scholarly journals Next-Generation Sequencing Confirms Presumed Nosocomial Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in the Netherlands

2016 ◽  
Vol 82 (14) ◽  
pp. 4081-4089 ◽  
Author(s):  
Thijs Bosch ◽  
Sandra Witteveen ◽  
Anja Haenen ◽  
Fabian Landman ◽  
Leo M. Schouls
Keyword(s):  
Health Care ◽  
Staphylococcus Aureus ◽  
Next Generation Sequencing ◽  
The Netherlands ◽  
Next Generation ◽  
Methicillin Resistant ◽  
Content Type ◽  
Dutch Health ◽  
Dutch Health Care ◽  
Generation Sequencing

ABSTRACTLivestock-associated methicillin-resistantStaphylococcus aureus(LA-MRSA) was detected in 2003 and rapidly became the predominant MRSA clade in the Netherlands. Studies have shown that transmissions are difficult to identify, since this MRSA variant represents a genetically homogenous clade when current typing techniques are used. Here, next-generation sequencing was performed on 206 LA-MRSA isolates to assess the capability of LA-MRSA to be transmitted between humans. The usefulness of single nucleotide variants (SNVs), the composition of the SCCmecregion, and the presence of plasmids to identify transmission of LA-MRSA were assessed. In total, 30 presumed putative nosocomial transmission events and 2 LA-MRSA outbreaks were studied; in most cases, SNV analysis revealed that the isolates of the index patient and the contact(s) clustered closely together. In three presumed events, the isolates did not cluster together, indicating that transmission was unlikely. The composition of the SCCmecregion corroborated these findings. However, plasmid identification did not support our SNV analysis, since different plasmids were present in several cases where SNV and SCCmecanalysis suggested that transmission was likely. Next-generation sequencing shows that transmission of LA-MRSA does occur in Dutch health care settings. Transmission was identified based on SNV analysis combined with epidemiological data and in the context of epidemiologically related and unrelated isolates. Analysis of the SCCmecregion provided limited, albeit useful, information to corroborate conclusions on transmissions, but plasmid identification did not.IMPORTANCEIn 2003, a variant of methicillin-resistantStaphylococcus aureus(MRSA) isolated from pigs was also found in pig farmers in France and the Netherlands. Soon thereafter, this livestock-associated MRSA (LA-MRSA) was identified in many other countries. Transmission of LA-MRSA between humans, particularly in the health care setting, is regarded to occur sporadically. Moreover, studies that describe LA-MRSA transmission used molecular characterization of isolates with limited discriminatory power, making the validity of the conclusion that transmission occurred questionable. In our study, we sequenced the complete genomes of 206 LA-MRSA isolates, obtained from more than 30 presumed LA-MRSA transmission events. Analysis of the data showed that transmission of LA-MRSA between humans had indeed occurred in more than 90% of these events. We conclude that transmission of LA-MRSA between humans does occur in Dutch health care settings; therefore, a decision to discontinue the search and destroy policy for LA-MRSA should be taken with caution.

scholarly journals Changing characteristics of livestock-associated meticillin-resistant Staphylococcus aureus isolated from humans – emergence of a subclade transmitted without livestock exposure, the Netherlands, 2003 to 2014

2016 ◽  
Vol 21 (21) ◽  
Author(s):  
Thijs Bosch ◽  
Martijn van Luit ◽  
Gerlinde N Pluister ◽  
Dineke Frentz ◽  
Anja Haenen ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Next Generation Sequencing ◽  
The Netherlands ◽  
Temporal Changes ◽  
Next Generation ◽  
Epidemiological Characteristics ◽  
Generation Sequencing

