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Article ; Online: Functional insights on probiotics activity in the gut from metagenomic data.

Wassenaar, T M

2021 Volume 12, Issue 6, Page(s) 613–615

MeSH term(s)	Metagenome ; Metagenomics ; Probiotics
Language	English
Publishing date	2021-10-22
Publishing country	Netherlands
Document type	Letter
ZDB-ID	2561259-1
ISSN	1876-2891 ; 1876-2883
ISSN (online)	1876-2891
ISSN	1876-2883
DOI	10.3920/BM2021.x002
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Article ; Online: 2019_nCoV/SARS-CoV-2: rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses.

Wassenaar, T M / Zou, Y

Letters in applied microbiology

2020 Volume 70, Issue 5, Page(s) 342–348

Abstract: The current outbreak of a novel severe acute respiratory syndrome-like coronavirus, 2019_nCoV (now named SARS-CoV-2), illustrated difficulties in identifying a novel coronavirus and its natural host, as the coding sequences of various Betacoronavirus ... ...

Abstract	The current outbreak of a novel severe acute respiratory syndrome-like coronavirus, 2019_nCoV (now named SARS-CoV-2), illustrated difficulties in identifying a novel coronavirus and its natural host, as the coding sequences of various Betacoronavirus species can be highly diverse. By means of whole-genome sequence comparisons, we demonstrate that the noncoding flanks of the viral genome can be used to correctly separate the recognized four betacoronavirus subspecies. The conservation would be sufficient to define target sequences that could, in theory, classify novel virus species into their subspecies. Only 253 upstream noncoding sequences of Sarbecovirus are sufficient to identify genetic similarities between species of this subgenus. Furthermore, it was investigated which bat species have commercial value in China, and would thus likely be handled for trading purposes. A number of coronavirus genomes have been published that were obtained from such bat species. These bats are used in Traditional Chinese Medicine, and their handling poses a potential risk to cause zoonotic coronavirus epidemics. SIGNIFICANCE AND IMPACT OF THE STUDY: The noncoding upstream and downstream flanks of coronavirus genomes allow for rapid classification of novel Betacoronavirus species and correct identification of genetic relationships. Although bats are the likely natural host of 2019_nCoV, the exact bat species that serves as the natural host of the virus remains as yet unknown. Chinese bat species with commercial value were identified as natural reservoirs of coronaviruses and are used in Traditional Chinese Medicine. Since their trading provides a potential risk for spreading zoonoses, a change in these practices is highly recommended.
MeSH term(s)	Animals ; Betacoronavirus/classification ; COVID-19 ; China/epidemiology ; Chiroptera/classification ; Chiroptera/virology ; Coronavirus Infections/etiology ; Coronavirus Infections/virology ; Genome, Viral ; Humans ; Medicine, Chinese Traditional/adverse effects ; Pandemics ; Phylogeny ; Pneumonia, Viral/etiology ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Zoonoses/virology
Keywords	covid19
Language	English
Publishing date	2020-02-28
Publishing country	England
Document type	Journal Article
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/lam.13285
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Article ; Online: How industrial bacterial cultures can be kept stable over time.

Wassenaar, T M / Zimmermann, K

Letters in applied microbiology

2020 Volume 71, Issue 3, Page(s) 220–228

Abstract: The tremendous variation that exists between bacterial species illustrates the power of evolution, which is the continuous process of mutation and selection over time. Even within a bacterial species, individual members can harbour an impressive degree ... ...

Abstract	The tremendous variation that exists between bacterial species illustrates the power of evolution, which is the continuous process of mutation and selection over time. Even within a bacterial species, individual members can harbour an impressive degree of genetic variation, depending on the species. The question then arises how similar the offspring of a given bacterial cell over time is, and how long it takes before differences are noticeable? Here we show that on the one hand one can expect random mutations to arise, as a result of various mechanisms. On the other hand, there are forces at play that keep the offspring of a cell genetically relatively constant, unless there is selection for a particular characteristic. The most common mechanisms behind mutations that can appear in a bacterial population are briefly introduced. Next, it is explained why nevertheless such mutations are rarely observed, as long as single colonies are randomly selected, unless selective pressures apply. Since quality control of industrial bacterial cultures is likely to depend heavily on genome sequencing in the near future, the accuracy of whole-genomic sequencing technologies is also discussed. It can be concluded that the bacteriologists who started picking single colonies from agar plates more than hundred years ago were unknowingly ingeneous, as their practice maintains a bacterial culture stable over time. SIGNIFICANCE AND IMPACT OF STUDY: The questions addressed here are relevant for industries that depend on live bacteria for (manufacturing of) their products, as they have to guard their bacterial cultures that remain unchanged over time. The explanation why randomly selection of single colonies keeps a population stable can be of use in bacteriology courses. The limitations of whole-genome sequencing are relevant to legislators to avoid overinterpretation of those data.
MeSH term(s)	Bacteria/genetics ; Gene Frequency/genetics ; Genetic Drift ; Genetic Variation/genetics ; Genome, Bacterial/genetics ; Mutation/genetics ; Selection, Genetic/genetics
Language	English
Publishing date	2020-06-21
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/lam.13309
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Article: How industrial bacterial cultures can be kept stable over time

