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Verschuuren TD, van Hout D, Arredondo-Alonso S, Fluit AC, Reuland EA, Top J, Schürch AC, Bosch T, Bonten MJM, Kluytmans JAJW, Willems RJL. Comparative genomics of ESBL-producing Escherichia coli (ESBL-Ec) reveals a similar distribution of the 10 most prevalent ESBL-Ec clones and ESBL genes among human community faecal and extra-intestinal infection isolates in the Netherlands (2014-17). J Antimicrob Chemother 2021; 76:901-908. [PMID: 33428729 PMCID: PMC7953314 DOI: 10.1093/jac/dkaa534] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/19/2020] [Indexed: 11/23/2022] Open
Abstract
INTRODUCTION The human gut microbiota is an important reservoir of ESBL-producing Escherichia coli (ESBL-Ec). Community surveillance studies of ESBL-Ec to monitor circulating clones and ESBL genes are logistically challenging and costly. OBJECTIVES To evaluate if isolates obtained in routine clinical practice can be used as an alternative to monitor the distribution of clones and ESBL genes circulating in the community. METHODS WGS was performed on 451 Dutch ESBL-Ec isolates (2014-17), including 162 community faeces and 289 urine and blood isolates. We compared proportions of 10 most frequently identified STs, PopPUNK-based sequence clusters (SCs) and ESBL gene subtypes and the degree of similarity using Czekanowski's proportional similarity index (PSI). RESULTS Nine out of 10 most prevalent STs and SCs and 8/10 most prevalent ESBL genes in clinical ESBL-Ec were also the most common types in community faeces. The proportions of ST131 (39% versus 23%) and SC131 (40% versus 25%) were higher in clinical isolates than in community faeces (P < 0.01). Within ST131, H30Rx (C2) subclade was more prevalent among clinical isolates (55% versus 26%, P < 0.01). The proportion of ESBL gene blaCTX-M-1 was lower in clinical isolates (5% versus 18%, P < 0.01). Czekanowski's PSI confirmed that the differences in ESBL-Ec from community faeces and clinical isolates were limited. CONCLUSIONS Distributions of the 10 most prevalent clones and ESBL genes from ESBL-Ec community gut colonization and extra-intestinal infection overlapped in majority, indicating that isolates from routine clinical practice could be used to monitor ESBL-Ec clones and ESBL genes in the community.
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Affiliation(s)
- T D Verschuuren
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - D van Hout
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - S Arredondo-Alonso
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A C Fluit
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - E A Reuland
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
- Saltro Diagnostic Center for Primary Care, Utrecht, The Netherlands
- The Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - J Top
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - A C Schürch
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - T Bosch
- The Netherlands Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - M J M Bonten
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - J A J W Kluytmans
- Julius Centre for Health Sciences and Primary Care, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - R J L Willems
- Department of Medical Microbiology, University Medical Centre Utrecht, Utrecht, The Netherlands
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Abdallah HM, Alnaiemi N, Reuland EA, Wintermans BB, Koek A, Abdelwahab AM, Samy A, Abdelsalam KW, Vandenbroucke-Grauls CMJE. Fecal carriage of extended-spectrum β-lactamase- and carbapenemase-producing Enterobacteriaceae in Egyptian patients with community-onset gastrointestinal complaints: a hospital -based cross-sectional study. Antimicrob Resist Infect Control 2017. [PMID: 28630686 PMCID: PMC5470242 DOI: 10.1186/s13756-017-0219-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [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: 12/21/2022] Open
Abstract
Objectives The aim of this study was to determine the prevalence of extended-spectrum β-lactamase (ESBL) and carbapenemase production among Enterobacteriaceae isolated from ambulatory patients with gastrointestinal complaints admitted to El-Ahrar General Hospital, Zagazig, Egypt in the period between January 2013 and May 2013. Methods One hundred and thirteen Enterobacteriaceae isolates were recovered from 100 consecutive Egyptian patients with community–onset gastrointestinal complaints. The fecal samples were plated directly on selective EbSA-ESBL Screening Agar and on MacConkey agar. Isolate identification was performed with matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS). Screening for ESBLs and carbapenemases production was done by both the automated VITEK®2 