Since 2007, livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) has become the predominant MRSA clade isolated from humans in the Netherlands. To assess possible temporal changes, we molecularly characterised over 9,000 LA-MRSA isolates submitted from 2003 to 2014 to the Dutch MRSA surveillance. After an initial rapid increase with a peak in 2009 (n = 1,368), the total number of submitted LA-MRSA isolates has been slowly decreasing to 968 in 2014 and over 80% of LA-MRSA belonged to one of three predominant MLVA/spa-types. Next generation sequencing (n=118) showed that MT569/t034 isolates were genetically more diverse than MT398/t011 and MT572/t108. Concurrent with the decrease in LA-MRSA, fewer people reported having contact with livestock and this was most prominent for people carrying MT569/t034 LA-MRSA. The proportion of LA-MRSA isolated from infection-related materials increased from 6% in 2009, to 13% in 2014 and most of these isolates originated from patients older than 50 years of age. Remarkably, 83% of these patients reported not having contact with livestock. The results reveal an ongoing change in the genotypic and epidemiological characteristics of Dutch LA-MRSA isolated from humans with the emergence of a LA-MRSA subclade independent of livestock exposure, suggesting LA-MRSA starts to resemble non-LA-MRSA in terms of transmissibility and pathogenicity.

scholarly journals Erratum: Legal approaches regarding health-care decisions involving minors: implications for next-generation sequencing

2017 ◽  
Vol 25 (5) ◽  
pp. 658-658 ◽  
Author(s):  
Karine Sénécal ◽  
Kristof Thys ◽  
Danya F Vears ◽  
Kristof Van Assche ◽  
Bartha M Knoppers ◽  
...  
Keyword(s):  
Health Care ◽  
Next Generation Sequencing ◽  
Next Generation ◽  
Health Care Decisions ◽  
Generation Sequencing

scholarly journals Draft Genome Sequence of Saccharomyces cerevisiae Strain Awamori Number 101, Commonly Used to Make Awamori, a Traditional Spirit, in Okinawa, Japan

2021 ◽  
Vol 10 (25) ◽  
Author(s):  
Masatoshi Tsukahara ◽  
Kotaro Ise ◽  
Maiko Nezuo ◽  
Haruna Azuma ◽  
Takeshi Akao ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Next Generation Sequencing ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Next Generation ◽  
Industrial Strain ◽  
Content Type ◽  
Short Reads ◽  
Generation Sequencing

We report here the draft genome sequence for Saccharomyces cerevisiae strain Awamori number 101, an industrial strain used for producing awamori, a distilled alcohol beverage. It was constructed by assembling the short reads obtained by next-generation sequencing. The 315 contigs constitute an 11.5-Mbp genome sequence coding 6,185 predicted proteins.

scholarly journals Next-Generation Sequencing and Bioinformatics Protocol for Malaria Drug Resistance Marker Surveillance

2018 ◽  
Vol 62 (4) ◽  
pp. e02474-17 ◽  
Author(s):  
Eldin Talundzic ◽  
Shashidhar Ravishankar ◽  
Julia Kelley ◽  
Dhruviben Patel ◽  
Mateusz Plucinski ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Next Generation Sequencing ◽  
Deep Sequencing ◽  
Artemisinin Resistance ◽  
The United States ◽  
Imported Malaria ◽  
Chloroquine Resistance ◽  
Next Generation ◽  
Content Type ◽  
Generation Sequencing

