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Article ; Online: Pre-processing tissue specimens with a tissue homogenizer: clinical and microbiological evaluation.

Yusuf, Erlangga / Pronk, Marieke / van Westreenen, Mireille

BMC microbiology

2021 Volume 21, Issue 1, Page(s) 202

Abstract: Background: Tissues are valuable specimens in diagnostic microbiology because they are often obtained by invasive methods, and effort should thus be taken to maximize microbiological yield. The objective of this study was to evaluate the added value of ... ...

Abstract	Background: Tissues are valuable specimens in diagnostic microbiology because they are often obtained by invasive methods, and effort should thus be taken to maximize microbiological yield. The objective of this study was to evaluate the added value of using tissue pre-processing (tissue homogenizer instrument gentleMACS Dissociator) in detecting microorganisms responsible for infections. Methods: We included 104 randomly collected tissue samples, 41 (39.4 %) bones and 63 (60.6 %) soft tissues, many of those (42/104 (40.4 %)) were of periprosthetic origins. We compared the agreement between pre-processing tissues using tissue homogenizer with routine microbiology diagnostic procedure, and we calculated the performance of these methods when clinical infections were used as reference standard. Results: There was no significant difference between the two methods (McNemar test, p = 0.3). Among the positive culture using both methods (n = 62), 61 (98.4 %) showed at least one similar microorganism. Exactly similar microorganisms were found in 42/62 (67.7 %) of the samples. From the included tissues, 55/ 104 (52.9 %) were deemed as infected. We found that the sensitivity of homogenized tissue procedure was lower (83.6 %) than when tissue was processed using tissue homogenizer (89.1 %). Sub-analysis on periprosthetic tissues and soft or bone tissues showed comparable results. Conclusions: The added value of GentleMACS Dissociator tissue homogenizer is limited in comparison to routine tissue processing.
MeSH term(s)	Bacterial Infections/diagnosis ; Bacterial Infections/microbiology ; Humans ; Microbiological Techniques/instrumentation ; Microbiological Techniques/methods ; Specimen Handling/methods
Language	English
Publishing date	2021-07-02
Publishing country	England
Document type	Journal Article
ISSN	1471-2180
ISSN (online)	1471-2180
DOI	10.1186/s12866-021-02271-6
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Article: An Update on Eight "New" Antibiotics against Multidrug-Resistant Gram-Negative Bacteria.

Yusuf, Erlangga / Bax, Hannelore I / Verkaik, Nelianne J / van Westreenen, Mireille

Journal of clinical medicine

2021 Volume 10, Issue 5

Abstract: Infections in the ICU are often caused by Gram-negative bacteria. When these microorganisms are resistant to third-generation cephalosporines (due to extended-spectrum (ESBL) or AmpC beta-lactamases) or to carbapenems (for example carbapenem producing ... ...

Abstract	Infections in the ICU are often caused by Gram-negative bacteria. When these microorganisms are resistant to third-generation cephalosporines (due to extended-spectrum (ESBL) or AmpC beta-lactamases) or to carbapenems (for example carbapenem producing Enterobacteriales (CPE)), the treatment options become limited. In the last six years, fortunately, there have been new antibiotics approved by the U.S. Food and Drug Administration (FDA) with predominant activities against Gram-negative bacteria. We aimed to review these antibiotics: plazomicin, eravacycline, temocillin, cefiderocol, ceftazidime/avibactam, ceftolozane/tazobactam, meropenem/vaborbactam, and imipenem/relebactam. Temocillin is an antibiotic that was only approved in Belgium and the UK several decades ago. We reviewed the in vitro activities of these new antibiotics, especially against ESBL and CPE microorganisms, potential side effects, and clinical studies in complicated urinary tract infections (cUTI), intra-abdominal infections (cIAI), and hospital-acquired pneumonia/ventilator-associatedpneumonia (HAP/VAP). All of these new antibiotics are active against ESBL, and almost all of them are active against CPE caused by KPC beta-lactamase, but only some of them are active against CPE due to MBL or OXA beta-lactamases. At present, all of these new antibiotics are approved by the U.S. Food and Drug Administration for cUTI (except eravacycline) and most of them for cIAI (eravacycline, ceftazidime/avibactam, ceftolozane/tazobactam, and imipenem/relebactam) and for HAP or VAP (cefiderocol, ceftazidime/avibactam, ceftolozane/tazobactam, and imipenem/relebactam).
Language	English
Publishing date	2021-03-04
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2662592-1
ISSN	2077-0383
ISSN	2077-0383
DOI	10.3390/jcm10051068
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Article ; Online: Confirmatory testing of