system with AST N198 and by disk diffusion method. Real-time PCR and sequencing were used to characterize the resistance genes. Phylogroups of the E. coli isolates were determined by a triplex PCR-based method. Results Of 100 patients screened for fecal colonization with extended-spectrum β-lactamase -producing Enterobacteriaceae (ESBL-E) and carbapenemase- producing Enterobacteriaceae (CPE), 68 were colonized with ESBL-E whereas five patients were positive for CPE. One hundred and thirteen Enterobacterceae isolates were recovered from 100 fecal samples, they belonged to E. coli (n = 72), Klebsiella pneumoniae (n = 23), Enterobacter cloacae(n = 3), Salmonella spp. (n = 1) and other Enterobacterceae isolates (n = 14). The blaCTX-M gene was detected in 89.04% (65/73) of the ESBL-producing Enterobacteriaceae, whereas blaSHV and blaTEM were detected in 30.14% (22/73) and 19.18% (14/73) respectively. Three out of 5 carbapenem-resistant isolates harbored New Delhi metallo-beta-lactamase (NDM) and 2 produced Verona integron-encoded metallo- beta -lactamase (VIM). Twenty-two (47.83%) of the ESBL positive isolates were multidrug resistant (MDR). Phylogenetic analysis showed that, of the 51 ESBL-EC isolates, 17 belonged to group B2, 13 to group D, 11 to group A and 10 to group B1. Conclusions Nearly two-thirds of the Enterobacteriaceae isolates recovered from feces of ambulatory patients with community–onset gastrointestinal complaints admitted to El-Ahrar General Hospital, Zagazig, Egypt were ESBL producers and one in every 20 patients included in our study was colonized by carbapenemase-producing Enterobacteriaceae. These high colonization rates are worrying, therefore prudent antimicrobial use should be adopted in Egyptian community settings.
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Affiliation(s)
- H M Abdallah
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.,Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - N Alnaiemi
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands.,Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands.,Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - E A Reuland
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - B B Wintermans
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - A Koek
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - A M Abdelwahab
- Department of Microbiology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - A Samy
- National Laboratory for Veterinary Quality Control on Poultry Production, Animal Health Research Institute, Dokki, Giza, Egypt
| | - K W Abdelsalam
- Department of Virology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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Reuland EA, Al Naiemi N, Kaiser AM, Heck M, Kluytmans JAJW, Savelkoul PHM, Elders PJM, Vandenbroucke-Grauls CMJE. Prevalence and risk factors for carriage of ESBL-producing Enterobacteriaceae in Amsterdam. J Antimicrob Chemother 2016; 71:1076-82. [PMID: 26755493 PMCID: PMC4790620 DOI: 10.1093/jac/dkv441] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Accepted: 11/19/2015] [Indexed: 01/28/2023] Open
Abstract
Objectives The objectives of this study were to determine the prevalence of carriage of ESBL-producing Enterobacteriaceae (ESBL-E) in a representative sample of the general adult Dutch community, to identify risk factors and to gain understanding of the epidemiology of these resistant strains. Methods Adults enrolled in five general practices in Amsterdam were approached by postal mail and asked to fill in a questionnaire and to collect a faecal sample. Samples were analysed for the presence of ESBL-E. ESBL genes were characterized by PCR and sequencing. Strains were typed using MLST and amplified fragment length polymorphism (AFLP) and plasmids were identified by PCR-based replicon typing. Risk factors for carriage were investigated by multivariate analysis. Results ESBL-E were found in 145/1695 (8.6%) samples; 91% were Escherichia coli. Most ESBL genes were of the CTX-M group (blaCTX-M-1 and blaCTX-M-15). MLST ST131 was predominant and mainly associated with CTX-M-15-producing E. coli. One isolate with reduced susceptibility to ertapenem produced OXA-48. In multivariate analyses, use of antimicrobial agents, use of antacids and travel to Africa, Asia and Northern America were associated with carriage of ESBL-E, in particular strains with blaCTX-M-14/15. Conclusions This study showed a high prevalence of ESBL-E carriage in the general Dutch community. Also, outside hospitals, the use of antibiotics was a risk factor; interestingly, use of antacids increased the risk of carriage. A major risk factor in the general population was travel to countries outside Europe, in particular to Asia, Africa and Northern America.