ABSTRACT The recent advances in next-generation sequencing technologies provide a new and effective way of tracking malaria drug-resistant parasites. To take advantage of this technology, an end-to-end Illumina targeted amplicon deep sequencing (TADS) and bioinformatics pipeline for molecular surveillance of drug resistance in P. falciparum, called malaria resistance surveillance (MaRS), was developed. TADS relies on PCR enriching genomic regions, specifically target genes of interest, prior to deep sequencing. MaRS enables researchers to simultaneously collect data on allele frequencies of multiple full-length P. falciparum drug resistance genes (crt, mdr1, k13, dhfr, dhps, and the cytochrome b gene), as well as the mitochondrial genome. Information is captured at the individual patient level for both known and potential new single nucleotide polymorphisms associated with drug resistance. The MaRS pipeline was validated using 245 imported malaria cases that were reported to the Centers for Disease Control and Prevention (CDC). The chloroquine resistance crt CVIET genotype (mutations underlined) was observed in 42% of samples, the highly pyrimethamine-resistant dhps IRN triple mutant in 92% of samples, and the sulfadoxine resistance dhps mutation SGEAA in 26% of samples. The mdr1 NFSND genotype was found in 40% of samples. With the exception of two cases imported from Cambodia, no artemisinin resistance k13 alleles were identified, and 99% of patients carried parasites susceptible to atovaquone-proguanil. Our goal is to implement MaRS at the CDC for routine surveillance of imported malaria cases in the United States and to aid in the adoption of this system at participating state public health laboratories, as well as by global partners.

scholarly journals Next generation sequencing characterizes HLA diversity in a registry population from the Netherlands

HLA ◽  
2019 ◽  
Vol 93 (6) ◽  
pp. 474-483 ◽  
Author(s):  
Lihua Hou ◽  
Elizabeth Enriquez ◽  
Misti Persaud ◽  
Noriko Steiner ◽  
Machteld Oudshoorn ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
The Netherlands ◽  
Next Generation ◽  
Generation Sequencing

scholarly journals Bloody coli: a Gene Cocktail in Escherichia coli O104:H4

mBio ◽  
2013 ◽  
Vol 4 (1) ◽  
Author(s):  
Fernando Baquero ◽  
Raquel Tobes
Keyword(s):  
Escherichia Coli ◽  
Next Generation Sequencing ◽  
Genetic Material ◽  
Next Generation ◽  
Content Type ◽  
Pathogenicity Genes ◽  
Sequencing Technologies ◽  
Population Sizes ◽  
Sequential Acquisition ◽  
Generation Sequencing

ABSTRACT A recent study published in mBio [Y. H. Grad et al., mBio 4(1):e00452-12, 2013] indicates that a rapid introgressive evolution has occurred in Escherichia coli O104:H4 by sequential acquisition of foreign genetic material involving pathogenicity traits. O104 genetic promiscuity cannot be readily explained by high population sizes. However, extensive interactions leading to cumulative assemblies of pathogenicity genes might be assured by small K-strategist populations exploiting particular intestinal niches. Next-generation sequencing technologies will be critical to detect particular “gene cocktails” as potentially pathogenic ensembles and to predict the risk of future outbreaks.

scholarly journals Improved Detection by Next-Generation Sequencing of Pyrazinamide Resistance in Mycobacterium tuberculosis Isolates

2015 ◽  
Vol 53 (12) ◽  
pp. 3779-3783 ◽  
Author(s):  
Nontuthuko E. Maningi ◽  
Luke T. Daum ◽  
John D. Rodriguez ◽  
Matsie Mphahlele ◽  
Remco P. H. Peters ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Next Generation Sequencing ◽  
Sanger Sequencing ◽  
Detection Sensitivity ◽  
Next Generation ◽  
Resistance Mutations ◽  
Coding Region ◽  
Content Type ◽  
Mdr Tb ◽  
Generation Sequencing

