic neighbours are arginine dihydrolase positivity, ornithine decarboxylase negativity and inability to produce acid aerobically from d-mannose, α-lactose and turanose. Acid is produced aerobically from trehalose. Based on these results, a novel species of the genus
Staphylococcus
is described and named
Staphylococcus
jettensis sp. nov. The type strain is SEQ110T ( = LMG 26879T = CCUG 62657T = DSM 26618T).
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Affiliation(s)
- Annelies De Bel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Koenraad Van Hoorde
- Faculty of Applied Bioscience Engineering, University College Ghent, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Fedoua Echahidi
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Evie De Brandt
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
| | - Peter Schumann
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7 B, 38124 Braunschweig, Germany
| | - Margareta Ieven
- Laboratory of Microbiology, Universitair Ziekenhuis Antwerpen, Wilrijkstraat 10, 2650 Edegem, Belgium
| | - Oriane Soetens
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Peter Vandamme
- Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, 9000 Ghent, Belgium
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10
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Van den Bossche D, De Bel A, De Smet D, Heylen O, Vekens E, Vandoorslaer K, Soetens O, Piérard D. Prevalence of Bordetella holmesii and Bordetella bronchiseptica in respiratory tract samples from Belgian patients with pertussis-like symptoms by sensitive culture method and mass spectrometry. Acta Clin Belg 2013; 68:341-8. [PMID: 24579240 DOI: 10.2143/acb.3341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Insertion sequences IS481 and IS1001 are targets for molecular detection of respectively Bordetella pertussis and Bordetella parapertussis. There is a raising concern about specificity of these targets due to sequence similarity with Bordetella holmesii and Bordetella bronchiseptica. The likelihood of false (para)pertussis diagnoses should be correlated with the prevalence of these organisms in the respiratory tract (RT). From October 2010 until September 2011, 2,207 RT samples were submitted to the Belgian reference laboratory for pertussis diagnosis. End-point IS481/IS 1001 PCR and culture were performed for B. pertussis and B. parapertussis. We developed a sensitive culture method followed by screening with matrix-assisted laser desorption/ionisation- time of flight mass spectrometry (MALDI-TOF MS) to look for B. holmesii and B. bronchiseptica in our samples,. Only one B. bronchiseptica and no B. holmesii were detected in RT samples from Belgian patients with pertussis-like symptoms.
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Affiliation(s)
- D Van den Bossche
- National Reference Centre for Bordetella Pertussis, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Belgium.
| | - A De Bel
- National Reference Centre for Bordetella Pertussis, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Belgium
| | - D De Smet
- National Reference Centre for Bordetella Pertussis, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Belgium
| | - O Heylen
- National Reference Centre for Bordetella Pertussis, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Belgium
| | - E Vekens
- National Reference Centre for Bordetella Pertussis, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Belgium
| | - K Vandoorslaer
- National Reference Centre for Bordetella Pertussis, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Belgium
| | - O Soetens
- National Reference Centre for Bordetella Pertussis, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Belgium
| | - D Piérard
- National Reference Centre for Bordetella Pertussis, Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Belgium
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11
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De Bel A, Wybo I, Vandoorslaer K, Rosseel P, Lauwers S, Piérard D. Acceptance criteria for identification results of Gram-negative rods by mass spectrometry. J Med Microbiol 2011; 60:684-686. [DOI: 10.1099/jmm.0.023184-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Annelies De Bel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Ingrid Wybo
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Kristof Vandoorslaer
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Paul Rosseel
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Sabine Lauwers
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
| | - Denis Piérard
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel (VUB), Laarbeeklaan 101, 1090 Brussels, Belgium
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12
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Wybo I, Piérard D, Ichiche M, Vandoorslaer K, Soetens O, Rosseel P, Lauwers S. P1947 Isolation of Microbacterium species in a case of dialysis-associated peritonitis. Int J Antimicrob Agents 2007. [DOI: 10.1016/s0924-8579(07)71786-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Wybo I, Piérard D, Verschraegen I, Reynders M, Vandoorslaer K, Claeys G, Delmée M, Glupczynski Y, Gordts B, Ieven M, Melin P, Struelens M, Verhaegen J, Lauwers S. Third Belgian multicentre survey of antibiotic susceptibility of anaerobic bacteria. J Antimicrob Chemother 2006; 59:132-9. [PMID: 17095529 DOI: 10.1093/jac/dkl458] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To collect recent data on the susceptibility of anaerobes and to compare them with results from previous studies. METHODS Four hundred and forty-three anaerobic clinical isolates from various body sites were prospectively collected from October 2003 to February 2005 in nine Belgian hospitals. MICs were determined for nine anti-anaerobic and three recently developed antibiotics. RESULTS Most gram-negative bacilli except Fusobacterium spp. were resistant to penicillin. Piperacillin/tazobactam, metronidazole, chloramphenicol, meropenem and amoxicillin/clavulanic acid were very active against all groups, but only 86% of Bacteroides fragilis group strains were susceptible to the latter. Cefoxitin, cefotetan and clindamycin were less active. In particular, only 62%, 52% and 48% of B. fragilis group strains were susceptible, respectively. Clindamycin shows a continuing decrease in activity, as 83% were still susceptible in 1987 and 66% in 1993-94. Anti-anaerobic activity of the new antibiotics is interesting, with MIC50 and MIC90 of 1 and >32 mg/L for moxifloxacin, 2 and 4 mg/L for linezolid and 0.5 and 8 mg/L for tigecycline. CONCLUSIONS The susceptibility of anaerobic bacteria remains stable in Belgium, except for clindamycin, which shows a continuous decrease in activity. However, for each of the tested antibiotics, at least a few resistant organisms were detected. Consequently, for severe infections involving anaerobic bacteria, it could be advisable to perform microbiological testing instead of relying on known susceptibility profiles. Periodically monitoring background susceptibility remains necessary to guide empirical therapy.
