Search

Your search keyword '"Schürch, Anita C."' showing total 226 results
Start Over Author "Schürch, Anita C."
226 results on '"Schürch, Anita C."'

1. Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements

Author

Kerkvliet, Jesse J., Bossers, Alex, Kers, Jannigje G., Meneses, Rodrigo, Willems, Rob J L, Schürch, Anita C., Kerkvliet, Jesse J., Bossers, Alex, Kers, Jannigje G., Meneses, Rodrigo, Willems, Rob J L, and Schürch, Anita C.

Abstract

Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing expe

Published
2024

2. PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli.

Author

MMB Research line 2, Infection & Immunity, Paganini, Julian A, Kerkvliet, Jesse J, Vader, Lisa, Plantinga, Nienke L, Meneses, Rodrigo, Corander, Jukka, Willems, Rob J L, Arredondo-Alonso, Sergio, Schürch, Anita C, MMB Research line 2, Infection & Immunity, Paganini, Julian A, Kerkvliet, Jesse J, Vader, Lisa, Plantinga, Nienke L, Meneses, Rodrigo, Corander, Jukka, Willems, Rob J L, Arredondo-Alonso, Sergio, and Schürch, Anita C

Published
2024

3. Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements

Author

IRAS OH Epidemiology Microbial Agents, IRAS – One Health Microbial, Kerkvliet, Jesse J., Bossers, Alex, Kers, Jannigje G., Meneses, Rodrigo, Willems, Rob J L, Schürch, Anita C., IRAS OH Epidemiology Microbial Agents, IRAS – One Health Microbial, Kerkvliet, Jesse J., Bossers, Alex, Kers, Jannigje G., Meneses, Rodrigo, Willems, Rob J L, and Schürch, Anita C.

Published
2024

5. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Author

Pöntinen, Anna K., Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R., Novais, Carla, Gladstone, Rebecca A., Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A., Jamrozy, Dorota, Bentley, Stephen D., Lanza, Val F., Torres, Carmen, Peixe, Luisa, Coque, Teresa M., Parkhill, Julian, Schürch, Anita C., Willems, Rob J. L., and Corander, Jukka

Published
2021
Full Text
View/download PDF

7. Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone

Author

Boralli, Camila Maria dos Santos, primary, Paganini, Julian Andres, additional, Meneses, Rodrigo Silva, additional, Mata, Camila Pacheco Silveira Martins da, additional, Leite, Edna Marilea Meireles, additional, Schürch, Anita C., additional, Paganelli, Fernanda L., additional, Willems, Rob J. L., additional, and Camargo, Ilana Lopes Baratella Cunha, additional

Published
2023
Full Text
View/download PDF

8. Mge-cluster: a reference-free approach for typing bacterial plasmids

Author

Infection & Immunity, MMB Research line 2, Arredondo-Alonso, Sergio, Gladstone, Rebecca A, Pöntinen, Anna K, Gama, João A, Schürch, Anita C, Lanza, Val F, Johnsen, Pål Jarle, Samuelsen, Ørjan, Tonkin-Hill, Gerry, Corander, Jukka, Infection & Immunity, MMB Research line 2, Arredondo-Alonso, Sergio, Gladstone, Rebecca A, Pöntinen, Anna K, Gama, João A, Schürch, Anita C, Lanza, Val F, Johnsen, Pål Jarle, Samuelsen, Ørjan, Tonkin-Hill, Gerry, and Corander, Jukka

Published
2023

9. Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone

Author

CMM Groep De Ridder, Cancer, MMB Research line 2, Infection & Immunity, Boralli, Camila Maria dos Santos, Paganini, Julian Andres, Meneses, Rodrigo Silva, Mata, Camila Pacheco Silveira Martins da, Leite, Edna Marilea Meireles, Schürch, Anita C., Paganelli, Fernanda L., Willems, Rob J.L., Camargo, Ilana Lopes Baratella Cunha, CMM Groep De Ridder, Cancer, MMB Research line 2, Infection & Immunity, Boralli, Camila Maria dos Santos, Paganini, Julian Andres, Meneses, Rodrigo Silva, Mata, Camila Pacheco Silveira Martins da, Leite, Edna Marilea Meireles, Schürch, Anita C., Paganelli, Fernanda L., Willems, Rob J.L., and Camargo, Ilana Lopes Baratella Cunha