Wassenaar, T.M / Zimmermann, K

Letters in applied microbiology. 2020 Sept., v. 71, no. 3

2020

Abstract	The tremendous variation that exists between bacterial species illustrates the power of evolution, which is the continuous process of mutation and selection over time. Even within a bacterial species, individual members can harbour an impressive degree of genetic variation, depending on the species. The question then arises how similar the offspring of a given bacterial cell over time is, and how long it takes before differences are noticeable? Here we show that on the one hand one can expect random mutations to arise, as a result of various mechanisms. On the other hand, there are forces at play that keep the offspring of a cell genetically relatively constant, unless there is selection for a particular characteristic. The most common mechanisms behind mutations that can appear in a bacterial population are briefly introduced. Next, it is explained why nevertheless such mutations are rarely observed, as long as single colonies are randomly selected, unless selective pressures apply. Since quality control of industrial bacterial cultures is likely to depend heavily on genome sequencing in the near future, the accuracy of whole‐genomic sequencing technologies is also discussed. It can be concluded that the bacteriologists who started picking single colonies from agar plates more than hundred years ago were unknowingly ingeneous, as their practice maintains a bacterial culture stable over time. SIGNIFICANCE AND IMPACT OF STUDY: The questions addressed here are relevant for industries that depend on live bacteria for (manufacturing of) their products, as they have to guard their bacterial cultures that remain unchanged over time. The explanation why randomly selection of single colonies keeps a population stable can be of use in bacteriology courses. The limitations of whole‐genome sequencing are relevant to legislators to avoid overinterpretation of those data.
Keywords	agar ; bacteria ; bacterial culture ; bacteriology ; evolution ; genetic variation ; genome ; mutation ; progeny ; quality control
Language	English
Dates of publication	2020-09
Size	p. 220-228.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	NAL-AP-2-clean ; REVIEW
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/lam.13309
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: 2019_nCoV/SARS‐CoV‐2

Wassenaar, T.M. / Zou, Y.

Letters in Applied Microbiology

rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses

2020 Volume 70, Issue 5, Page(s) 342–348

Keywords	Applied Microbiology and Biotechnology ; covid19
Language	English
Publisher	Wiley
Publishing country	us
Document type	Article ; Online
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/lam.13285
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Article ; Online: BCG vaccination early in life does not improve COVID-19 outcome of elderly populations, based on nationally reported data.

Wassenaar, T M / Buzard, G S / Newman, D J

Letters in applied microbiology

2020 Volume 71, Issue 5, Page(s) 498–505

Abstract: The reported numbers of Covid-19 cases and deaths were compared for 18 countries (14 in Western Europe, plus Australia, Brazil, Israel and the USA) to assess the effect of historic and current national BCG immunizations. In view of the high death rate ... ...

Abstract	The reported numbers of Covid-19 cases and deaths were compared for 18 countries (14 in Western Europe, plus Australia, Brazil, Israel and the USA) to assess the effect of historic and current national BCG immunizations. In view of the high death rate for Covid-19 patients over 70 years of age, and given the fact that BCG vaccination is typically given early in life, we compared countries that had introduced BCG in the 1950s with those that had not. No effect on Covid-19 case fatality rate (CFR) or number of deaths per population could be demonstrated. Since some countries test for Covid-19 more than others, the effect of tests performed per million population on reported deaths per million was also assessed, but again did not demonstrate an effect of BCG vaccination in the 1950s. Whether countries had never used the vaccine, had historically used it but since ceased to do so, or were presently vaccinating with BCG did not correlate with national total number of deaths or CFR. We conclude that there is currently no evidence for a beneficial effect of BCG vaccination on Covid-19 reported cases or fatalities.
MeSH term(s)	Aged ; Aged, 80 and over ; Australia/epidemiology ; BCG Vaccine/administration & dosage ; BCG Vaccine/immunology ; Betacoronavirus/physiology ; Brazil/epidemiology ; COVID-19 ; Coronavirus Infections/epidemiology ; Coronavirus Infections/immunology ; Coronavirus Infections/mortality ; Coronavirus Infections/virology ; Europe/epidemiology ; Female ; Humans ; Male ; Pandemics/prevention & control ; Pneumonia, Viral/epidemiology ; Pneumonia, Viral/immunology ; Pneumonia, Viral/mortality ; Pneumonia, Viral/virology ; SARS-CoV-2 ; Vaccination
Chemical Substances	BCG Vaccine
Keywords	covid19
Language	English
Publishing date	2020-08-14
Publishing country	England
Document type	Journal Article
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/lam.13365
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Article: 2019_nCoV/SARS-CoV-2: rapid classification of betacoronaviruses and identification of Traditional Chinese Medicine as potential origin of zoonotic coronaviruses

