‘Cyclical Bias’ in Microbiome Research Revealed by A Portable Germ-Free Housing System Using Nested Isolation

Germ-Free (GF) research has required highly technical pressurized HEPA-ventilation anchored systems for decades. Herein, we validated a GF system that can be easily implemented and portable using Nested Isolation (NesTiso). GF-standards can be achieved housing mice in non-HEPA-static cages, which only need to be nested ‘one-cage-inside-another’ resembling ‘Russian dolls’. After 2 years of monitoring ~100,000 GF-mouse-days, NesTiso showed mice can be maintained GF for life (>1.3 years), with low animal daily-contamination-probability risk (1 every 867 days), allowing the expansion of GF research with unprecedented freedom and mobility. At the cage level, with 23,360 GF cage-days, the probability of having a cage contamination in NesTiso cages opened in biosafety hoods was statistically identical to that of opening cages inside (the ‘gold standard’) multi-cage pressurized GF isolators. When validating the benefits of using NesTiso in mouse microbiome research, our experiments unexpectedly revealed that the mouse fecal microbiota composition within the ‘bedding material’ of conventional SPF-cages suffers cyclical selection bias as moist/feces/diet/organic content (‘soiledness’) increases over time (e.g., favoring microbiome abundances of Bacillales, Burkholderiales, Pseudomonadales; and cultivable Enterococcus faecalis over Lactobacillus murinus and Escherichia coli), which in turn cyclically influences the gut microbiome dynamics of caged mice. Culture ‘co-streaking’ assays showed that cohoused mice exhibiting different fecal microbiota/hemolytic profiles in clean bedding (high-within-cage individual diversity) ‘cyclically and transiently appear identical’ (less diverse) as bedding soiledness increases, and recurs. Strategies are proposed to minimize this novel functional form of cyclical bedding-dependent microbiome selection bias.
REFERENCE:
Rodriguez-Palacios, Alexander et al. “‘Cyclical Bias’ in Microbiome Research Revealed by A Portable Germ-Free Housing System Using Nested Isolation.” Scientific Reports 8 (2018): 3801. PMC. Web. 2 Apr. 2018.


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Qualitative Analysis of Origins and Evolution of an Elastomeric #Respirator Program

Elastomeric respirators (elastomerics) may serve as one alternative to disposable N95 respirator use in healthcare. We explored factors which drove elastomeric adoption and continued use in a large academic medical center. We conducted semi-structured and focus group interviews in 2015 with a) 11 leadership key informants (KIs) with involvement in the respiratory protection program (RPP) when elastomerics were introduced and b) 11 healthcare workers (HCWs) recruited from hospital departments assigned to use elastomerics. Interview transcripts and responses were open-coded to capture emergent themes, which were collapsed into broader categories and iteratively refined. Factors identified by leadership KIs as influencing elastomeric adoption included: 1) N95 shortages during 2009’s H1N1 influenza pandemic and 2) the presence of trained, certified safety professionals who were familiar with respiratory protection requirements. Factors identified as influencing ongoing use of elastomerics included: 1) cleaning/decontamination practices, 2) storage, 3) safety culture, 4) HCW respirator knowledge, and 5) risk perception. HCW users expressed dissatisfaction related to breathing, communication and cleaning of elastomerics. Other themes included convenience use of N95s rather than assigned elastomerics, despite perceptions that elastomerics are more protective. Through semi-structured and focus group interviews, we learned that 1) leadership introduced elastomerics due to necessity but now face challenges related to ongoing use, and 2) HCWs were not satisfied with elastomerics for routine care and preferentially used N95s because they were conveniently available at point of use. Although the impetus behind incorporation of elastomerics was clear, the most complex themes related to sustainability of this form of RPP. These themes were used to inform a broader questionnaire and will address the utility of elastomerics as a feasible and acceptable practical alternative to N95s in healthcare.
REFERENCE:
Hines, Stella E et al. “Qualitative Analysis of Origins and Evolution of an Elastomeric Respirator-Based Hospital Respiratory Protection Program.” Journal of the International Society for Respiratory Protection 34.2 (2017): 95–110. Print.

