Alien Registration- Bowden, James J. (Ashland, Aroostook County)

https://digitalmaine.com/alien_docs/27426/thumbnail.jp

Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit

BACKGROUND  Strategies to prevent Staphylococcus aureus infection in hospitals focus on patient-to-patient transmission. We used whole-genome sequencing to investigate the role of colonized patients as the source of new S. aureus acquisitions, and the reliability of identifying patient-to-patient transmission using the conventional approach of spa typing and overlapping patient stay. METHODS Over 14 months, all unselected patients admitted to an adult intensive care unit (ICU) were serially screened for S. aureus. All available isolates (n = 275) were spa typed and underwent whole-genome sequencing to investigate their relatedness at high resolution. RESULTS Staphylococcus aureus was carried by 185 of 1109 patients sampled within 24 hours of ICU admission (16.7%); 59 (5.3%) patients carried methicillin-resistant S. aureus (MRSA). Forty-four S. aureus (22 MRSA) acquisitions while on ICU were detected. Isolates were available for genetic analysis from 37 acquisitions. Whole-genome sequencing indicated that 7 of these 37 (18.9%) were transmissions from other colonized patients. Conventional methods (spa typing combined with overlapping patient stay) falsely identified 3 patient-to-patient transmissions (all MRSA) and failed to detect 2 acquisitions and 4 transmissions (2 MRSA). CONCLUSIONS Only a minority of S. aureus acquisitions can be explained by patient-to-patient transmission. Whole-genome sequencing provides the resolution to disprove transmission events indicated by conventional methods and also to reveal otherwise unsuspected transmission events. Whole-genome sequencing should replace conventional methods for detection of nosocomial S. aureus transmission

Genomic tools reveal complex social organization of an invasive large mammal (\u3ci\u3eSus scrofa\u3c/i\u3e)

A comprehensive understanding of sociality in wildlife is vital to optimizing conservation and management efforts. However, sociality is complicated, especially for widely distributed species that exhibit substantive behavioral plasticity. Invasive wild pigs (Sus scrofa), often representing hybrids of European wild boar and domestic pigs, are among the most adaptable and widely distributed large mammals. The social structure of wild pigs is believed to be similar to European wild boar, consisting of matriarchal groups (sounders) and solitary males. However, wild pig social structure is understudied and largely limited to visual observations. Using a hierarchical approach, we incorporated genomic tools to describe wild pig social group composition in two disparate ecoregions within their invaded range in North America. The most common social unit was sounders, which are characterized as the association of two or more breeding-aged wild pigs with or without dependent offspring. In addition to sounders, pseudo-solitary females and male-dominated bachelor groups were observed at a greater frequency than previously reported. Though primarily composed of close female kin, some sounders included unrelated females. Bachelor groups were predominantly composed of young, dispersal-aged males and almost always included only close kin. Collectively, our study suggests social organization of wild pigs in their invaded range is similar to that observed among wild boar but is complex, dynamic, and likely variable across invaded habitats

Structural Plasticity of the Semliki Forest Virus Glycome upon Interspecies Transmission

Cross-species viral transmission subjects parent and progeny alphaviruses to differential post-translational processing of viral envelope glycoproteins. Alphavirus biogenesis has been extensively studied, and the Semliki Forest virus E1 and E2 glycoproteins have been shown to exhibit differing degrees of processing of N-linked glycans. However the composition of these glycans, including that arising from different host cells, has not been determined. Here we determined the chemical composition of the glycans from the prototypic alphavirus, Semliki Forest virus, propagated in both arthropod and rodent cell lines, by using ion-mobility mass spectrometry and collision-induced dissociation analysis. We observe that both the membrane-proximal E1 fusion glycoprotein and the protruding E2 attachment glycoprotein display heterogeneous glycosylation that contains N-linked glycans exhibiting both limited and extensive processing. However, E1 contained predominantly highly processed glycans dependent on the host cell, with rodent and mosquito-derived E1 exhibiting complex-type and paucimannose-type glycosylation, respectively. In contrast, the protruding E2 attachment glycoprotein primarily contained conserved under-processed oligomannose-type structures when produced in both rodent and mosquito cell lines. It is likely that glycan processing of E2 is structurally restricted by steric-hindrance imposed by local viral protein structure. This contrasts E1, which presents glycans characteristic of the host cell and is accessible to enzymes. We integrated our findings with previous cryo-electron microscopy and crystallographic analyses to produce a detailed model of the glycosylated mature virion surface. Taken together, these data reveal the degree to which virally encoded protein structure and cellular processing enzymes shape the virion glycome during interspecies transmission of Semliki Forest virus

Hyporheic Exchange and Water Chemistry of Two Arctic Tundra Streams of Contrasting Geomorphology

