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Author Alexander W Friedrich

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Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium.

Paola Lisotto, Erwin C Raangs, Natacha Couto, Sigrid Rosema, Mariëtte Lokate, Xuewei Zhou, Alexander W Friedrich, John W A Rossen, Hermie J M Harmsen, Erik Bathoorn, Monika A Chlebowicz-Fliss,

<h4>Background</h4>Vancomycin-resistant enterococci (VRE) are successful nosocomial pathogens able to cause hospital outbreaks. In the Netherlands, core-genome MLST (cgMLST) based on short-read sequencing is often used for molecular typing. Long-read sequencing is more rapid and provides useful information about the genome's structural composition but lacks the precision required for SNP-based typing ... Read more >>

BMC Genomics (BMC genomics)
[2021, 22(1):758]

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[We still have to continue to test, test, test].

Bert Mulder, Ginny Mooij, Marino van Zelst, Alexander W Friedrich,

Testing for COVID-19 is performed curatively for disease detection and as screening tool to prevent spread for public health and infection prevention. Testing for access is an important additional measure to provide information about asymptomatic or pre-symptomatic infection. In a recent meta-analysis 42.8% showed no symptoms with an estimated percentage ... Read more >>

Ned Tijdschr Geneeskd (Nederlands tijdschrift voor geneeskunde)
[2021, 165:]

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Molecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks.

Paola Lisotto, Natacha Couto, Sigrid Rosema, Mariëtte Lokate, Xuewei Zhou, Erik Bathoorn, Hermie J M Harmsen, Alexander W Friedrich, John W A Rossen, Monika A Chlebowicz-Fliss,

<b>Background:</b> Vancomycin-resistant <i>Enterococcus faecium</i> (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2021, 12:728356]

Cited: 1 time

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Pseudomonas aeruginosa and Staphylococcus aureus virulence factors as biomarkers of infection.

Artur J Sabat, Daniele Pantano, Viktoria Akkerboom, Erik Bathoorn, Alexander W Friedrich,

The gold standard for the diagnosis of bacterial infections in clinical samples is based on culture tests that are time-consuming and labor-intense. For these reasons, an extraordinary effort has been made to identify biomarkers as the tools for sensitive, rapid and accurate identification of pathogenic microorganisms. Moreover, biomarkers have been ... Read more >>

Biol Chem (Biological chemistry)
[2021, 402(12):1565-1573]

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Misidentification of meticillin-resistant Staphylococcus aureus by the Cepheid Xpert MRSA NxG assay, the Netherlands, February to March 2021.

Artur J Sabat, Erik Bathoorn, Monika A Chlebowicz-Fliss, Viktoria Akkerboom, Inge Kamphuis, Claudy Oliveira Dos Santos, Alexander W Friedrich,

We describe two false-negative results in the detection of meticillin-resistant <i>Staphylococcus aureus</i> (MRSA) of sequence type 398 and <i>spa</i> type t011 using the Cepheid Xpert MRSA NxG assay. The isolates were recovered in late February and early March 2021 from two patients in different hospitals in the northern Netherlands. Variations ... Read more >>

Euro Surveill (Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin)
[2021, 26(37):]

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Staphylococcal cassette chromosome mec containing a novel mec gene complex, B4.

Artur J Sabat, Erik Bathoorn, Karsten Becker, Viktoria Akkerboom, Madalina Miskoski, Tim Durfee, Alexander W Friedrich,

<h4>Objectives</h4>To describe a new subclass of mec class B complex identified in Staphylococcus epidermidis.<h4>Methods</h4>Four S. epidermidis isolates obtained from bloodstream infections in patients at University Medical Center Groningen (UMCG) were analysed by phenotypic antibiotic susceptibility testing and WGS.<h4>Results</h4>Sequence analysis revealed a new staphylococcal cassette chromosome mec (SCCmec) structure in isolate ... Read more >>

J Antimicrob Chemother (The Journal of antimicrobial chemotherapy)
[2021, 76(8):1986-1990]

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Bdellovibrio bacteriovorus: a potential 'living antibiotic' to control bacterial pathogens.

Francis M Cavallo, Lorea Jordana, Alexander W Friedrich, Corinna Glasner, Jan Maarten van Dijl,

<i>Bdellovibrio bacteriovorus</i> is a small Deltaproteobacterium which, since its discovery, has distinguished itself for the unique ability to prey on other Gram-negative bacteria. The studies on this particular "predatory bacterium", have gained momentum in response to the rising problem of antibiotic resistance, because it could be applied as a potential ... Read more >>

Crit Rev Microbiol (Critical reviews in microbiology)
[2021, 47(5):630-646]

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Predominance of CTX-M-15-producing ST131 strains among ESBL-producing Escherichia coli isolated from asylum seekers in the Netherlands.

