Extensive screening reveals previously undiscovered aminoglycoside resistance genes in human pathogens.

Antibiotic resistance is a growing threat to human health, caused in part by pathogens accumulating antibiotic resistance genes (ARGs) through horizontal gene transfer. New ARGs are typically not recognized until they have become widely disseminated, which limits our ability to reduce their spread. In this study, we use large-scale computational screening of bacterial genomes to identify previously undiscovered mobile ARGs in pathogens. From ~1 million genomes, we predict 1,071,815 genes encoding 34,053 unique aminoglycoside-modifying enzymes (AMEs). These cluster into 7,612 families (<70% amino acid identity) of which 88 are previously described. Fifty new AME families are associated with mobile genetic elements and pathogenic hosts. From these, 24 of 28 experimentally tested AMEs confer resistance to aminoglycoside(s) in Escherichia coli, with 17 providing resistance above clinical breakpoints. This study greatly expands the range of clinically relevant aminoglycoside resistance determinants and demonstrates that computational methods enable early discovery of potentially emerging ARGs.

A global synthesis of high-resolution stable isotope data from benthic foraminifera of the last deglaciation.

We present the first version of the Ocean Circulation and Carbon Cycling (OC3) working group database, of oxygen and carbon stable isotope ratios from benthic foraminifera in deep ocean sediment cores from the Last Glacial Maximum (LGM, 23-19 ky) to the Holocene (<10 ky) with a particular focus on the early last deglaciation (19-15 ky BP). It includes 287 globally distributed coring sites, with metadata, isotopic and chronostratigraphic information, and age models. A quality check was performed for all data and age models, and sites with at least millennial resolution were preferred. Deep water mass structure as well as differences between the early deglaciation and LGM are captured by the data, even though its coverage is still sparse in many regions. We find high correlations among time series calculated with different age models at sites that allow such analysis. The database provides a useful dynamical approach to map physical and biogeochemical changes of the ocean throughout the last deglaciation.

Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.

BACKGROUND: Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants. RESULTS: A reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs. CONCLUSIONS: Our results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.

Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes.

Macrolides are broad-spectrum antibiotics used to treat a range of infections. Resistance to macrolides is often conferred by mobile resistance genes encoding Erm methyltransferases or Mph phosphotransferases. New erm and mph genes keep being discovered in clinical settings but their origins remain unknown, as is the type of macrolide resistance genes that will appear in the future. In this study, we used optimized hidden Markov models to characterize the macrolide resistome. Over 16 terabases of genomic and metagenomic data, representing a large taxonomic diversity (11 030 species) and diverse environments (1944 metagenomic samples), were searched for the presence of erm and mph genes. From this data, we predicted 28 340 macrolide resistance genes encoding 2892 unique protein sequences, which were clustered into 663 gene families (<70 % amino acid identity), of which 619 (94 %) were previously uncharacterized. This included six new resistance gene families, which were located on mobile genetic elements in pathogens. The function of ten predicted new resistance genes were experimentally validated in Escherichia coli using a growth assay. Among the ten tested genes, seven conferred increased resistance to erythromycin, with five genes additionally conferring increased resistance to azithromycin, showing that our models can be used to predict new functional resistance genes. Our analysis also showed that macrolide resistance genes have diverse origins and have transferred horizontally over large phylogenetic distances into human pathogens. This study expands the known macrolide resistome more than ten-fold, provides insights into its evolution, and demonstrates how computational screening can identify new resistance genes before they become a significant clinical problem.

Laser-induced corneal injury: validation of a computer model to predict thresholds.

The exposure and emission limits of ICNIRP, IEC 60825-1 and ANSI Z136.1 to protect the cornea are based on a limited number of in-vivo studies. To broaden the database, a computer model was developed to predict injury thresholds in the wavelength range from 1050 nm to 10.6 µm and was validated by comparison with all applicable experimental threshold data (ED50) with exposure duration between 1.7 ns and 100 s. The model predictions compare favorably with the in-vivo data with an average ratio of computer prediction to ED50 of 0.94 (standard deviation ± 30%) and a maximum deviation of less than 2. This computer model can be used to improve exposure limits or for a quantitative risk analysis of a given exposure of the cornea.

Consistently dated Atlantic sediment cores over the last 40 thousand years.