The North Slope of Alaska’s Brooks Range is underlain by continuous permafrost, but an active layer of thawed sediments develops at the tundra surface and beneath streambeds during the summer, facilitating hyporheic exchange. Our goal was to understand how active layer extent and stream geomorphology influence hyporheic exchange and nutrient chemistry. We studied two arctic tundra streams of contrasting geomorphology: a high-gradient, alluvial stream with riffle-pool sequences and a low-gradient, peat-bottomed stream with large deep pools connected by deep runs. Hyporheic exchange occurred to ~50 cm beneath the alluvial streambed and to only ~15 cm beneath the peat streambed. The thaw bulb was deeper than the hyporheic exchange zone in both stream types. The hyporheic zone was a net source of ammonium and soluble reactive phosphorus in both stream types. The hyporheic zone was a net source of nitrate in the alluvial stream, but a net nitrate sink in the peat stream. The mass flux of nutrients regenerated from the hyporheic zones in these two streams was a small portion of the surface water mass flux. Although small, hyporheic sources of regenerated nutrients help maintain the in-stream nutrient balance. If future warming in the arctic increases the depth of the thaw bulb, it may not increase the vertical extent of hyporheic exchange. The greater impacts on annual contributions of hyporheic regeneration are likely to be due to longer thawed seasons, increased sediment temperatures or changes in geomorphology

Influence of Morphology and Permafrost Dynamics on Hyporheic Exchange in Arctic Headwater Streams under Warming Climate Conditions

We investigated surface-subsurface (hyporheic) exchange in two morphologically distinct arctic headwater streams experiencing warming (thawing) sub-channel conditions. Empirically parameterized and calibrated groundwater flow models were used to assess the influence of sub-channel thaw on hyporheic exchange. Average thaw depths were at least two-fold greater under the higher-energy, alluvial stream than under the lowenergy, peat-lined stream. Alluvial hyporheic exchange had shorter residence times and longer flowpaths that occurred across greater portions of the thawed sediments. For both reaches, the morphologic (longitudinal bed topography) and hydraulic conditions (surface and groundwater flow properties) set the potential for hyporheic flow. Simulations of deeper thaw, as predicted under a warming arctic climate, only influence hyporheic exchange until a threshold depth. This depth is primarily determined by the hydraulic head gradients imposed by the stream morphology. Therefore, arctic hyporheic exchange extent is likely to be independent of greater sub-stream thaw depths

The use of human papillomavirus DNA methylation in cervical intraepithelial neoplasia : A systematic review and meta-analysis

Background: Methylation of viral DNA has been proposed as a novel biomarker for triage of human papillomavirus (HPV) positive women at screening. This systematic review and meta-analysis aims to assess how methylation levels change with disease severity and to determine diagnostic test accuracy (DTA) in detecting high-grade cervical intra-epithelial neoplasia (CIN). Methods: We performed searches in MEDLINE, EMBASE and CENTRAL from inception to October 2019. Studies were eligible if they explored HPV methylation levels in HPV positive women. Data were extracted in duplicate and requested from authors where necessary. Random-effects models and a bivariate mixed-effects binary regression model were applied to determine pooled effect estimates. Findings: 44 studies with 8819 high-risk HPV positive women were eligible. The pooled estimates for positive methylation rate in HPV16 L1 gene were higher for high-grade CIN (>= CIN2/high-grade squamous intra-epithelial lesion (HSIL) (95% confidence interval (95%CI:72.7% (47 8-92.2))) vs. low-grade CIN (= CIN2/HSIL vs. = CIN2/HSIL vs. Interpretation: Higher HPV methylation is associated with increased disease severity, whilst HPV16 L1/L2 genes demonstrated high diagnostic accuracy to detect high-grade CIN in HPV16 positive women. Direct clinical use is limited by the need for a multi-genotype and standardised assays. Next-generation multiplex HPV sequencing assays are under development and allow potential for rapid, automated and low-cost methylation testing. (C) 2019 The Authors. Published by Elsevier B.V.Peer reviewe

Evaluation of the Effect of Hydrated Lime on the Scavenging of Feral Swine (\u3ci\u3eSus Scrofa\u3c/i\u3e) Carcasses and Implications for Managing Carcass-Based Transmission of African Swine Fever Virus

African swine fever (ASF) is a devastating hemorrhagic disease marked by extensive morbidity and mortality in infected swine. The recent global movement of African swine fever virus (ASFV) in domestic and wild swine (Sus scrofa) populations has initiated preparedness and response planning activities within many ASF-free countries. Within the US, feral swine are of utmost concern because they are susceptible to infection, are wide-spread, and are known to interact with domestic swine populations. African swine fever virus is particularly hardy and can remain viable in contaminated carcasses for weeks to months; therefore, carcass-based transmission plays an important role in the epidemiology of ASF. Proper disposal of ASF-infected carcasses has been demonstrated to be paramount to curbing an ASF outbreak in wild boar in Europe; preparedness efforts in the US anticipate carcass management being an essential component of control if an introduction were to occur. Due to environmental conditions, geographic features, or limited personnel, immediately removing every carcass from the landscape may not be viable. Hydrated lime converts to calcium carbonate, forming a sterile crust that may be used to minimize pathogen amplification. Any disturbance by scavenging animals to the sterile crust would nullify the effect of the hydrated lime; therefore, this pilot project aimed to evaluate the behavior of scavenging animals relative to hydrated lime-covered feral swine carcasses on the landscape. At two of the three study sites, hydrated limetreated carcasses were scavenged less frequently compared to the control carcasses. Additionally, the median time to scavenging was 1 d and 6 d for control versus hydrated lime-treated carcasses, respectively. While results of this study are preliminary, hydrated lime may be used to deter carcass disruption via scavenging in the event that the carcass cannot be immediately removed from the landscape