Christina Louka, Sofanne J Ravensbergen, Alewijn Ott, Xuewei Zhou, Silvia García-Cobos, Alexander W Friedrich, Spyros Pournaras, Sigrid Rosema, John W Rossen, Ymkje Stienstra, Erik Bathoorn,

<h4>Objectives</h4>Numerous studies show increased prevalence of MDR bacteria amongst asylum seekers, but data on the molecular profiles of such strains are limited. We aimed to evaluate the molecular profiles of ESBL-producing Escherichia coli (ESBL-E. coli) strains isolated from asylum seekers and investigate their phylogenetic relatedness.<h4>Methods</h4>WGS data of ESBL-E. coli isolates ... Read more >>

J Antimicrob Chemother (The Journal of antimicrobial chemotherapy)
[2021, 76(1):70-76]

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Enterococcus faecium: from microbiological insights to practical recommendations for infection control and diagnostics.

Xuewei Zhou, Rob J L Willems, Alexander W Friedrich, John W A Rossen, Erik Bathoorn,

Early in its evolution, Enterococcus faecium acquired traits that allowed it to become a successful nosocomial pathogen. E. faecium inherent tenacity to build resistance to antibiotics and environmental stressors that allows the species to thrive in hospital environments. The continual wide use of antibiotics in medicine has been an important ... Read more >>

Antimicrob Resist Infect Control (Antimicrobial resistance and infection control)
[2020, 9(1):130]

Cited: 12 times

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Detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicons in Enterobacteriaceae using PlasmidSPAdes assembly of short-read sequence data.

Joep J J M Stohr, Marjolein F Q Kluytmans-van den Bergh, Ronald Wedema, Alexander W Friedrich, Jan A J W Kluytmans, John W A Rossen,

Knowledge of the epidemiology of plasmids is essential for understanding the evolution and spread of antimicrobial resistance. PlasmidSPAdes attempts to reconstruct plasmids using short-read sequence data. Accurate detection of extended-spectrum beta-lactamase (ESBL) genes and plasmid replicon genes is a prerequisite for the use of plasmid assembly tools to investigate the ... Read more >>

Microb Genom (Microbial genomics)
[2020, 6(7):]

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Improved diagnostic policy for respiratory tract infections essential for patient management in the emergency department.

Randy Poelman, Johan van der Meer, Corina van der Spek, Annelies Riezebos-Brilman, Marjolein Knoester, Coretta Van Leer-Buter, Alexander W Friedrich, Hubert G Niesters,

<b>Aim:</b> Establishing an optimal diagnostic policy for patients with respiratory tract infections, at the emergency department (ED) of a university hospital in The Netherlands. <b>Methods:</b> Adult patients were sampled at admission, during the respiratory season (2014-2015). The FilmArray-RP was implemented at the clinical virology laboratory. Diagnostics were provided from 8 ... Read more >>

Future Microbiol (Future microbiology)
[2020, 15:623-632]

Cited: 2 times

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Prevention and Control of Multidrug-Resistant Bacteria in The Netherlands and Germany-The Impact of Healthcare Structures.

Robin Köck, Karsten Becker, Evgeny A Idelevich, Annette Jurke, Corinna Glasner, Ron Hendrix, Alexander W Friedrich,

The Netherlands and Germany are neighbouring countries within the European Union but are differently affected by multidrug-resistant microorganisms (MDRO). In this narrative review, we summarize data about antibiotic use, the occurrence of MDRO and healthcare-associated infections in these two countries, as well as data about organizational and structural differences between ... Read more >>

Int J Environ Res Public Health (International journal of environmental research and public health)
[2020, 17(7):]

Cited: 2 times

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Decreasing prevalence of contamination with extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) in retail chicken meat in the Netherlands.

Pepijn Huizinga, Marjolein Kluytmans-van den Bergh, John W Rossen, Ina Willemsen, Carlo Verhulst, Paul H M Savelkoul, Alexander W Friedrich, Silvia García-Cobos, Jan Kluytmans,

Retail chicken meat is a potential source of extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E). In the past decade, vast national efforts were undertaken to decrease the antibiotic use in the veterinary sector, resulting in a 58% decrease in antibiotic sales in the sector between 2009 and 2014. This decrease in antibiotic use ... Read more >>

PLoS One (PloS one)
[2019, 14(12):e0226828]

Cited: 1 time

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Incidence, clinical implications and impact on public health of infections with Shigella spp. and entero-invasive Escherichia coli (EIEC): results of a multicenter cross-sectional study in the Netherlands during 2016-2017.