Tielemans, Myrte / van Westreenen, Mireille / Klaassen, Corné / Götz, Hannelore M

Sexually transmitted infections

2021 Volume 98, Issue 2, Page(s) 121–124

Abstract: Objectives: European guidelines advise the use of dual nucleic acid amplification tests (NAAT) in order to minimise the inappropriate diagnosis of : Methods: Apart from urogenital testing, extragenital (oropharyngeal/anorectal) testing was performed ... ...

Abstract	Objectives: European guidelines advise the use of dual nucleic acid amplification tests (NAAT) in order to minimise the inappropriate diagnosis of Methods: Apart from urogenital testing, extragenital (oropharyngeal/anorectal) testing was performed for men who have sex with men (MSM) and according to sexual exposure for women and heterosexual men. Ng detection using NAAT was performed using BD Viper and for confirmatory testing BD MAX. Sexual transmitted infection consultation data were merged with diagnostic data from August 2015 through May 2016. Results: In women (n=4175), oral testing was performed in 84% and 22% were tested anally. In MSM (n=1828), these percentages were 97% and 96%, respectively. Heterosexual men (n=3089) were tested urogenitally. After confirmatory testing, oropharyngeal positivity rates decreased from 7.3% (95% CI 6.5 to 8.2) to 1.5% (95% CI 1.1 to 1.8) in women and from 13.9% (95% CI 12.3 to 15.5) to 5.4% (95% CI 4.3 to 6.4) in MSM. Anorectal positivity rates decreased from 2.6% (95% CI 1.6 to 3.7) to 1.8% (95% CI 0.9 to 2.6) in women and from 9.3% (95% CI 7.9 to 10.7) to 7.2% (95% CI 6.0 to 8.5) in MSM. Urogenital Ng-positivity rate ranged between 3.0% and 4.4% and after confirmation between 2.3% and 3.9%. When confirming oropharyngeal samples, Ng-positivity was 3.8% in women, 3.0% in heterosexual men and 12.5% in MSM. Additional confirmation of urogenital and anorectal samples led to 3.0% Ng positivity in women, 2.7% in heterosexual men and 11.4% in MSM. Conclusions: Confirmation of urogenital and anorectal samples reduced the Ng-positivity rates, especially for women. However, as there is no gold standard for the confirmation of Ng infection, the dilemma within public health settings is to choose between two evils: missing diagnoses or overtreatment. In view of the large decrease in oropharyngeal positivity, confirmation Ng-positivity in oropharyngeal samples remains essential to avoid unnecessary treatment.
MeSH term(s)	Cross-Sectional Studies ; Female ; Gonorrhea/diagnosis ; Gonorrhea/drug therapy ; Gonorrhea/epidemiology ; Heterosexuality/statistics & numerical data ; Homosexuality, Male/statistics & numerical data ; Humans ; Male ; Molecular Diagnostic Techniques/methods ; Molecular Diagnostic Techniques/standards ; Neisseria gonorrhoeae/genetics ; Neisseria gonorrhoeae/isolation & purification ; Netherlands/epidemiology ; Prevalence ; Retrospective Studies ; Sexual Behavior ; Sexual Health
Language	English
Publishing date	2021-02-25
Publishing country	England
Document type	Journal Article
ZDB-ID	1420303-0
ISSN	1472-3263 ; 1368-4973
ISSN (online)	1472-3263
ISSN	1368-4973
DOI	10.1136/sextrans-2020-054525
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Article ; Online: Bacteria in Extracorporeal Membrane Oxygenation Circuit Clots of a Patient With Persistent Bacteremia: A Case Report.