Rapid changes in ocean circulation and climate have been observed in marine-sediment and ice cores over the last glacial period and deglaciation, highlighting the non-linear character of the climate system and underlining the possibility of rapid climate shifts in response to anthropogenic greenhouse gas forcing. To date, these rapid changes in climate and ocean circulation are still not fully explained. One obstacle hindering progress in our understanding of the interactions between past ocean circulation and climate changes is the difficulty of accurately dating marine cores. Here, we present a set of 92 marine sediment cores from the Atlantic Ocean for which we have established age-depth models that are consistent with the Greenland GICC05 ice core chronology, and computed the associated dating uncertainties, using a new deposition modeling technique. This is the first set of consistently dated marine sediment cores enabling paleoclimate scientists to evaluate leads/lags between circulation and climate changes over vast regions of the Atlantic Ocean. Moreover, this data set is of direct use in paleoclimate modeling studies.

Patient Perspectives on Sharing Anonymized Personal Health Data Using a Digital System for Dynamic Consent and Research Feedback: A Qualitative Study.

BACKGROUND: Electronic health records are widely acknowledged to provide an important opportunity to anonymize patient-level health care data and collate across populations to support research. Nonetheless, in the wake of public and policy concerns about security and inappropriate use of data, conventional approaches toward data governance may no longer be sufficient to respect and protect individual privacy. One proposed solution to improve transparency and public trust is known as Dynamic Consent, which uses information technology to facilitate a more explicit and accessible opportunity to opt out. In this case, patients can tailor preferences about whom they share their data with and can change their preferences reliably at any time. Furthermore, electronic systems provide opportunities for informing patients about data recipients and the results of research to which their data have contributed. OBJECTIVE: To explore patient perspectives on the use of anonymized health care data for research purposes. To evaluate patient perceptions of a Dynamic Consent model and electronic system to enable and implement ongoing communication and collaboration between patients and researchers. METHODS: A total of 26 qualitative interviews and three focus groups were conducted that included a video presentation explaining the reuse of anonymized electronic patient records for research. Slides and tablet devices were used to introduce the Dynamic Consent system for discussion. A total of 35 patients with chronic rheumatic disease with varying levels of illness and social deprivation were recruited from a rheumatology outpatient clinic; 5 participants were recruited from a patient and public involvement health research network. RESULTS: Patients were supportive of sharing their anonymized electronic patient record for research, but noted a lack of transparency and awareness around the use of data, making it difficult to secure public trust. While there were general concerns about detrimental consequences of data falling into the wrong hands, such as insurance companies, 39 out of 40 (98%) participants generally considered that the altruistic benefits of sharing health care data outweighed the risks. Views were mostly positive about the use of an electronic interface to enable greater control over consent choices, although some patients were happy to share their data without further engagement. Participants were particularly enthusiastic about the system as a means of enabling feedback regarding data recipients and associated research results, noting that this would improve trust and public engagement in research. This underlines the importance of patient and public involvement and engagement throughout the research process, including the reuse of anonymized health care data for research. More than half of patients found the touch screen interface easy to use, although a significant minority, especially those with limited access to technology, expressed some trepidation and felt they may need support to use the system. CONCLUSIONS: Patients from a range of socioeconomic backgrounds viewed a digital system for Dynamic Consent positively, in particular, feedback about data recipients and research results. Implementation of a digital Dynamic Consent system would require careful interface design and would need to be located within a robust data infrastructure; it has the potential to improve trust and engagement in electronic medical record research.

Dynamic consent: a possible solution to improve patient confidence and trust in how electronic patient records are used in medical research.

With one million people treated every 36 hours, routinely collected UK National Health Service (NHS) health data has huge potential for medical research. Advances in data acquisition from electronic patient records (EPRs) means such data are increasingly digital and can be anonymised for research purposes. NHS England's care.data initiative recently sought to increase the amount and availability of such data. However, controversy and uncertainty following the care.data public awareness campaign led to a delay in rollout, indicating that the success of EPR data for medical research may be threatened by a loss of patient and public trust. The sharing of sensitive health care data can only be done through maintaining such trust in a constantly evolving ethicolegal and political landscape. We propose that a dynamic consent model, whereby patients can electronically control consent through time and receive information about the uses of their data, provides a transparent, flexible, and user-friendly means to maintain public trust. This could leverage the huge potential of the EPR for medical research and, ultimately, patient and societal benefit.

Dynamic consent: a patient interface for twenty-first century research networks.