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https://www.youtube.com/watch?v=BRDApYgvDqQ

LAB RULES - Dua Lipa "New Rules" Parody

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Mechanisms of ultraviolet disinfection and chlorination of Escherichia coli

Traditional culture methods may underestimate the tolerance of microorganisms to disinfectants because of the existence of viable but nonculturable or sublethally injured cells after disinfection. The selection of a strict method is crucial for the evaluation of disinfection performance. The actions of 2 typical disinfectants - ultraviolet (UV) and chlorine - on the fecal indicator Escherichia coli were investigated by the detection of culturability, membrane permeability, metabolic activity, deoxyribonucleic acid (DNA), and messenger ribonucleic acid (mRNA). During UV disinfection, the irreversible damages in the cell membrane and cellular adenosine triphosphate (ATP) were negligible at low UV doses (<80mJ/cm2). However, membrane permeability was damaged at low doses of chlorine (<5mg/L), leading to leakage of cellular ATP. Our study showed that a slight lesion in DNA was detected even at high doses of UV (400mJ/cm2) and chlorine (>5mg/L) treatments. The decay of mRNA was more rapid than that of DNA. The degradation level of mRNA depended on the choice of target genes. After exposure to 50mJ/cm2 UV dose or 5mg/L chlorine for 30min, the DNA damage repair function (RecA mRNA) was inhibited. The mRNA involved in the DNA damage repair function can be a potential indicator of bacterial viability.
REFERENCE:
Xu L, Zhang C, Xu P, Wang XC. Mechanisms of ultraviolet disinfection and chlorination of Escherichia coli: Culturability, membrane permeability, metabolism, and genetic damage. J Environ Sci (China). 2018 Mar;65:356-366. doi:  10.1016/j.jes.2017.07.006. Epub 2017 Jul 16.

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Guidance for Evaluating the Safety of Experimental Releases of Mosquitoes

Experimental releases of mosquitoes are performed to understand characteristics of populations related to the biology, ability to transmit pathogens, and ultimately their control. In this article, we discuss considerations related to the safety of experimental releases of living mosquitoes, applying principles of good practice in vector biology that protect human health and comfort. We describe specific factors of experimental releases of mosquitoes that we believe are critical to inform institutional biosafety committees and similar review boards to which proposals to conduct mosquito release experiments have been submitted. In this study, “experimental releases” means those that do not significantly increase vector capacity or nuisance biting relative to the unperturbed natural baseline. This document specifically does not address releases of mosquitoes for ongoing control programs or trials of new control methods for which broader assessments of risk are required. It also does not address releases of transgenic or exotic (non-native) mosquito species, both of which require particular regulatory approval. Experimental releases may include females and males and evaluation must consider their effects based on the number released, their genotype and phenotype, the environment into which they are released, and postrelease collection activities. We consider whether increases of disease transmission and nuisance biting might result from proposed experimental releases against the backdrop of natural population size variation. We recommend that experimental releases be conducted in a manner that can be reasonably argued to have insignificant negative effects. Reviewers of proposals for experimental releases should expect applicants to provide such an argument based on evidence from similar studies and their planned activities. This document provides guidance for creating and evaluating such proposals.
REFERENCE;
Benedict, Mark Q. et al. “Guidance for Evaluating the Safety of Experimental Releases of Mosquitoes, Emphasizing Mark-Release-Recapture Techniques.” Vector Borne and Zoonotic Diseases 18.1 (2018): 39–48. PMC. Web. 23 Mar. 2018.