Maaike J C van den Beld, Esther Warmelink, Alexander W Friedrich, Frans A G Reubsaet, Maarten Schipper, Richard F de Boer, Daan W Notermans, Mariska W F Petrignani, Evert van Zanten, John W A Rossen, Ingrid H M Friesema, A M D Mirjam Kooistra-Smid, ,

BACKGROUND:Shigella spp. and entero-invasive E. coli (EIEC) use the same invasive mechanism to cause diarrheal diseases. Public health regulations apply only to Shigella spp. infections, but are hampered by the lack of simple methods to distinguish them from EIEC. In the last decades, molecular methods for detecting Shigella spp. and ... Read more >>

BMC Infect Dis (BMC infectious diseases)
[2019, 19(1):1037]

Cited: 5 times

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Development of a reference data set for assigning Streptococcus and Enterococcus species based on next generation sequencing of the 16S-23S rRNA region.

Maja Kosecka-Strojek, Artur J Sabat, Viktoria Akkerboom, Anna M D Mirjam Kooistra-Smid, Jacek Miedzobrodzki, Alexander W Friedrich,

<h4>Background</h4>Many members of <i>Streptococcus</i> and <i>Enterococcus</i> genera are clinically relevant opportunistic pathogens warranting accurate and rapid identification for targeted therapy. Currently, the developed method based on next generation sequencing (NGS) of the 16S-23S rRNA region proved to be a rapid, reliable and precise approach for species identification directly from polymicrobial ... Read more >>

Antimicrob Resist Infect Control (Antimicrobial resistance and infection control)
[2019, 8:178]

Cited: 1 time

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Reduced Fitness Costs of mcr-1.2 Compared to Mutated pmrB in Isogenic Colistin-Resistant KPC-3-Producing Klebsiella pneumoniae.

Cesira Giordano, Adrian Klak, Simona Barnini, Monika A Chlebowicz, Mariacristina Menconi, John W Rossen, Alexander W Friedrich, Erik Bathoorn,

In the present study, we provide the results of a detailed genomic analysis and the growth characteristics of a colistin-resistant KPC-3-producing Klebsiella pneumoniae sequence type 512 (ST512) isolate (the colR-KPC3-KP isolate) with a mutated pmrB and isogenic isolates of colR-KPC3-KP with mcr-1.2 isolated from an immunocompromised patient. From 2014 to ... Read more >>

mSphere (mSphere)
[2019, 4(6):]

Cited: 2 times

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Development and Validation of a Reference Data Set for Assigning Staphylococcus Species Based on Next-Generation Sequencing of the 16S-23S rRNA Region.

Maja Kosecka-Strojek, Artur J Sabat, Viktoria Akkerboom, Karsten Becker, Evert van Zanten, Guido Wisselink, Jacek Miedzobrodzki, Anna M D Mirjam Kooistra-Smid, Alexander W Friedrich,

Many members of the <i>Staphylococcus</i> genus are clinically relevant opportunistic pathogens that warrant accurate and rapid identification for targeted therapy. The aim of this study was to develop a careful assignment scheme for staphylococcal species based on next-generation sequencing (NGS) of the 16S-23S rRNA region. All reference staphylococcal strains were ... Read more >>

Front Cell Infect Microbiol (Frontiers in cellular and infection microbiology)
[2019, 9:278]

Cited: 4 times

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Applied shotgun metagenomics approach for the genetic characterization of dengue viruses.

Erley Lizarazo, Natacha Couto, Maria Vincenti-Gonzalez, Erwin C Raangs, Zoraida Velasco, Sarah Bethencourt, Thomas Jaenisch, Alexander W Friedrich, Adriana Tami, John W Rossen,

Dengue virus (DENV), an arthropod-borne virus, has rapidly spread in recent years. DENV diagnosis is performed through virus serology, isolation or molecular detection, while genotyping is usually done through Sanger sequencing of the envelope gene. This study aimed to optimize the use of shotgun metagenomics and subsequent bioinformatics analysis to ... Read more >>

J Biotechnol (Journal of biotechnology)
[2019, 306S:100009]

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Daptomycin Resistant Staphylococcus aureus Clinical Strain With Novel Non-synonymous Mutations in the mprF and vraS Genes: A New Insight Into Daptomycin Resistance.

Artur J Sabat, Marco Tinelli, Hajo Grundmann, Viktoria Akkerboom, Monica Monaco, Maria Del Grosso, Giulia Errico, Annalisa Pantosti, Alexander W Friedrich,

<b>Objectives:</b> Daptomycin (DAP) resistance in <i>Staphylococcus aureus</i> is uncommon but there are increasing reports of the emergence of resistance during DAP therapy. Most clinical DAP-resistant <i>S. aureus</i> isolates investigated carried mutations in the <i>mprF</i> gene. The aim of this study was to identify mutations between a clinical pair of methicillin-susceptible ... Read more >>

Front Microbiol (Frontiers in microbiology)
[2018, 9:2705]

Cited: 10 times

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European external quality assessments for identification, molecular typing and characterization of Staphylococcus aureus.