Biomedical research is being transformed through the application of information technologies that allow ever greater amounts of data to be shared on an unprecedented scale. However, the methods for involving participants have not kept pace with changes in research capability. In an era when information is shared digitally at the global level, mechanisms of informed consent remain static, paper-based and organised around national boundaries and legal frameworks. Dynamic consent (DC) is both a specific project and a wider concept that offers a new approach to consent; one designed to meet the needs of the twenty-first century research landscape. At the heart of DC is a personalised, digital communication interface that connects researchers and participants, placing participants at the heart of decision making. The interface facilitates two-way communication to stimulate a more engaged, informed and scientifically literate participant population where individuals can tailor and manage their own consent preferences. The technical architecture of DC includes components that can securely encrypt sensitive data and allow participant consent preferences to travel with their data and samples when they are shared with third parties. In addition to improving transparency and public trust, this system benefits researchers by streamlining recruitment and enabling more efficient participant recontact. DC has mainly been developed in biobanking contexts, but it also has potential application in other domains for a variety of purposes.

Laser-induced retinal damage threshold for repetitive-pulse exposure to 100-µs pulses.

The laser-induced retinal injury thresholds for repetitive-pulse exposures to 100-µs-duration pulses at a wavelength of 532 nm have been determined for exposures of up to 1000 pulses in an in vivo model. The ED50 was measured for pulse repetition frequencies of 50 and 1000 Hz. Exposures to collimated beams producing a minimal retinal beam spot and to divergent beams producing a 100-µm-diameter retinal beam spot were considered. The ED50 for a 100-µs exposure was measured to be 12.8 µJ total intraocular energy for a minimal retinal beam spot exposure and 18.1 µJ total intraocular energy for a 100-µm-diameter retinal beam spot. The threshold for exposures to N > 1 pulse was found to be the same for both pulse repetition frequencies. The variation of the ED50 with the number of pulses is described well by the probability summation model, in which each pulse is considered an independent event. This is consistent with a threshold-level damage mechanism of microcavitation for single-pulse 100-µs-duration exposures. The data support the maximum permissible exposure levels for repetitive-pulse exposure promulgated in the most recent laser safety guidelines.

Damage threshold from large retinal spot size repetitive-pulse laser exposures.

The retinal damage thresholds for large spot size, multiple-pulse exposures to a Q-switched, frequency doubled Nd:YAG laser (532 nm wavelength, 7 ns pulses) have been measured for 100 µm and 500 µm retinal irradiance diameters. The ED50, expressed as energy per pulse, varies only weakly with the number of pulses, n, for these extended spot sizes. The previously reported threshold for a multiple-pulse exposure for a 900 µm retinal spot size also shows the same weak dependence on the number of pulses. The multiple-pulse ED50 for an extended spot-size exposure does not follow the n dependence exhibited by small spot size exposures produced by a collimated beam. Curves derived by using probability-summation models provide a better fit to the data.

A new understanding of multiple-pulsed laser-induced retinal injury thresholds.

Laser safety standards committees have struggled for years to formulate adequately a sound method for treating repetitive-pulse laser exposures. Safety standards for lamps and LEDs have ignored this issue because averaged irradiance appeared to treat the issue adequately for large retinal image sizes and skin exposures. Several authors have recently questioned the current approach of three test conditions (i.e., limiting single-pulse exposure, average irradiance, and a single-pulse-reduction factor) as still insufficient to treat pulses of unequal energies or certain pulse groupings. Schulmeister et al. employed thermal modeling to show that a total-on-time pulse (TOTP) rule was conservative. Lund further developed the approach of probability summation proposed by Menendez et al. to explain pulse-additivity, whereby additivity is the result of an increasing probability of detecting injury with multiple pulse exposures. This latter argument relates the increase in detection probability to the slope of the probit curve for the threshold studies. Since the uncertainty in the threshold for producing an ophthalmoscopically detectable minimal visible lesion (MVL) is large for retinal exposure to a collimated laser beam, safety committees traditionally applied large risk reduction factors ("safety factors") of one order of magnitude when deriving intrabeam, "point-source" exposure limits. This reduction factor took into account the probability of visually detecting the low-contrast lesion among other factors. The reduction factor is smaller for large spot sizes where these difficulties are quite reduced. Thus the N⁻°·²5 reduction factor may result from the difficulties in detecting the lesion. Recent studies on repetitive pulse exposures in both animal and in vitro (retinal explant) models support this interpretation of the available data.