Published
2023

11. Consistent typing of plasmids with the mge-cluster pipeline

Author

Arredondo-Alonso, Sergio, primary, Gladstone, Rebecca A., additional, Pöntinen, Anna K., additional, Gama, João A., additional, Schürch, Anita C., additional, Lanza, Val F., additional, Johnsen, Pål Jarle, additional, Samuelsen, Ørjan, additional, Tonkin-Hill, Gerry, additional, and Corander, Jukka, additional

Published
2022
Full Text
View/download PDF

13. Characterization of bla KPC-2 and bla NDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone.

Author

Boralli, Camila Maria dos Santos, Paganini, Julian Andres, Meneses, Rodrigo Silva, Mata, Camila Pacheco Silveira Martins da, Leite, Edna Marilea Meireles, Schürch, Anita C., Paganelli, Fernanda L., Willems, Rob J. L., and Camargo, Ilana Lopes Baratella Cunha

Subjects
KLEBSIELLA pneumoniae, ESCHERICHIA coli, MOLECULAR cloning, PULSED-field gel electrophoresis, PLASMIDS, WHOLE genome sequencing
Abstract

The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids' transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem. [ABSTRACT FROM AUTHOR]

Published
2023
Full Text
View/download PDF

16. A high-throughput multiplexing and selection strategy to complete bacterial genomes

Author

MMB Research line 2, Infection & Immunity, Pöntinen, Anna K, Cléon, François, Gladstone, Rebecca A, Schürch, Anita C, Johnsen, Pål J, Samuelsen, Ørjan, Corander, Jukka, MMB Research line 2, Infection & Immunity, Pöntinen, Anna K, Cléon, François, Gladstone, Rebecca A, Schürch, Anita C, Johnsen, Pål J, Samuelsen, Ørjan, and Corander, Jukka

Published
2021

17. Recovering escherichia coli plasmids in the absence of long-read sequencing data

Author

Infection & Immunity, MMB Research line 2, MMB opleiding Arts microbioloog, Biostatistiek Onderzoek, Paganini, Julian A., Plantinga, Nienke L., Arredondo-alonso, Sergio, Willems, Rob J.L., Schürch, Anita C., Infection & Immunity, MMB Research line 2, MMB opleiding Arts microbioloog, Biostatistiek Onderzoek, Paganini, Julian A., Plantinga, Nienke L., Arredondo-alonso, Sergio, Willems, Rob J.L., and Schürch, Anita C.

Published
2021

18. Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era

Author

MMB Research line 2, Infection & Immunity, Pöntinen, Anna K, Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R, Novais, Carla, Gladstone, Rebecca A, Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A, Jamrozy, Dorota, Bentley, Stephen D, Lanza, Val F, Torres, Carmen, Peixe, Luisa, Coque, Teresa M, Parkhill, Julian, Schürch, Anita C, Willems, Rob J L, Corander, Jukka, MMB Research line 2, Infection & Immunity, Pöntinen, Anna K, Top, Janetta, Arredondo-Alonso, Sergio, Tonkin-Hill, Gerry, Freitas, Ana R, Novais, Carla, Gladstone, Rebecca A, Pesonen, Maiju, Meneses, Rodrigo, Pesonen, Henri, Lees, John A, Jamrozy, Dorota, Bentley, Stephen D, Lanza, Val F, Torres, Carmen, Peixe, Luisa, Coque, Teresa M, Parkhill, Julian, Schürch, Anita C, Willems, Rob J L, and Corander, Jukka

Published
2021

20. gplas: a comprehensive tool for plasmid analysis using short-read graphs

Author

Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, Schürch, Anita C, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, and Schürch, Anita C