Drop, Joppe G / Verhage, Latisha / van Westreenen, Mireille / Wildschut, Enno D / de Hoog, Matthijs / van Beusekom, Heleen / van Ommen, C Heleen

ASAIO journal (American Society for Artificial Internal Organs : 1992)

2023 Volume 69, Issue 11, Page(s) e463–e466

Abstract: A neonate with pulmonary hypertension was supported with extracorporeal membrane oxygenation (ECMO). During ECMO support, the patient developed Enterococcus faecalis bacteremia, treated with targeted antibiotics. Despite the maximum dose of antibiotics, ... ...

Abstract	A neonate with pulmonary hypertension was supported with extracorporeal membrane oxygenation (ECMO). During ECMO support, the patient developed Enterococcus faecalis bacteremia, treated with targeted antibiotics. Despite the maximum dose of antibiotics, routine blood cultures remained positive throughout the ECMO treatment. A circuit change was performed due to buildup of thrombotic material and disseminated intravascular coagulation (DIC) inside the circuit. Thrombus formation was more extensive in the first than the second circuit. Gram-positive diplococci were present in all initial circuit clots and gram-positive masses surrounded by fibrin were found inside thrombi of the second circuit. Scanning electron microscopy (SEM) revealed a dense fibrin network with embedded red blood cells and bacteria in the first circuit. In the second circuit, SEM analysis revealed scattered micro thrombi. Polymerase chain reaction for identification of bacteria in the thrombus of the first circuit showed the same bacteria as found in blood cultures and did not achieve a sufficient signal in the second circuit. This case report shows that bacteria can nestle in thrombi of an ECMO circuit and that there is a rationale for a circuit change in a patient with persistent positive blood cultures and DIC.
MeSH term(s)	Infant, Newborn ; Humans ; Extracorporeal Membrane Oxygenation/adverse effects ; Thrombosis/etiology ; Fibrin ; Bacteria ; Bacteremia/complications ; Anti-Bacterial Agents/therapeutic use
Chemical Substances	Fibrin (9001-31-4) ; Anti-Bacterial Agents
Language	English
Publishing date	2023-05-17
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	759982-1
ISSN	1538-943X ; 0162-1432 ; 1058-2916
ISSN (online)	1538-943X
ISSN	0162-1432 ; 1058-2916
DOI	10.1097/MAT.0000000000001980
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Zs.B 2435: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 2021: Bestellungen von Artikeln über das Online-Bestellformular ab Jg. 2022: Lesesaal (EG)

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Article ; Online: Evidence of cat-to-human transmission of

Sips, Gregorius J / van Dijk, Marloes A M / van Westreenen, Mireille / van der Graaf-van Bloois, Linda / Duim, Birgitta / Broens, Els M

Journal of medical microbiology

2023 Volume 72, Issue 2

Abstract: Introduction. ...

Abstract	Introduction.
MeSH term(s)	Humans ; Female ; Cats ; Animals ; Middle Aged ; Coagulase ; Staphylococcus ; Felis ; Virulence Factors/genetics ; Staphylococcal Infections/veterinary ; Staphylococcal Infections/microbiology ; Cat Diseases
Chemical Substances	Coagulase ; Virulence Factors
Language	English
Publishing date	2023-02-10
Publishing country	England
Document type	Case Reports ; Journal Article
ZDB-ID	218356-0
ISSN	1473-5644 ; 0022-2615
ISSN (online)	1473-5644
ISSN	0022-2615
DOI	10.1099/jmm.0.001661
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Article ; Online: Increased incidence of

Bolluyt, Dita C / Euser, Sjoerd M / Souverein, Dennis / van Rossum, Annemarie Mc / Kalpoe, Jayant / van Westreenen, Mireille / Goeijenbier, Marco / Snijders, Dominic / Eggink, Dirk / Jongenotter, Femke / van Lelyveld, Steven Fl / van Houten, Marlies A

Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

2024 Volume 29, Issue 4

Abstract: Mycoplasma ... ...