Transgenic overexpression of the presynaptic choline transporter elevates acetylcholine levels and augments motor endurance.

The hemicholinium-3 (HC-3) sensitive, high-affinity choline transporter (CHT) sustains cholinergic signaling via the presynaptic uptake of choline derived from dietary sources or from acetylcholinesterase (AChE)-mediated hydrolysis of acetylcholine (ACh). Loss of cholinergic signaling capacity is associated with cognitive and motor deficits in humans and in animal models. Whereas genetic elimination of CHT has revealed the critical nature of CHT in maintaining ACh stores and sustaining cholinergic signaling, the consequences of elevating CHT expression have yet to be studied. Using bacterial artificial chromosome (BAC)-mediated transgenic methods, we generated mice with integrated additional copies of the mouse Slc5a7 gene. BAC-CHT mice are viable, appear to develop normally, and breed at wild-type (WT) rates. Biochemical studies revealed a 2 to 3-fold elevation in CHT protein levels in the CNS and periphery, paralleled by significant increases in [(3)H]HC-3 binding and synaptosomal choline transport activity. Elevations of ACh in the BAC-CHT mice occurred without compensatory changes in the activity of either choline acetyltransferase (ChAT) or AChE. Immunohistochemistry for CHT in BAC-CHT brain sections revealed markedly elevated CHT expression in the cell bodies of cholinergic neurons and in axons projecting to regions known to receive cholinergic innervation. Behaviorally, BAC-CHT mice exhibited diminished fatigue and increased speeds on the treadmill test without evidence of increased strength. Finally, BAC-CHT mice displayed elevated horizontal activity in the open field test, diminished spontaneous alteration in the Y-maze, and reduced time in the open arms of the elevated plus maze. Together, these studies provide biochemical, pharmacological and behavioral evidence that CHT protein expression and activity can be elevated beyond that seen in wild-type animals. BAC-CHT mice thus represent a novel tool to examine both the positive and negative impact of constitutively elevated cholinergic signaling capacity.

From patients to partners: participant-centric initiatives in biomedical research.

Advances in computing technology and bioinformatics mean that medical research is increasingly characterized by large international consortia of researchers that are reliant on large data sets and biobanks. These trends raise a number of challenges for obtaining consent, protecting participant privacy concerns and maintaining public trust. Participant-centred initiatives (PCIs) use social media technologies to address these immediate concerns, but they also provide the basis for long-term interactive partnerships. Here, we give an overview of this rapidly moving field by providing an analysis of the different PCI approaches, as well as the benefits and challenges of implementing PCIs.

Review of thresholds and recommendations for revised exposure limits for laser and optical radiation for thermally induced retinal injury.

Exposure limits (ELs) for laser and optical broadband radiation that are derived to protect the retina from adverse thermally-induced effects vary as a function of wavelength, exposure duration, and retinal irradiance diameter (spot size) expressed as the angular subtense α. A review of ex vivo injury threshold data shows that, in the ns regime, the microcavitation-induced damage mechanism results in retinal injury thresholds below thermal denaturation-induced thresholds. This appears to be the reason that the injury thresholds for retinal spot sizes of about 80 µm (α = 6 mrad) and pulse durations of about 5 ns in the green wavelength range are very close to current ELs, calling for a reduction of the EL in the ns regime. The ELs, expressed in terms of retinal radiant exposure or radiance dose, currently exhibit a 1/α dependence up to a retinal spot size of 100 mrad, referred to as αmax. For α ≥ αmax, the EL is a constant retinal radiant exposure (no α dependence) for any given exposure duration. Recent ex vivo, computer model, and non-human primate in vivo threshold data provide a more complete assessment of the retinal irradiance diameter dependence for a wide range of exposure durations. The transition of the 1/α dependence to a constant retinal radiant exposure (or constant radiance dose) is not a constant αmax but varies as a function of the exposure duration. The value of αmax of 100 mrad reflects the spot size dependence of the injury thresholds only for longer duration exposures. The injury threshold data suggest that αmax could increase as a function of the exposure duration, starting in the range of 5 mrad in the µs regime, which would increase the EL for pulsed exposure and extended sources by up to a factor of 20, while still assuring an appropriate reduction factor between the injury threshold and the exposure limit.