Abstract

SUMMARY: Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data are often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and network partitioning based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short-read sequence data.AVAILABILITY AND IMPLEMENTATION: Gplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at https://gitlab.com/sirarredondo/gplas.git.SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Published
2020

21. Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Author

van Hout, Denise, Verschuuren, Tess D, Bruijning-Verhagen, Patricia C J, Bosch, Thijs, Schürch, Anita C, Willems, Rob J L, Bonten, Marc J M, Kluytmans, Jan A J W, van Hout, Denise, Verschuuren, Tess D, Bruijning-Verhagen, Patricia C J, Bosch, Thijs, Schürch, Anita C, Willems, Rob J L, Bonten, Marc J M, and Kluytmans, Jan A J W

Published
2020

22. gplas: a comprehensive tool for plasmid analysis using short-read graphs

Author

Sub Mathematical Modeling, Mathematical Modeling, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, Schürch, Anita C, Sub Mathematical Modeling, Mathematical Modeling, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R C, Corander, Jukka, Willems, Rob J L, and Schürch, Anita C

Published
2020

23. Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 - 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Author

Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Child Health, MMB Research line 2, Epi Infectieziekten, MMB, van Hout, Denise, Verschuuren, Tess D, Bruijning-Verhagen, Patricia C J, Bosch, Thijs, Schürch, Anita C, Willems, Rob J L, Bonten, Marc J M, Kluytmans, Jan A J W, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, Child Health, MMB Research line 2, Epi Infectieziekten, MMB, van Hout, Denise, Verschuuren, Tess D, Bruijning-Verhagen, Patricia C J, Bosch, Thijs, Schürch, Anita C, Willems, Rob J L, Bonten, Marc J M, and Kluytmans, Jan A J W

Published
2020

24. Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, enterococcus faecium

Author

MMB Research line 2, Infection & Immunity, Top, Janetta, Arredondo-Alonso, Sergio, Schürch, Anita C., Puranen, Santeri, Pesonen, Maiju, Pensar, Johan, Willems, Rob J.L., Corander, Jukka, MMB Research line 2, Infection & Immunity, Top, Janetta, Arredondo-Alonso, Sergio, Schürch, Anita C., Puranen, Santeri, Pesonen, Maiju, Pensar, Johan, Willems, Rob J.L., and Corander, Jukka

Published
2020

25. gplas: a comprehensive tool for plasmid analysis using short-read graphs

Author

MMB RZN, MMB Research line 2, Epi Hart- en Vaatziekten Team 2, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB, UMC Utrecht, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R.C., Corander, Jukka, Willems, Rob J.L., Schürch, Anita C., MMB RZN, MMB Research line 2, Epi Hart- en Vaatziekten Team 2, Epi Infectieziekten Team 1, Infection & Immunity, JC onderzoeksprogramma Infectieziekten, MMB, UMC Utrecht, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R.C., Corander, Jukka, Willems, Rob J.L., and Schürch, Anita C.

Published
2020

29. Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Author

van Hout, Denise, primary, Verschuuren, Tess D., additional, Bruijning-Verhagen, Patricia C. J., additional, Bosch, Thijs, additional, Schürch, Anita C., additional, Willems, Rob J. L., additional, Bonten, Marc J. M., additional, and Kluytmans, Jan A. J. W., additional

Published
2020
Full Text
View/download PDF

31. high-throughput multiplexing and selection strategy to complete bacterial genomes.

Author

Arredondo-Alonso, Sergio, Pöntinen, Anna K, Cléon, François, Gladstone, Rebecca A, Schürch, Anita C, Johnsen, Pål J, Samuelsen, Ørjan, and Corander, Jukka

Subjects
BACTERIAL genomes, NUCLEOTIDE sequencing, ESCHERICHIA coli, REPLICONS, GENOMES
Abstract