Abstract	Mycoplasma pneumoniae
MeSH term(s)	Child ; Humans ; Adult ; Pneumonia, Mycoplasma/epidemiology ; Pneumonia, Mycoplasma/diagnosis ; Netherlands/epidemiology ; Incidence ; Mycoplasma pneumoniae ; Hospitals
Language	English
Publishing date	2024-01-11
Publishing country	Sweden
Document type	Journal Article
ZDB-ID	1338803-4
ISSN	1560-7917 ; 1025-496X
ISSN (online)	1560-7917
ISSN	1025-496X
DOI	10.2807/1560-7917.ES.2024.29.4.2300724
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Article ; Online: The accuracy of four commercial broth microdilution tests in the determination of the minimum inhibitory concentration of colistin.

Yusuf, Erlangga / van Westreenen, Mireille / Goessens, Wil / Croughs, Peter

Annals of clinical microbiology and antimicrobials

2020 Volume 19, Issue 1, Page(s) 42

Abstract: Colistin is considered as one of the last-resort antibiotics and reliable antimicrobial susceptibility testing is therefore crucial. The reference standard for AST according to EUCAST and CLSI is broth microdilution (BMD). However, BMD is labor intensive ...

Abstract	Colistin is considered as one of the last-resort antibiotics and reliable antimicrobial susceptibility testing is therefore crucial. The reference standard for AST according to EUCAST and CLSI is broth microdilution (BMD). However, BMD is labor intensive to perform. Commercial antimicrobial susceptibility tests derived from BMD method are available. We investigated the performance of four different commercial tests: Sensititre™, SensiTest™ Colistin, Micronaut MIC Strip Colistin and UMIC Colistin using 70 clinical isolates (half of them was deemed by VITEK2 as resistant), including isolates from cystic fibrosis patients and mcr-1 bearing isolates. We used two reference standards: BMD and composite MIC as determined by all four tests. Sensititre™ had essential agreement (EA, defined as minimum inhibitory concentration within ± 1 dilution) of 87% and 89% compared to BMD and composite reference standard, respectively. For SensiTest™, the EA's were 93% and 90%. For UMIC, 87% and 90%, and for Micronaut, 83% and 84%. All four tests demonstrated categorical agreement (CA) above 90%. CA for SensiTest™ and Micronaut was both 96%, UMIC 94%, and Sensititre™ 93%. All tests were reproducible as tested in two quality control isolates. In conclusion, in clinical isolates from a large referral center, the four commercial tests for determination of colistin minimum inhibitory concentrations showed acceptable performance.
MeSH term(s)	Anti-Bacterial Agents/pharmacokinetics ; Colistin/pharmacology ; Cystic Fibrosis/microbiology ; Drug Resistance, Bacterial/genetics ; Humans ; Microbial Sensitivity Tests/methods ; Reproducibility of Results ; Sensitivity and Specificity
Chemical Substances	Anti-Bacterial Agents ; Colistin (Z67X93HJG1)
Language	English
Publishing date	2020-09-14
Publishing country	England
Document type	Journal Article
ZDB-ID	2097873-X
ISSN	1476-0711 ; 1476-0711
ISSN (online)	1476-0711
ISSN	1476-0711
DOI	10.1186/s12941-020-00383-x
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Article ; Online: Less Is More: When to Repeat Antimicrobial Susceptibility Testing.