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Recommendations for Laboratory Containment and Management of Gene Drive Systems in Arthropods

V

ersatile molecular tools for creating driving transgenes and other invasive genetic factors present regulatory, ethical, and environmental challenges that should be addressed to ensure their safe use. In this article, we discuss driving transgenes and invasive genetic factors that can potentially spread after their introduction into a small proportion of individuals in a population. The potential of invasive genetic factors to increase their number in natural populations presents challenges that require additional safety measures not provided by previous recommendations regarding accidental release of arthropods. In addition to providing physical containment, invasive genetic factors require greater attention to strain management, including their distribution and identity confirmation. In this study, we focus on insects containing such factors with recommendations for investigators who are creating them, institutional biosafety committees charged with ensuring safety, funding agencies providing support, those managing insectaries handling these materials who are responsible for containment, and other persons who will be receiving insects—transgenic or not—from these facilities. We give specific examples of efforts to modify mosquitoes for mosquito-borne disease control, but similar considerations are relevant to other arthropods that are important to human health, the environment, and agriculture.
REFERENCE:
Benedict, Mark Q. et al. “Recommendations for Laboratory Containment and Management of Gene Drive Systems in Arthropods.” Vector Borne and Zoonotic Diseases 18.1 (2018): 2–13. PMC. Web. 23 Mar. 2018.
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A New Approach to Evaluating the Risk–Benefit Equation for Dual-Use and Gain-of-Function Research of Concern

In the twenty-first century, biology faces a problem that has previously vexed other disciplines such as physics, namely the prospect that its knowledge domain could be used to generate biological agents with altered properties that enhanced their weapon potential. Biological weapons bring the additional dimension that these could be self-replicating, easy to manufacture and synthesized with commonly available expertise. This resulted in increasing concern about the type of research done and communicated, despite the fact that such research often has direct societal benefits, bringing the dual-use dilemma to biology. The conundrum of dual use research of concern was crystallized by the so-called “gain-of-function” type of experiments in which avian influenza viruses were endowed with new properties in the laboratory such as increased virulence and the capacity for mammalian transmission. After more than a decade of intensive discussion and controversy involving biological experiments with dual-use potential, there is no consensus on the issue except for the need to carry out such experiments in the safest conditions possible. In this essay, we review the topic with the hindsight of several years and suggest that instead of prescribing prohibitions and experimental limitations the focus should be on the importance of scientific questions at hand. We posit that the importance of a scientific question for medical and scientific progress provides a benchmark to determine the acceptable level of risk in biological experimentation.

REFERENCE:
Imperiale, Michael J., and Arturo Casadevall. “A New Approach to Evaluating the Risk–Benefit Equation for Dual-Use and Gain-of-Function Research of Concern.” Frontiers in Bioengineering and Biotechnology 6 (2018): 21. PMC. Web. 23 Mar. 2018.

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Re-creation of Horsepox Virus: Dual use research of concern #DURC #Viruela

mSphere is publishing two commentaries on a controversial topic: should the horsepox virus have been reconstructed? A group led by David Evans at University of Alberta was funded by the company Tonix Pharmaceuticals, Inc., in New York to build this virus as a potential step toward a new smallpox vaccine (1).
This work occurs at a time when much attention is being paid to dual use research of concern (DURC): research that is performed due to its potential benefit, but the results of which could potentially be misused for nefarious purposes. In this case, the debate focuses on the benefit of a new smallpox vaccine versus the risk that someone may unleash variola virus itself, the causative agent of smallpox, on a largely unvaccinated human population. There is no argument against the fact that the eradication of smallpox was one of the greatest achievements of the public health community.
The two articles posted today come from Gregory Koblentz at George Mason University, who argues that this work was poorly justified on two fronts, scientifically and commercially (2), and from Diane DiEuliis and Gigi Gronvall from National Defense University and the Center for Health Security at Johns Hopkins University Bloomberg School of Public Health, respectively, who discuss this study in the larger context of how the risks and benefits of dual use research are assessed and managed (3). (mSphere asked the leadership of Tonix to submit a manuscript, but we received no response.)
It is our intent at mSphere to publish similar pairs of articles on controversial and cutting edge topics in the future. We are keeping our eyes open for such opportunities and welcome your ideas for potential areas that should be addressed.
These are important discussions to have, not just among those of us who pay daily attention to biosafety and biosecurity, but among the broader scientific community as a whole and especially the microbial science community. I think you will find these articles to be both thoughtful and thought-provoking.