Background Bacterial whole-genome sequencing based on short-read technologies often results in a draft assembly formed by contiguous sequences. The introduction of long-read sequencing technologies permits those contiguous sequences to be unambiguously bridged into complete genomes. However, the elevated costs associated with long-read sequencing frequently limit the number of bacterial isolates that can be long-read sequenced. Here we evaluated the recently released 96 barcoding kit from Oxford Nanopore Technologies (ONT) to generate complete genomes on a high-throughput basis. In addition, we propose an isolate selection strategy that optimizes a representative selection of isolates for long-read sequencing considering as input large-scale bacterial collections. Results Despite an uneven distribution of long reads per barcode, near-complete chromosomal sequences (assembly contiguity = 0.89) were generated for 96 Escherichia coli isolates with associated short-read sequencing data. The assembly contiguity of the plasmid replicons was even higher (0.98), which indicated the suitability of the multiplexing strategy for studies focused on resolving plasmid sequences. We benchmarked hybrid and ONT-only assemblies and showed that the combination of ONT sequencing data with short-read sequencing data is still highly desirable (i) to perform an unbiased selection of isolates for long-read sequencing, (ii) to achieve an optimal genome accuracy and completeness, and (iii) to include small plasmids underrepresented in the ONT library. Conclusions The proposed long-read isolate selection ensures the completion of bacterial genomes that span the genome diversity inherent in large collections of bacterial isolates. We show the potential of using this multiplexing approach to close bacterial genomes on a high-throughput basis. [ABSTRACT FROM AUTHOR]

Published
2021
Full Text
View/download PDF

32. Prevalence, risk factors and genetic characterisation of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE): a community-based cross-sectional study, the Netherlands, 2014 to 2016

Author

van den Bunt, Gerrita, van Pelt, Wilfrid, Hidalgo, Laura, Scharringa, Jelle, de Greeff, Sabine C, Schürch, Anita C, Mughini-Gras, Lapo, Bonten, Marc J M, and Fluit, Ad C

Subjects
genetic characterization, prevalence, risk factors, general community, Extended Spectrum Beta-Lactamase (ESBL)
Abstract

BackgroundThe epidemiology of carriage of extended-spectrum beta-lactamase-producing (ESBL-E) and carbapenemase-producing Enterobacteriaceae (CPE) in the general population is unknown.AimIn this observational study, the prevalence and risk factors for intestinal ESBL-E and CPE carriage in the Dutch general population were determined. ESBL-E were characterised.MethodsFrom 2014 to 2016, ca 2,000 residents were invited monthly to complete a questionnaire and provide a faecal sample, which was tested for ESBL-E. The first 1,758 samples were also tested for CPE. Risk factors for ESBL-E carriage were identified by multivariable logistic regression analysis. ESBL-E isolates underwent whole genome sequencing.ResultsOf 47,957 individuals invited, 4,177 (8.7%) completed the questionnaire and provided a faecal sample. ESBL-E were detected in 186 (4.5%) individuals, resulting in an adjusted prevalence of 5.0% (95% confidence interval (CI):3.4-6.6%). Risk factors were: born outside the Netherlands (odds ratio (OR): 1.99; 95% CI: 1.16-4.54), eating in restaurants > 20 times/year (OR: 1.70; 95% CI: 1.04-2.76), antibiotic use

Published
2019

33. Design of the EPIGENEC Study: Assessing the EPIdemiology and GENetics of Escherichia coli in the Netherlands

Author

Hout, Denise van, Verschuuren, Tess D., Bruijning-Verhagen, Patricia C. J., Bosch, Thijs, Ascelijn Reuland, E., Fluit, Ad C., Schürch, Anita C., Willems, Rob J. L., de Greeff, Sabine C., Veen, Annemarie van ’t, Kluytmans, Jan A. J. W., and Bonten, Marc J. M.