Sarink, Maarten J / Bode, Lonneke G M / Croughs, Peter / de Steenwinkel, Jurriaan E M / Verkaik, Nelianne J / van Westreenen, Mireille / Vogel, Marius / Yusuf, Erlangga

Journal of clinical microbiology

2023 Volume 61, Issue 8, Page(s) e0046323

Abstract: This study investigated the frequency of change of the antimicrobial susceptibility pattern when the same isolate was found in the same patient in various situations. We used laboratory data collected over a period of 8 years (January 2014 to December ... ...

Abstract	This study investigated the frequency of change of the antimicrobial susceptibility pattern when the same isolate was found in the same patient in various situations. We used laboratory data collected over a period of 8 years (January 2014 to December 2021) at the clinical microbiology laboratory of a tertiary hospital for Escherichia coli, Klebsiella pneumoniae, Enterobacter spp., Pseudomonas aeruginosa, and Staphylococcus aureus. Antimicrobial susceptibility tests (AST) were performed using Vitek 2 automated system. We determined essential agreement and categorical agreement, and introduced the new terms essential MIC increase and change from nonresistant to resistant to present changes in antimicrobial susceptibility over time. During the study period, 18,501 successive AST were included. The risk for S. aureus to be resistant to any antibiotic upon repeated culture was <10% during a follow-up of 30 days. For Enterobacterales, this risk was approximately 10% during a follow-up of 7 days. For P. aeruginosa, this risk was higher. The longer the follow-up period, the higher the risk that the bacteria would show phenotypic resistance. We also found that some drug-bug combinations were more likely to develop phenotypical resistance (i.e., E. coli/amoxicillin-clavulanic acid and E. coli/cefuroxime). A potential consequence of our finding is that if we regard a risk of resistance below 10% as acceptable, it may be feasible to omit follow-up AST within 7 days for the microorganisms investigated in this study. This approach saves money, time, and will reduce laboratory waste. Further studies are needed to determine whether these savings are in balance with the small possibility of treating patients with inadequate antibiotics.
MeSH term(s)	Humans ; Escherichia coli ; Staphylococcus aureus ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria ; Pseudomonas aeruginosa ; Microbial Sensitivity Tests
Chemical Substances	Anti-Bacterial Agents
Language	English
Publishing date	2023-07-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	390499-4
ISSN	1098-660X ; 0095-1137
ISSN (online)	1098-660X
ISSN	0095-1137
DOI	10.1128/jcm.00463-23
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Article ; Online: Characterization of clinical Ralstonia strains and their taxonomic position.

Fluit, Ad C / Bayjanov, Jumamurat R / Aguilar, María Díez / Cantón, Rafael / Tunney, Michael M / Elborn, J Stuart / van Westreenen, Mireille / Ekkelenkamp, Miquel B

Antonie van Leeuwenhoek

2021 Volume 114, Issue 10, Page(s) 1721–1733

Abstract: To improve understanding of the role of Ralstonia in cystic fibrosis (CF), whole genomes of 18 strains from clinical samples were sequenced using Illumina technology. Sequences were analysed by core genome Multi-Locus Sequence Typing, Average Nucleotide ... ...