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Affiliation(s)
- Ingrid Wybo
- Academisch Ziekenhuis Vrije Universiteit Brussel, 1090 Brussels, Belgium.
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14
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Detry G, Pierard D, Vandoorslaer K, Wauters G, Avesani V, Glupczynski Y. Septicemia due to Solobacterium moorei in a patient with multiple myeloma. Anaerobe 2006; 12:160-2. [PMID: 16723262 DOI: 10.1016/j.anaerobe.2006.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2005] [Revised: 04/08/2006] [Accepted: 04/16/2006] [Indexed: 10/24/2022]
Abstract
We report a case of bacteremia caused by Solobacterium moorei, an anaerobic, non-sporulated Gram-positive bacillus in a patient with a multiple myeloma. The source of infection was presumably related to multiple dento-alveolar abscesses. This is the first recovery of S. moorei from blood cultures.
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Affiliation(s)
- G Detry
- Department of Microbiology, Catholic University of Louvain, Mont-Godinne University Hospital, Yvoir, Belgium
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15
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Piérard D, Wybo I, Vandoorslaer K, Roebben E, Rosseel P, Lauwers S. In vitro activity of ertapenem against anaerobes isolated from the respiratory tract. ACTA ACUST UNITED AC 2003; 51:508-11. [PMID: 14568599 DOI: 10.1016/s0369-8114(03)00152-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Ertapenem is a novel parenteral carbapenem with a long serum half-life. Its spectrum of activity is similar to that of imipenem and meropenem against Gram-positive bacteria, Enterobacteriaceae and fastidious Gram-negative bacteria but it is less active against Pseudomonas aeruginosa and Acinetobacter spp. Several studies were performed in the United States but only one European study has shown that ertapenem has an excellent activity against anaerobes. The objectives of the present study were to test the activity of ertapenem against anaerobes isolated prospectively from the lower and upper respiratory tracts, and to compare their susceptibility with that of anaerobic isolates from other body sites. Fifty-three isolates from the respiratory tract, as well as 50 isolates from various other body sites were tested with E-tests against six antibiotics. For respiratory isolates and for isolates from other sites, MIC 90 values (mg/l) were, respectively, >32 and >32 for penicillin, 0.38 and 0.75 for amoxicillin/clavulanate, 48 and >256 for ceftriaxone, 0.12 and 0.75 for ertapenem, 12 and >256 for clindamycin and 2 and 12 for moxifloxacin. The higher susceptibility of respiratory tract isolates was mainly due to the different distribution of isolated species: only three respiratory isolates but 22 other isolates belonged to the Bacteroides fragilis group. This study confirms the excellent anti-anaerobic activity of ertapenem against anaerobic isolates from the respiratory tract.
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Affiliation(s)
- Denis Piérard
- Département de Microbiologie, Hôpital Académique V.U.B., Laarbeeklaan 101, B-1090 Brussels, Belgium.
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Foulon I, Piérard D, Muyldermans G, Vandoorslaer K, Soetens O, Rosseel P, Lauwers S. Prevalence of fragilysin gene in Bacteroides fragilis isolates from blood and other extraintestinal samples. J Clin Microbiol 2003; 41:4428-30. [PMID: 12958284 PMCID: PMC193814 DOI: 10.1128/jcm.41.9.4428-4430.2003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Of 166 Bacteroides fragilis isolates, 26.2% of 103 isolates from blood and 20.6% of 63 extraintestinal isolates harbored the fragilysin gene (difference not statistically significant). Clinical characteristics and evolution were comparable in patients with B. fragilis bacteremia with or without this enterotoxin. Fragilysin seems not to be an important virulence factor in B. fragilis disease.
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Affiliation(s)
- Ina Foulon
- Department of Microbiology, Academisch Ziekenhuis Vrije Universiteit Brussel, Brussels, Belgium
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