Tachycardia, reduced vagal capacity, and age-dependent ventricular dysfunction arising from diminished expression of the presynaptic choline transporter.

Healthy cardiovascular function relies on a balanced and responsive integration of noradrenergic and cholinergic innervation of the heart. High-affinity choline uptake by cholinergic terminals is pivotal for efficient ACh production and release. To date, the cardiovascular impact of diminished choline transporter (CHT) expression has not been directly examined, largely due to the transporter's inaccessibility in vivo. Here, we describe findings from cardiovascular experiments using transgenic mice that bear a CHT genetic deficiency. Whereas CHT knockout (CHT(-/-)) mice exhibit early postnatal lethality, CHT heterozygous (CHT(+/-)) mice survive, grow, and reproduce normally and exhibit normal spontaneous behaviors. However, the CHT(+/-) mouse heart displays significantly reduced levels of high-affinity choline uptake accompanied by significantly reduced levels of ACh. Telemeterized recordings of cardiovascular function in these mice revealed tachycardia and hypertension at rest. After treadmill exercise, CHT(+/-) mice exhibited slower heart rate recovery, consistent with a diminished cholinergic reserve, a contention validated through direct vagal nerve stimulation. Echocardiographic and histological experiments revealed an age-dependent decrease in fractional shortening, increased left ventricular dimensions, and increased ventricular fibrosis, consistent with ventricular dysfunction. These cardiovascular phenotypes of CHT(+/-) mice encourage an evaluation of humans bearing reduced CHT expression for their resiliency in maintaining proper heart function as well as risk for cardiovascular disease.

Holocene glacier fluctuations in the Peruvian Andes indicate northern climate linkages.

The role of the tropics in triggering, transmitting, and amplifying interhemispheric climate signals remains a key debate in paleoclimatology. Tropical glacier fluctuations provide important insight on regional paleoclimatic trends and forcings, but robust chronologies are scarce. Here, we report precise moraine ages from the Cordillera Vilcabamba (13 degrees 20'S) of southern Peru that indicate prominent glacial events and associated climatic shifts in the outer tropics during the early Holocene and late in the "Little Ice Age" period. Our glacier chronologies differ from the New Zealand record but are broadly correlative with well-dated glacial records in Europe, suggesting climate linkages between the tropics and the North Atlantic region.

Thermal lensing in ocular media exposed to continuous-wave near-infrared radiation: the 1150-1350-nm region.

Ocular damage threshold data remain sparse in the continuous wave (CW), near-infrared (NIR) radiation region save for the 1300-nm area that has been investigated in the past several decades. The 1300-nm ocular damage data have yielded unusual characteristics where CW retinal damage was observed in rabbit models, but never in nonhuman primate models. This paper reviews the existing 1300-nm ocular damage threshold data in terms of the fundamental criteria of an action spectrum to assist in explaining laser-tissue effects from near-infrared radiation in the eye. Reviewing the action spectrum criteria and existing NIR retinal lesion data lend evidence toward the significant presence of thermal lensing in ocular media affecting damage, a relatively unexplored mechanism of laser-tissue interaction.

Ex vivo and computer model study on retinal thermal laser-induced damage in the visible wavelength range.

Excised bovine eyes are used as models for threshold determination of 532-nm laser-induced thermal damage of the retina in the pulse duration regime of 100 micros to 2 s for varying laser spot size diameters. The thresholds as determined by fluorescence viability staining compare well with the prediction of an extended Thompson-Gerstman computer model. Both models compare well with published Rhesus monkey threshold data. A previously unknown variation of the spot size dependence is seen for different pulse durations, which allows for a more complete understanding of the retinal thermal damage. Current International Commission on Nonionized Radiation Protection (ICNIRP), American National Standards Institute (ANS), and International Electromechanical Commission (IEC) laser and incoherent optical radiation exposure limits can be increased for extended sources for pulsed exposures. We conclude that the damage mechanism at threshold detected at 24 and 1 h for the nonhuman primate model is retinal pigment epithelium (RPE) cell damage and not thermal coagulation of the sensory retina. This work validates the bovine ex vivo and computer models for prediction of thresholds of thermally induced damage in the time domain of 10 micros to 2 s, which provides the basis for safety analysis of more complicated retinal exposure scenarios such as repetitive pulses, nonconstant retinal irradiance profiles, and scanned exposure.