Wassenaar, T M / Zou, Y

Lett Appl Microbiol

Abstract	The current outbreak of a novel severe acute respiratory syndrome-like coronavirus, 2019_nCoV (now named SARS-CoV-2), illustrated difficulties in identifying a novel coronavirus and its natural host, as the coding sequences of various Betacoronavirus species can be highly diverse. By means of whole-genome sequence comparisons, we demonstrate that the noncoding flanks of the viral genome can be used to correctly separate the recognized four betacoronavirus subspecies. The conservation would be sufficient to define target sequences that could, in theory, classify novel virus species into their subspecies. Only 253 upstream noncoding sequences of Sarbecovirus are sufficient to identify genetic similarities between species of this subgenus. Furthermore, it was investigated which bat species have commercial value in China, and would thus likely be handled for trading purposes. A number of coronavirus genomes have been published that were obtained from such bat species. These bats are used in Traditional Chinese Medicine, and their handling poses a potential risk to cause zoonotic coronavirus epidemics. SIGNIFICANCE AND IMPACT OF THE STUDY: The noncoding upstream and downstream flanks of coronavirus genomes allow for rapid classification of novel Betacoronavirus species and correct identification of genetic relationships. Although bats are the likely natural host of 2019_nCoV, the exact bat species that serves as the natural host of the virus remains as yet unknown. Chinese bat species with commercial value were identified as natural reservoirs of coronaviruses and are used in Traditional Chinese Medicine. Since their trading provides a potential risk for spreading zoonoses, a change in these practices is highly recommended.
Keywords	covid19
Publisher	WHO
Document type	Article
Note	WHO #Covidence: #4187
Database	COVID19

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Article ; Online: The mobile dso-gene-sso element in rolling-circle plasmids of staphylococci reflects the evolutionary history of its resistance gene.

Wassenaar, T M / Cabal, A

Letters in applied microbiology

2017 Volume 65, Issue 3, Page(s) 192–198

Abstract: The qacC and lnuA genes of Staphylococcus species were recently proposed to comprise a mobile element when residing on rolling-circle plasmids. Here we present other examples of resistance genes on staphylococcal rolling-circle plasmids, including fosB ... ...

Abstract	The qacC and lnuA genes of Staphylococcus species were recently proposed to comprise a mobile element when residing on rolling-circle plasmids. Here we present other examples of resistance genes on staphylococcal rolling-circle plasmids, including fosB producing resistance to fosfomycin, cat resulting in resistance to chloramphenicol and cadB for resistance to the toxic heavy metal cadmium. For three of these genes (qacC, lnuA and fosB), evidence was obtained that the genes have spread between different plasmid backgrounds. The lack of mutations in qacC suggests that the spread occurred relatively recently, while the build up of mutations in lnuA and fosB suggests their mobilization occurred in the more distant past. These observations can be explained by the use of the respective antibiotics over time. However, the cat and cadB genes sequences analysed had not collected any mutations, an observation that is not completely understood but possible explanations are discussed. Significance and impact of the study: We have analysed five resistance genes in Staphylococcus aureus that are positioned between the replication elements of rolling-circle plasmids. For three of these genes, evidence was obtained indicative of recent mobilization. The historical use of the antibiotics to which the genes produce resistance could be related to the number of mutations collected in these genes. However, two other resistance genes have not collected any mutations over time, and the reasons for this are discussed. The analyses presented provide insights into the spread and evolution of antibiotic resistance genes.
Language	English
Publishing date	2017-09
Publishing country	England
Document type	Journal Article
ZDB-ID	632584-1
ISSN	1472-765X ; 0266-8254
ISSN (online)	1472-765X
ISSN	0266-8254
DOI	10.1111/lam.12767
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Article ; Online: Generalist-Specialist Collaboration in Primary Care for Frail Older Persons: A Promising Model for the Future.

Vrijmoeth, Talitha / Wassenaar, Annelies / Koopmans, Raymond T C M / Nieuwboer, Minke S / Perry, Marieke

Journal of the American Medical Directors Association

2021 Volume 23, Issue 2, Page(s) 288–296.e3

Abstract: Objectives: The complex care needs of frail older persons living at home is a major challenge for health care systems worldwide. One possible solution is to employ a primary care physician (PCP) with additional geriatric expertise. In the Netherlands, ... ...