REFERENCES:

1. Noyce RS, Lederman S, Evans DH. 2018. Construction of an infectious horsepox virus vaccine from chemically synthesized DNA fragments. PLoS One 13:e0188453. doi:10.1371/journal.pone.0188453.
2. Koblentz GD. 2018. A critical analysis of the scientific and commercial rationales for the de novo synthesis of horsepox virus. mSphere 3:e00040-18. doi:10.1128/mSphere.00040-18. [Cross Ref]
3. DiEuliis D, Gronvall GK. 2018. A holistic assessment of the risks and benefits of the synthesis of horsepox virus. mSphere 3:e00074-18. doi:10.1128/mSphere.00074-18.
4. Imperiale, Michael J. “Re-Creation of Horsepox Virus.” mSphere 3.2 (2018): e00079–18. PMC. Web. 23 Mar. 2018.

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Recreational Water and Infection

This paper reviews the latest evidence provided by epidemiological studies and quantitative microbial risk assessments (QMRAs) of infection risk from recreational water use. Studies for review were selected following a PubMed search for articles published between January 2010 and April 2014. Epidemiological studies show a generally elevated risk of gastrointestinal illness in bathers compared to non-bathers but often no clear association with water quality as measured by faecal indicator bacteria; this is especially true where study sites are impacted by non-point source pollution. Evidence from QMRAs support the lack of a consistent water quality association for non-point source-impacted beaches. It is suggested that source attribution, through quantified microbial source apportionment, linked with appropriate use of microbial source tracking methods should be employed as an integral part of future epidemiological surveys.

REFERENCE:
Fewtrell L, Kay D. Recreational Water and Infection: A Review of Recent Findings. Curr Environ Health Rep. 2015 Mar;2(1):85-94. doi: 10.1007/s40572-014-0036-6. Review.

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Analysis of the risk of acquiring infections from recreational exposure to seawater

Background: Numerous illnesses are associated with bathing in natural waters, although it is assumed that the risk of illness among bathers exposed to relatively clean waters found in high-income countries is negligible. A systematic review was carried out to quantify the increased risk of experiencing a range of adverse health outcomes among bathers exposed to coastal water compared with non-bathers.
Methods: In all 6919 potentially relevant titles and abstracts were screened, and from these 40 studies were eligible for inclusion in the review. Odds ratios (OR) were extracted from 19 of these reports and combined in random-effect meta-analyses for the following adverse health outcomes: incident cases of any illness, ear infections, gastrointestinal illness and infections caused by specific microorganisms.
Results: There is an increased risk of experiencing symptoms of any illness [OR = 1.86, 95% confidence interval (CI): 1.31 to 2.64, P = 0.001] and ear ailments (OR = 2.05, 95% CI: 1.49 to 2.82, P < 0.001) in bathers compared with non-bathers. There is also an increased risk of experiencing gastrointestinal ailments (OR = 1.29, 95% CI: 1.12 to 1.49, P < 0.001).
Conclusions:  This is the first systematic review to evaluate evidence on the increased risk of acquiring illnesses from bathing in seawater compared with non-bathers. Our results support the notion that infections are acquired from bathing in coastal waters, and that bathers have a greater risk of experiencing a variety of illnesses compared with non-bathers.

REFERENCES:
Leonard AFC, et al. Is it safe to go back into the water? A systematic review and meta-analysis of the risk of acquiring infections from recreational exposure to seawater. Int J Epidemiol. 2018 Feb 26.  doi: 10.1093/ije/dyx281.

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