Abstract	To improve understanding of the role of Ralstonia in cystic fibrosis (CF), whole genomes of 18 strains from clinical samples were sequenced using Illumina technology. Sequences were analysed by core genome Multi-Locus Sequence Typing, Average Nucleotide Identity based on BLAST (ANIb), RAST annotation, and by ResFinder. Phylogenetic analysis was performed for the 16S rRNA gene, and the OXA-22 and OXA-60 ß-lactamase families. The minimal inhibitory concentrations (MICs) were determined using broth microdilution. ANIb data for the 18 isolates and 54 strains from GenBank, supported by phylogenetic analysis, showed that 8 groups of clusters (A-H), as well as subgroups that should be considered as species or subspecies. Groups A-C contain strains previously identified as Ralstonia solanacearum and Ralstonia pseudosolanacearum. We propose that group A is a novel species. Group B and C are Ralstonia syzygii, Ralstonia solanacearum, respectively. Group D is composed of Ralstonia mannitolilytica and Group E of Ralstonia pickettii. Group F and G should be considered novel species. Group H strains belong to R. insidiosa. OXA-22 and OXA-60 family ß-lactamases were encoded by all strains. Co-trimoxazole generally showed high activity with low MICs (≤1 mg/l) as did ciprofloxacin (≤0.12 mg/l). MICs against the other antibiotics were more variable, but generally high. RAST annotation revealed limited differences between the strains, and virulence factors were not identified. The taxonomy of the genus Ralstonia is in need of revision, but sequencing additional isolates is needed. Antibiotic resistance levels are high. Annotation did not identify potential virulence factors.
MeSH term(s)	Humans ; Multilocus Sequence Typing ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ralstonia/genetics
Chemical Substances	RNA, Ribosomal, 16S
Language	English
Publishing date	2021-08-31
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	214861-4
ISSN	1572-9699 ; 0003-6072
ISSN (online)	1572-9699
ISSN	0003-6072
DOI	10.1007/s10482-021-01637-0
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Article: Characterization of clinical Ralstonia strains and their taxonomic position

Fluit, Ad C. / Bayjanov, Jumamurat R. / Aguilar, María Díez / Cantón, Rafael / Tunney, Michael M. / Elborn, J. Stuart / van Westreenen, Mireille / Ekkelenkamp, Miquel B.

Antonie van Leeuwenhoek. 2021 Oct., v. 114, no. 10

2021

Abstract	To improve understanding of the role of Ralstonia in cystic fibrosis (CF), whole genomes of 18 strains from clinical samples were sequenced using Illumina technology. Sequences were analysed by core genome Multi-Locus Sequence Typing, Average Nucleotide Identity based on BLAST (ANIb), RAST annotation, and by ResFinder. Phylogenetic analysis was performed for the 16S rRNA gene, and the OXA-22 and OXA-60 ß-lactamase families. The minimal inhibitory concentrations (MICs) were determined using broth microdilution. ANIb data for the 18 isolates and 54 strains from GenBank, supported by phylogenetic analysis, showed that 8 groups of clusters (A-H), as well as subgroups that should be considered as species or subspecies. Groups A-C contain strains previously identified as Ralstonia solanacearum and Ralstonia pseudosolanacearum. We propose that group A is a novel species. Group B and C are Ralstonia syzygii, Ralstonia solanacearum, respectively. Group D is composed of Ralstonia mannitolilytica and Group E of Ralstonia pickettii. Group F and G should be considered novel species. Group H strains belong to R. insidiosa. OXA-22 and OXA-60 family ß-lactamases were encoded by all strains. Co-trimoxazole generally showed high activity with low MICs (≤1 mg/l) as did ciprofloxacin (≤0.12 mg/l). MICs against the other antibiotics were more variable, but generally high. RAST annotation revealed limited differences between the strains, and virulence factors were not identified. The taxonomy of the genus Ralstonia is in need of revision, but sequencing additional isolates is needed. Antibiotic resistance levels are high. Annotation did not identify potential virulence factors.
Keywords	Ralstonia mannitolilytica ; Ralstonia pickettii ; Ralstonia solanacearum ; Ralstonia syzygii ; antibiotic resistance ; ciprofloxacin ; cystic fibrosis ; genes ; minimum inhibitory concentration ; multilocus sequence typing ; phylogeny ; taxonomy ; virulence
Language	English
Dates of publication	2021-10
Size	p. 1721-1733.
Publishing place	Springer International Publishing
Document type	Article
ZDB-ID	214861-4
ISSN	1572-9699 ; 0003-6072
ISSN (online)	1572-9699
ISSN	0003-6072
DOI	10.1007/s10482-021-01637-0
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