Abstract	Objectives: The complex care needs of frail older persons living at home is a major challenge for health care systems worldwide. One possible solution is to employ a primary care physician (PCP) with additional geriatric expertise. In the Netherlands, elderly care physicians (ECPs), who traditionally work in nursing homes, are increasingly encouraged to utilize their expertise within primary care. However, little is known about how PCPs and ECPs collaborate. Therefore, we aimed to unravel the nature of the current PCP-ECP collaboration in primary care for frail older persons, and to identify key concepts for success. Design: A qualitative multiple case study with semistructured interviews. Setting and participants: A selection of 22 participants from 7 "established collaboration practices" within the primary care setting in the Netherlands, including at least 1 ECP, 1 PCP, and 1 other health care professional for every included established collaboration practice. Methods: Transcripts of individual interviews were analyzed using largely double and independent open and axial coding, and formulation of themes and subthemes. Results: Data analysis revealed 4 key concepts for success: (1) clarification of roles and expectations (ie, patient-centered care and embedding in existing care networks), (2) trust, respect, and familiarity as drivers for collaboration (ie, mutual trust through knowing each other and having shared goals); (3) framework for regular communication (ie, structural meetings and a shared vision); and (4) government, payer, and organization support (ie, financial support and emphasis on the collaboration's urgency by organizations and national policy makers). Conclusions and implications: For a successful generalist-specialist collaboration, health care professionals need to invest in building relationships and mutual trust, and incorporating their efforts in the existing care networks to guarantee patient-centeredness. When provided with reimbursement and appreciation, this collaboration is a promising change in general practice to improve the care and outcomes of frail older persons.
MeSH term(s)	Aged ; Aged, 80 and over ; Delivery of Health Care ; Frail Elderly ; Health Personnel ; Humans ; Patient-Centered Care ; Qualitative Research
Language	English
Publishing date	2021-12-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2171030-2
ISSN	1538-9375 ; 1525-8610
ISSN (online)	1538-9375
ISSN	1525-8610
DOI	10.1016/j.jamda.2021.12.016
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Article ; Online: Screening and prioritising persistent, mobile and toxic chemicals

Julia Hartmann / Emiel Rorije / Pim N. H. Wassenaar / Eric Verbruggen

Environmental Sciences Europe, Vol 35, Iss 1, Pp 1-

development and application of a robust scoring system

2023 Volume 15

Abstract: ... M) and toxic (T) chemicals. Such chemicals, like some polyfluoroalkyl acids (PFAAs), are of concern ... given a continuous score for P, M and T potential based on the modelled indicators (low to moderate potential is ... of the chemicals receiving high scores (≥ 0.33) for all three (P-, M- and T-) indicators and 4% getting very high ...

Abstract	Abstract Background Lately scientific and societal concern has emerged about persistent (P), mobile (M) and toxic (T) chemicals. Such chemicals, like some polyfluoroalkyl acids (PFAAs), are of concern due to their high mobility and persistence in aquatic compartments which relates to long-term biotic exposure and difficult removal from drinking water. In this study, a screening approach for identification of PMT chemicals was developed and applied to 6158 diverse chemicals. Results Chemicals are given a continuous score for P, M and T potential based on the modelled indicators (low to moderate potential is a score of 0–0.33, high potential is a score of 0.33–0.5 and very high potential a score of 0.5–1). The P score was based on the estimated aquatic environmental half life and the M score on the chemical’s organic carbon/water partition coefficient (K oc) using respectively the BIOWIN3 and KocWIN QSAR models of EPISuite™. The T score was based on the indicators for five human health endpoints: carcinogenicity (c), mutaganicity (m), reprotoxicity (r), endocrine disruption (ED) and general repeated dose systemic toxicity. Structural alerts for these endpoints taken from the OECD QSAR Toolbox™ and Toxtree™ were used as indicators of potential (human) toxicity. Chemical similarity values to Substances of Very High Concern (SVHC) with c, m and/or r properties were also included. Value functions were developed to translate the presence of alerts and similarity to the existing SVHCs to values between 0 and 1. Subsequently, all values were also aggregated to an overall PMT score, again ranging from 0 to 1. Applying the approach to chemicals from the Inventory of Existing Commercial chemical Substances, which are also REACH registered, resulted in 15% of the chemicals receiving high scores (≥ 0.33) for all three (P-, M- and T-) indicators and 4% getting very high scores (≥ 0.5) for both the P- and M-indicators. Conclusions The approach confirmed the properties of chemicals classified as SVHC due to PMT properties (e.g. ...
Keywords	Contaminants of emerging concern ; Emerging contaminants ; Drinking water ; Continuous screening approach ; Multi-criteria decision analysis ; Prioritisation ; Environmental sciences ; GE1-350 ; Environmental law ; K3581-3598
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	SpringerOpen
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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