Subjects
microbiology, bacterial infections and mycoses
Abstract

Background: Infections caused by E. coli cause considerable disease burden and range from frequently occurring and relatively innocent urinary tract infection (UTI) to severe bloodstream infection (BSI). The incidence of infections caused by ESBL-producing E. coli (ESBL-PEc) is increasing, justifying surveillance and development of preventive strategies in several domains. Faecal carriage is universal and believed to be the most important reservoir for E. coli from which infections can originate. It is currently unknown to what extent Dutch E. coli carriage strains in the community reflect isolates causing disease. In this study, we will perform comparative genomics to infer the population structures of human-derived ESBL-PEc from community- and hospital-acquired infections and from community-based faecal carriage samples in the Netherlands. Furthermore, we will describe the molecular epidemiology of E. coli isolates causing invasive disease (BSI). Methods: This study uses four different microbiological data sources: 1) ESBL-PEc from patients with community-acquired UTI tested in primary care between May and November 2017, 2) ESBL-PEc from urine cultures obtained from patients hospitalized between January 2014 and December 2016, 3) E. coli from blood cultures obtained from patients hospitalized between January 2014 and December 2016, and 4) ESBL-PEc from faecal samples collected in a national population- prevalence study performed between January 2014 and January 2017. Clinical epidemiological data was collected from all patients and all isolates were subjected to whole genome sequencing. Discussion: The EPIGENEC study (EPIdemiology and GENetics of E. coli) will describe the molecular epidemiology of E. coli BSI and assess the genomic population structure of ESBL-PEc strains from community-acquired and nosocomial infections, and of ESBL-PEc reflecting community-based faecal carriage. Information from these studies may assist in optimizing surveillance strategies and determining targets and potential impact of future new preventive measures.

Published
2019

34. Corrigendum : Mlplasmids: A user-friendly tool to predict plasmid-and chromosome-derived sequences for single species, (Microbial Genomics), (2018), 4, 10.1099/mgen.0.000224

Author

Arredondo-Alonso, Sergio, Rogers, Malbert R.C., Braat, Johanna C., Verschuuren, Tess D., Top, Janetta, Corander, Jukka, Willems, Rob J.L., and Schürch, Anita C.

Subjects
Medicine(all), Published Erratum, Journal Article
Abstract

There was an error in the Funding information section in the published article. The Funding information section should include the following sentence: ‘This study was supported by the Joint Programming Initiative in Antimicrobial Resistance (JPIAMR Third call, STARCS, JPIAMR2016-AC16/00039 to SA, RJLW).’ The author apologizes for any inconvenience caused.

Published
2019

35. gplas: a comprehensive tool for plasmid analysis using short-read graphs

Author

Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R.C., Corander, Jukka, Willems, Rob JL, Schürch, Anita C., Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R.C., Corander, Jukka, Willems, Rob JL, and Schürch, Anita C.

Abstract

Summary Plasmids can horizontally transmit genetic traits, enabling rapid bacterial adaptation to new environments and hosts. Short-read whole-genome sequencing data is often applied to large-scale bacterial comparative genomics projects but the reconstruction of plasmids from these data is facing severe limitations, such as the inability to distinguish plasmids from each other in a bacterial genome. We developed gplas, a new approach to reliably separate plasmid contigs into discrete components using sequence composition, coverage, assembly graph information and clustering based on a pruned network of plasmid unitigs. Gplas facilitates the analysis of large numbers of bacterial isolates and allows a detailed analysis of plasmid epidemiology based solely on short read sequence data. Availability and implementation Gplas is written in R, Bash and uses a Snakemake pipeline as a workflow management system. Gplas is available under the GNU General Public License v3.0 at Contact a.c.schurch{at}umcutrecht.nl

Published
2019

36. Sequence-Based Epidemiology of an OXA-48 Plasmid during Hospital Outbreak

Author

Hidalgo, Laura, de Been, Mark, Rogers, Malbert R C, Schürch, Anita C, Scharringa, Jelle, van der Zee, Anneke, Bonten, Marc J M, Fluit, Ad C, Hidalgo, Laura, de Been, Mark, Rogers, Malbert R C, Schürch, Anita C, Scharringa, Jelle, van der Zee, Anneke, Bonten, Marc J M, and Fluit, Ad C

Published
2019

38. gplas: a comprehensive tool for plasmid analysis using short-read graphs

Author

Sub Mathematical Modeling, Mathematical Modeling, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R.C., Corander, Jukka, Willems, Rob JL, Schürch, Anita C., Sub Mathematical Modeling, Mathematical Modeling, Arredondo-Alonso, Sergio, Bootsma, Martin, Hein, Yaïr, Rogers, Malbert R.C., Corander, Jukka, Willems, Rob JL, and Schürch, Anita C.