Ariane Deplano, Magali Dodémont, Olivier Denis, Henrik Westh, Heidi Gumpert, Anders Rhod Larsen, Jesper Larsen, Angela Kearns, Bruno Pichon, Franziska Layer, Berit Schulte, Christiane Wolz, Iris Spiliopoulou, Gráinne Brennan, Joanna Empel, Waleria Hryniewicz, Herminia de Lencastre, Nuno Alexandre Faria, Irina Codita, Artur J Sabat, Alexander W Friedrich, Ruud H Deurenberg, Anne Tristan, Frédéric Laurent, François Vandenesch,

<h4>Objectives</h4>We present the results of two European external quality assessments (EQAs) conducted in 2014 and 2016 under the auspices of the Study Group on Staphylococci and Staphylococcal Infections of ESCMID. The objective was to assess the performance of participating centres in characterizing Staphylococcus aureus using their standard in-house phenotypic and ... Read more >>

J Antimicrob Chemother (The Journal of antimicrobial chemotherapy)
[2018, 73(10):2662-2666]

Cited: 1 time

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Antimicrobial Resistance in Class 1 Integron-Positive Shiga Toxin-Producing Escherichia coli Isolated from Cattle, Pigs, Food and Farm Environment.

Rocío Colello, Alejandra Krüger, José Di Conza, John W A Rossen, Alexander W Friedrich, Gabriel Gutkind, Analía I Etcheverría, Nora L Padola,

The aim of this study was to investigate the presence of class 1 integrons in a collection of Shiga toxin-producing <i>Escherichia coli</i> (STEC) from different origins and to characterize pheno- and genotypically the antimicrobial resistance associated to them. A collection of 649 isolates were screened for the class 1 integrase ... Read more >>

Microorganisms (Microorganisms)
[2018, 6(4):]

Cited: 2 times

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Joint Genomic and Proteomic Analysis Identifies Meta-Trait Characteristics of Virulent and Non-virulent Staphylococcus aureus Strains.

Emilia A Bonar, Michal Bukowski, Marcin Hydzik, Urszula Jankowska, Sylwia Kedracka-Krok, Magdalena Groborz, Grzegorz Dubin, Viktoria Akkerboom, Jacek Miedzobrodzki, Artur J Sabat, Alexander W Friedrich, Benedykt Wladyka,

<i>Staphylococcus aureus</i> is an opportunistic pathogen of humans and warm-blooded animals and presents a growing threat in terms of multi-drug resistance. Despite numerous studies, the basis of staphylococcal virulence and switching between commensal and pathogenic phenotypes is not fully understood. Using genomics, we show here that <i>S. aureus</i> strains exhibiting ... Read more >>

Front Cell Infect Microbiol (Frontiers in cellular and infection microbiology)
[2018, 8:313]

Cited: 4 times

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Extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) isolated from bean sprouts in the Netherlands.

Pepijn Huizinga, Eefje Schrauwen, Silvia García-Cobos, Ina Willemsen, Carlo Verhulst, Alexander W Friedrich, Paul H M Savelkoul, John W Rossen, Jan Kluytmans,

Community-acquired carriage and infections due to extended-spectrum beta-lactamase producing Enterobacteriaceae (ESBL-E) are increasing worldwide, resulting in increased morbidity, mortality and healthcare costs. The origins of community-acquired ESBL-E carriage and infections remain unclear. Bean sprouts are a potential source of Enterobacteriaceae for the community, as illustrated by outbreaks of pathogenic Enterobacteriaceae ... Read more >>

PLoS One (PloS one)
[2018, 13(8):e0203338]

Cited: 5 times

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ESCMID postgraduate education course: regional capacity building for integration of next-generation sequencing in the clinical microlab.

Yair Motro, João André Carriço, Alexander W Friedrich, John W A Rossen, Jacob Moran-Gilad,

Microbes Infect (Microbes and infection)
[2018, 20(5):275-280]

Cited: 1 time

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Defining Multidrug Resistance of Gram-Negative Bacteria in the Dutch-German Border Region-Impact of National Guidelines.

Robin Köck, Philipp Siemer, Jutta Esser, Stefanie Kampmeier, Matthijs S Berends, Corinna Glasner, Jan P Arends, Karsten Becker, Alexander W Friedrich,

Preventing the spread of multidrug-resistant Gram-negative bacteria (MDRGNB) is a public health priority. However, the definition of MDRGNB applied for planning infection prevention measures such as barrier precautions differs depending on national guidelines. This is particularly relevant in the Dutch-German border region, where patients are transferred between healthcare facilities located ... Read more >>

Microorganisms (Microorganisms)
[2018, 6(1):]

Cited: 6 times

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