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Affiliation(s)
- E A Reuland
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - N Al Naiemi
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands Laboratory for Medical Microbiology and Public Health, Hengelo, The Netherlands Medical Microbiology and Infection Control, Ziekenhuisgroep Twente, Almelo, The Netherlands
| | - A M Kaiser
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - M Heck
- Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - J A J W Kluytmans
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands Department of Medical Microbiology and Infection Control, Amphia Hospital, Breda, The Netherlands Department of Medical Microbiology, St Elisabeth Hospital, Tilburg, The Netherlands
| | - P H M Savelkoul
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, The Netherlands
| | - P J M Elders
- EMGO Institute for Health and Care Research, VU University Medical Center, Amsterdam, The Netherlands
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Abdallah HM, Reuland EA, Wintermans BB, al Naiemi N, Koek A, Abdelwahab AM, Ammar AM, Mohamed AA, Vandenbroucke-Grauls CMJE. Extended-Spectrum β-Lactamases and/or Carbapenemases-Producing Enterobacteriaceae Isolated from Retail Chicken Meat in Zagazig, Egypt. PLoS One 2015; 10:e0136052. [PMID: 26284654 PMCID: PMC4540287 DOI: 10.1371/journal.pone.0136052] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 07/30/2015] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVES The aim of the present study was to determine the prevalence and to characterize extended-spectrum β-lactamases- and/or carbapenemases-producing Enterobacteriaceae among Enterobacteriaceae isolated from retail chicken meat in Zagazig, Egypt. METHODS One hundred and six Enterobacteriaceae isolates were collected from retail chicken meat samples purchased in Zagazig, Egypt in 2013. Species identification was done by MALDI-TOF MS. Screening for ESBL-E was performed by inoculation of isolates recovered from meat samples onto the EbSA (Cepheid Benelux, Apeldoorn, the Netherlands) selective screening agar. ESBL production was confirmed by combination disc diffusion test with clavulanic acid (Rosco, Taastrup, Denmark). Carbapenemases production was confirmed with double disk synergy tests. Resistance genes were characterized by PCR with specific primers for TEM, SHV, and CTX-M and carbapenemases (KPC, NDM, OXA-48, IMP and VIM). PCR products of CTX-M genes were purified and sequenced. Phylogenetic grouping of E. coli was performed by a PCR-based method. RESULTS Of these 106 isolates 69 (65.09%) were ESBL producers. Twelve (11.32%) of these isolates were also phenotypically class B carbapenemases producer. TEM genes were detected in 61 (57.55%) isolates. 49 (46.23%) isolates harbored CTX-M genes, and 25 (23.58%) carried genes of the SHV family. All CPE belonged to the NDM group. The predominant CTX-M sequence type was CTX-M-15 (89.80%). The majority (80%) of the ESBL-EC belonged to low virulence phylogroups A and B1. CONCLUSIONS This is the first study from Egypt reporting high rates of ESBLs and carbapenemases (65.09% and 11.32%, respectively) in Enterobacteriaceae isolated from retail chicken meat. These results raise serious concerns about public health and food safety as retail meat could serve as a reservoir for these resistant bacteria which could be transferred to humans through the food chain.
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Affiliation(s)
- H. M. Abdallah
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- * E-mail:
| | - E. A. Reuland
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - B. B. Wintermans
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - N. al Naiemi
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Laboratory for Medical Microbiology and Public Health, Hengelo, the Netherlands
- Microbiology and Infection Control, Ziekenhuisgroep Twente, Almelo, Amsterdam, the Netherlands
| | - A. Koek
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - A. M. Abdelwahab
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - A. M. Ammar
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Zagazig University, Egypt
| | - A. A. Mohamed
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Zagazig University, Egypt
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Abdallah HM, Wintermans BB, Reuland EA, Koek A, al Naiemi N, Ammar AM, Mohamed AA, Vandenbroucke-Grauls CMJE. Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Enterobacteriaceae Isolated from Egyptian Patients with Suspected Blood Stream Infection. PLoS One 2015; 10:e0128120. [PMID: 26001049 PMCID: PMC4441433 DOI: 10.1371/journal.pone.0128120] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/23/2015] [Indexed: 01/08/2023] Open
Abstract
Objectives The aim of the study was to investigate the prevalence of extended-spectrum β-lactamase and carbapenemase production among Enterobacteriaceae isolated from Egyptian patients with suspected blood stream infection. Methods Ninety-four Enterobacteriaceae blood culture isolates from Egyptian patients with suspected blood stream infection were collected, one isolate per patient. Identification of bacterial isolates was performed with MALDI-TOF (MS-based Vitek MS system, bioMerieux). Screening for ESBLs and carbapenemases production was done with the Vitek 2 system (bioMérieux). ESBL production was confirmed using the combined disk diffusion method for cefotaxime, ceftazidime, and cefepime, all with and without clavulanic acid (Rosco). Real-time PCR and sequencing were used to characterize the resistance genes. The phylogenetic groups of E. coli were identified by a PCR-based method. Results Of the 94 Enterobacteriaceae isolates 46 (48.93%) showed an ESBL phenotype. One Enterobacter spp isolate was ESBL-producer and meropenem-resistant. The genetic analysis showed that CTX-M was present in 89.13% (41/46) of the ESBL-producing Enterobacteriaceae, whereas TEM and SHV were detected in 56.52% (26/46) and 21.74% (10/46) respectively (47.83%) of the ESBL-producing isolates were multidrug resistant (MDR). Eleven out of 30 ESBL-producing E-coli isolates were assigned to phylogroup B2, followed by groups B1 (8 isolates), A (6 isolates) and D (5 isolates). Conclusions The high ESBL-E rates (48.93%) found in this study together with the identification of one carbapenem-resistant Enterobacter spp isolate is worrisome. Our results indicate that systems for monitoring and detection of ESBL-producing bacteria in Egyptian hospitals have to be established. Also strict hospital infection control policies with the restriction of the consumption of extended-spectrum cephalosporins are necessary.