Published
2019

39. Prevalence, risk factors and genetic characterisation of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE): a community-based cross-sectional study, the Netherlands, 2014 to 2016

Author

One Health Microbieel, dIRAS RA-I&I I&I, van den Bunt, Gerrita, van Pelt, Wilfrid, Hidalgo, Laura, Scharringa, Jelle, de Greeff, Sabine C, Schürch, Anita C, Mughini-Gras, Lapo, Bonten, Marc J M, Fluit, Ad C, One Health Microbieel, dIRAS RA-I&I I&I, van den Bunt, Gerrita, van Pelt, Wilfrid, Hidalgo, Laura, Scharringa, Jelle, de Greeff, Sabine C, Schürch, Anita C, Mughini-Gras, Lapo, Bonten, Marc J M, and Fluit, Ad C

Published
2019

40. Draft Genome Sequence of Haemophilus haemolyticus Strain 16/010 O, Isolated from a Sputum Sample from a Cystic Fibrosis Patient

Author

MMB Research line 2, Infection & Immunity, MMB, MMB Medische Staf, Fluit, Ad C, Bayjanov, Jumamurat R, Tunney, Michael, Elborn, J Stuart, Rogers, Malbert R C, Schürch, Anita C, Ekkelenkamp, Miquel B, MMB Research line 2, Infection & Immunity, MMB, MMB Medische Staf, Fluit, Ad C, Bayjanov, Jumamurat R, Tunney, Michael, Elborn, J Stuart, Rogers, Malbert R C, Schürch, Anita C, and Ekkelenkamp, Miquel B

Published
2019

41. Sequence-Based Epidemiology of an OXA-48 Plasmid during Hospital Outbreak

Author

Infection & Immunity, MMB, MMB Research line 2, Epi Infectieziekten, JC onderzoeksprogramma Infectieziekten, Hidalgo, Laura, de Been, Mark, Rogers, Malbert R C, Schürch, Anita C, Scharringa, Jelle, van der Zee, Anneke, Bonten, Marc J M, Fluit, Ad C, Infection & Immunity, MMB, MMB Research line 2, Epi Infectieziekten, JC onderzoeksprogramma Infectieziekten, Hidalgo, Laura, de Been, Mark, Rogers, Malbert R C, Schürch, Anita C, Scharringa, Jelle, van der Zee, Anneke, Bonten, Marc J M, and Fluit, Ad C

Published
2019

42. Corrigendum: Mlplasmids: A user-friendly tool to predict plasmid-and chromosome-derived sequences for single species, (Microbial Genomics), (2018), 4, 10.1099/mgen.0.000224

Author

MMB Research line 2, MMB, Epi Infectieziekten Team 1, JC onderzoeksprogramma Infectieziekten, Infection & Immunity, Arredondo-Alonso, Sergio, Rogers, Malbert R.C., Braat, Johanna C., Verschuuren, Tess D., Top, Janetta, Corander, Jukka, Willems, Rob J.L., Schürch, Anita C., MMB Research line 2, MMB, Epi Infectieziekten Team 1, JC onderzoeksprogramma Infectieziekten, Infection & Immunity, Arredondo-Alonso, Sergio, Rogers, Malbert R.C., Braat, Johanna C., Verschuuren, Tess D., Top, Janetta, Corander, Jukka, Willems, Rob J.L., and Schürch, Anita C.