The technical limitations of common tests used for detecting pyrazinamide (PZA) resistance inMycobacterium tuberculosisisolates pose challenges for comprehensive and accurate descriptions of drug resistance in patients with multidrug-resistant tuberculosis (MDR-TB). In this study, a 606-bp fragment (comprising thepncAcoding region plus the promoter) was sequenced using Ion Torrent next-generation sequencing (NGS) to detect associated PZA resistance mutations in 88 recultured MDR-TB isolates from an archived series collected in 2001. These 88 isolates were previously Sanger sequenced, with 55 (61%) designated as carrying the wild-typepncAgene and 33 (37%) showing mutations. PZA susceptibility of the isolates was also determined using the Bactec 460 TB system and the Wayne test. In this study, isolates were recultured and susceptibility testing was performed in Bactec 960 MGIT. Concordance between NGS and MGIT results was 93% (n= 88), and concordance values between the Bactec 460, the Wayne test, orpncAgene Sanger sequencing and NGS results were 82% (n= 88), 83% (n= 88), and 89% (n= 88), respectively. NGS confirmed the majority ofpncAmutations detected by Sanger sequencing but revealed several new and mixed-strain mutations that resolved discordancy in other phenotypic results. Importantly, in 53% (18/34) of these isolates,pncAmutations were located in the 151 to 360 region and warrant further exploration. In these isolates, with their known resistance to rifampin, NGS ofpncAimproved PZA resistance detection sensitivity to 97% and specificity to 94% using NGS as the gold standard and helped to resolve discordant results from conventional methodologies.

scholarly journals Propionibacterium acnes: Disease-Causing Agent or Common Contaminant? Detection in Diverse Patient Samples by Next-Generation Sequencing

2016 ◽  
Vol 54 (4) ◽  
pp. 980-987 ◽  
Author(s):  
Sarah Mollerup ◽  
Jens Friis-Nielsen ◽  
Lasse Vinner ◽  
Thomas Arn Hansen ◽  
Stine Raith Richter ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Propionibacterium Acnes ◽  
Opportunistic Pathogen ◽  
Next Generation Sequencing Data ◽  
Clinical Samples ◽  
Next Generation ◽  
Sequencing Data ◽  
Tissue Samples ◽  
Content Type ◽  
Generation Sequencing

Propionibacterium acnesis the most abundant bacterium on human skin, particularly in sebaceous areas.P. acnesis suggested to be an opportunistic pathogen involved in the development of diverse medical conditions but is also a proven contaminant of human clinical samples and surgical wounds. Its significance as a pathogen is consequently a matter of debate. In the present study, we investigated the presence ofP. acnesDNA in 250 next-generation sequencing data sets generated from 180 samples of 20 different sample types, mostly of cancerous origin. The samples were subjected to either microbial enrichment, involving nuclease treatment to reduce the amount of host nucleic acids, or shotgun sequencing. We detected high proportions ofP. acnesDNA in enriched samples, particularly skin tissue-derived and other tissue samples, with the levels being higher in enriched samples than in shotgun-sequenced samples.P. acnesreads were detected in most samples analyzed, though the proportions in most shotgun-sequenced samples were low. Our results show thatP. acnescan be detected in practically all sample types when molecular methods, such as next-generation sequencing, are employed. The possibility of contamination from the patient or other sources, including laboratory reagents or environment, should therefore always be considered carefully whenP. acnesis detected in clinical samples. We advocate that detection ofP. acnesalways be accompanied by experiments validating the association between this bacterium and any clinical condition.

scholarly journals The politics of health-care reform in the Netherlands since 2006

2011 ◽  
Vol 6 (1) ◽  
pp. 125-134 ◽  
Author(s):  
Hans Maarse ◽  
Aggie Paulus
Keyword(s):  
Health Care ◽  
The Netherlands ◽  
Health Care Reform ◽  
Political Context ◽  
Market Reform ◽  
The Political ◽  
Political Resistance ◽  
Dutch Health ◽  
Dutch Health Care ◽  
Political Compromise

AbstractThis article comments on Schut and van de Ven's overview of the results of purchaser competition in Dutch health care, which concludes that the glass can be seen as half full or half empty. Although it is true that results have been achieved, we believe that the evidence is incomplete and in some respects flimsy. More importantly, however, Schut and van de Ven neglect the political context of the market reform introduced in 2006. The reform is far from finished and there has been a constant need for political compromise. Optimism about the market's potential also seems to be on the wane. Several insurer and provider initiatives have provoked political resistance. As a result, there are good reasons to argue that the reform's future is uncertain.

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