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Affiliation(s)
- H. M. Abdallah
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
- * E-mail:
| | - B. B. Wintermans
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - E. A. Reuland
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - A Koek
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
| | - N. al Naiemi
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands
- Laboratory for Medical Microbiology and Public Health, Hengelo, the Netherlands
- Microbiology and Infection Control, Ziekenhuisgroep Twente, Almelo, Amsterdam, the Netherlands
| | - A. M. Ammar
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - A. A. Mohamed
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
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Reuland EA, Al Naiemi N, Raadsen SA, Savelkoul PHM, Kluytmans JAJW, Vandenbroucke-Grauls CMJE. Prevalence of ESBL-producing Enterobacteriaceae in raw vegetables. Eur J Clin Microbiol Infect Dis 2014; 33:1843-6. [PMID: 24848131 PMCID: PMC4182617 DOI: 10.1007/s10096-014-2142-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 04/24/2014] [Indexed: 12/01/2022]
Abstract
To determine whether extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae (ESBL-E) are present in retail raw vegetables in Amsterdam, the Netherlands, we collected 119 samples of 15 different types of vegetables from various sources. After culture, strain identification and susceptibility testing, ESBL-encoding genes were characterised by a microarray. Four of the 15 vegetable types were contaminated with ESBL-E. Seven samples (6 %) yielded ESBL-E. Three blaCTX-M-15, one blaCTX-M-1, two genes of the CTX-M-9 group and one SHV ESBL-encoding gene were found. The ESBL genes were similar to what is found in enterobacterial strains from human origin. Therefore, raw vegetables might be a source of resistance genes for the enterobacterial strains found in humans.
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Affiliation(s)
- E A Reuland
- Department of Medical Microbiology and Infection Control, VU University Medical Center, P.O. Box 7057, 1007 MB, Amsterdam, The Netherlands,
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Wintermans BB, Reuland EA, Wintermans RGF, Bergmans AMC, Kluytmans JAJW. The cost-effectiveness of ESBL detection: towards molecular detection methods? Clin Microbiol Infect 2012; 19:662-5. [PMID: 22971154 DOI: 10.1111/j.1469-0691.2012.03998.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Correct detection of extended-spectrum beta-lactamases (ESBLs) is crucial for infection control and antibiotic choice. We performed a study to determine the cost-effectiveness of phenotypical testing, which can be inaccurate, and genotypical tests, which are considered to be more reliable but also more expensive. All patients that had been in isolation in the Amphia hospital because of the detection of ESBL according to the ESBL Etest were included in the survey. All strains were retested using the double disk confirmation test (DDCT) and a genotypical method. This was a commercially available microarray (Check-Points). Discordant results were confirmed by PCR and sequencing. In total 174 patients were included. In 24 of 174 (14%) patients, ESBL carriage could not be confirmed with the microarray. This was verified with PCR and sequencing. The mean duration of isolation was 15 days, adding up to a total number of isolation days of 2571. False-positive results according to the microarray resulted in a total of 279 days of unnecessary isolation for the Etest and 151 days for the DDCT. Using Etest to detect the presence of ESBL results in a false-positive outcome in 14% of the cases. This results in unnecessary isolation of patients, which can be omitted by using a genotypic method.
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Affiliation(s)
- B B Wintermans
- Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, the Netherlands.
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