Published
2019

44. Prevalence, risk factors and genetic characterisation of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae (ESBL-E and CPE): a community-based cross-sectional study, the Netherlands, 2014 to 2016

Author

van den Bunt, Gerrita, primary, van Pelt, Wilfrid, additional, Hidalgo, Laura, additional, Scharringa, Jelle, additional, de Greeff, Sabine C., additional, Schürch, Anita C., additional, Mughini-Gras, Lapo, additional, Bonten, Marc J.M., additional, and Fluit, Ad C., additional

Published
2019
Full Text
View/download PDF

45. Extended-spectrum beta-lactamase (ESBL)-producing and non-ESBL-producing Escherichia coli isolates causing bacteremia in the Netherlands (2014 – 2016) differ in clonal distribution, antimicrobial resistance gene and virulence gene content

Author

van Hout, Denise, primary, Verschuuren, Tess D., additional, Bruijning-Verhagen, Patricia C.J., additional, Bosch, Thijs, additional, Schürch, Anita C., additional, Willems, Rob J.L., additional, Bonten, Marc J.M., additional, and Kluytmans, Jan A.J.W., additional

Published
2019
Full Text
View/download PDF

47. Design of the EPIGENEC Study: Assessing the EPIdemiology and GENetics of Escherichia coli in the Netherlands

Author

van Hout, Denise, primary, Verschuuren, Tess D., additional, Bruijning-Verhagen, Patricia C.J., additional, Bosch, Thijs, additional, Reuland, E. Ascelijn, additional, Fluit, Ad C., additional, Schürch, Anita C., additional, Willems, Rob J.L., additional, de Greeff, Sabine C., additional, van ’t Veen, Annemarie, additional, Kluytmans, Jan A.J.W., additional, and Bonten, Marc J.M., additional

Published
2019
Full Text
View/download PDF

49. mlplasmids: a user-friendly tool to predict plasmid- and chromosome-derived sequences for single species

Author

MMB Research line 2, MMB, Epi Infectieziekten Team 1, JC onderzoeksprogramma Infectieziekten, Infection & Immunity, Arredondo-Alonso, Sergio, Rogers, Malbert R.C., Braat, Johanna C., Verschuuren, Tess D., Top, Janetta, Corander, Jukka, Willems, Rob J.L., Schürch, Anita C., MMB Research line 2, MMB, Epi Infectieziekten Team 1, JC onderzoeksprogramma Infectieziekten, Infection & Immunity, Arredondo-Alonso, Sergio, Rogers, Malbert R.C., Braat, Johanna C., Verschuuren, Tess D., Top, Janetta, Corander, Jukka, Willems, Rob J.L., and Schürch, Anita C.

Published
2018

50. Challenges and opportunities for whole-genome sequencing–based surveillance of antibiotic resistance

Author

Schürch, Anita C. and van Schaik, Willem

Subjects
Klebsiella pneumoniae, antibiotic resistance, History and Philosophy of Science, Biochemistry, Genetics and Molecular Biology(all), genomics, bioinformatics, mcr-1
Abstract

Infections caused by drug-resistant bacteria are increasingly reported across the planet, and drug-resistant bacteria are recognized to be a major threat to public health and modern medicine. In this review, we discuss how whole-genome sequencing (WGS)–based approaches can contribute to the surveillance of the emergence and spread of antibiotic resistance. We outline the characteristics of sequencing technologies that are currently most used for WGS (Illumina short-read technologies and the long-read sequencing platforms developed by Pacific Biosciences and Oxford Nanopore). The challenges posed by the analysis of sequencing data sets for antimicrobial-resistance determinants and the solutions offered by modern bioinformatics tools are discussed. Finally, we illustrate the power of WGS-based surveillance of antimicrobial resistance by summarizing recent studies on the spread of the multidrug-resistant opportunistic pathogen Klebsiella pneumoniae and the transferable colistin-resistance gene mcr-1, in which high-throughput WGS analyses played essential roles. The implementation of WGS for surveillance of antibiotic-resistant bacteria is technically feasible and cost effective and provides actionable results with reference to infection control. Consequently, the time has come for laboratories to implement routine genome sequencing as part of their surveillance programs for antibiotic-resistant bacteria.

Published
2017

Catalog

Books, media, physical & digital resources
See catalog results