Comparison of two culture techniques used to detect environmental contamination with Salmonella enterica in a large-animal hospital

Salmonellosis is a common healthcare-associated infection in large-animal hospitals, and surveillance for Salmonella is an integral part of comprehensive infection control programmes in populations at risk. The present study compares the effectiveness of two culture techniques for recovery of Salmonella from environmental samples obtained in a large-animal referral veterinary hospital during a Salmonella outbreak. Environmental samples were collected using household cleaning cloths that were incubated overnight in buffered peptone water (BPW). Aliquots of BPW were then processed using two different selective enrichment and culture techniques. In the first technique (TBG-RV-XLT4) samples were incubated at 43 °C in tetrathionate broth and then Rappaport-Vassiliadis broth before plating on XLT4 agar. The second technique (SEL-XLD) involved incubation at 37 °C in selenite broth before plating on XLD agar. Salmonella was recovered from 49.7% (73/147) of samples using the TBG-RV-XLT4 technique, but only 10.2% (15/147) of samples using the SEL-XLD method. Fourteen samples (9.5%) were culture-positive using both methods, and 73 (49.7%) were culture-negative using both techniques. There were discordant results for 60 samples, including 59 that were only culture-positive using the TBG-RV-XLT4 method, and one sample that was only culturepositive using the SEL-XLD method. Salmonella was much more likely to be recovered using the TBG-RV-XLT4 method, and there appeared to be five times more false-negative results using the SEL-XLD technique. Environmental contamination with Salmonella may be underestimated by certain culture techniques, which may impair efforts to control spread in veterinary hospitals

Shoreline Management Plan with Habitat Enhancement for Town of Saxis, Virginia

The goal of the present study is to identify the best course of action to manage shoreline erosion in Saxis and to provide a detailed Shoreline Management Plan with Habitat Enhancement which can be presented to potential State and Federal funding agencies. While the Plan itself will not resolve the erosion conditions in Saxis, it will allow the Town to market its need and the method of resolution of this need, to agencies and leaders with the resources to implement the Plan’s suggested actions. The shoreline management plan will provide the necessary level of shoreline stabilization while minimizing adverse impacts to estuarine habitat and providing maximum habitat enhancement opportunities. The habitats needed to fulfill the life history requirements of target species desirable for Saxis Island were emphasized in the Plan. The Plan also will present opportunities to enhance local fisheries and provide increased opportunities in eco-tourism

Site 1220

Site 1220 (10°10.600´N, 142°45.503´W; 5218 meters below sea level (mbsl); Fig. F1) forms a southerly component of the 56-Ma transect drilled during Leg 199. It is situated about midway between the Clipperton and Clarion Fracture Zones in typical abyssal hill topography. On the basis of regional magnetic anomalies, we anticipated basement age at Site 1220 to be equivalent to Chron C25n (~56 Ma; Cande et al., 1989), slightly older than at Site 1219. At the outset of drilling at Site 1220, our estimate for total sediment depth was ~225 meters below seafloor (mbsf) (Fig. F2). Based upon a fixed hotspot model (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles), Site 1220 should have been located ~3° south of the equator at 56 Ma and in an equatorial position at 40 Ma. Thus, Site 1220 should have been situated underneath the South Equatorial Current in the early Eocene. A nearby piston core (EW9709-13PC) taken during the site survey cruise recovered >16 m of red clay, with the base of the core dated as middle-early Miocene on the basis of radiolarian biostratigraphy (Lyle, 2000). Site 1220 will be used to study equatorial ocean circulation from the late Paleocene through the late Eocene during the early Cenozoic thermal maximum. Sediment records from this site will help to define the calcite compensation depth (CCD) and lysocline during the Paleocene-Eocene and Eocene-Oligocene transitions. In this and other respects, Site 1220 will act as an interesting analog to Site 1218. Both sites are thought to have been located on the equator at ~40 Ma, but the older crustal age anticipated at Site 1220 dictates a greater paleowater depth than for contemporaneous sediments accumulating at Site 1218

Site 1216

Site 1216 (21°27.16´N, 139°28.79´W; 5152 meters below sea level [mbsl]; Fig. F1) is situated in abyssal hill topography south of the Molokai Fracture Zone and two small associated unnamed parasitic fracture zones (Fig. F2). Based on magnetic lineations, Site 1216 appears to be situated on normal ocean crust formed during the C25r magnetic anomaly (~57 Ma; Atwater and Severinghaus, 1989). Site 1216 was chosen for drilling because it is near the thickest section of lower Eocene sediments along the 56-Ma transect, which was based upon the seismic stratigraphy of seismic reflection data acquired on site survey cruise EW9709 during transits between the proposed drill sites (Lyle et al., this volume; Moore et al., 2002). The Cenozoic history of sedimentation in this region was poorly constrained prior to Leg 199, being largely based on two Deep Sea Drilling Project (DSDP) drill sites (40 and 41) and piston core data (EW9709-3PC) from ~1.5° in latitude to the south. Based on data from these drill sites, we expected the sedimentary sequence at Site 1216 to comprise red clays (a mixture of wind-blown dust and authigenic precipitates) overlying a biogenic sediment section composed of an upper middle Eocene radiolarian ooze and lower carbonate ooze deposited when the site was near the ridge crest in the late Paleocene and early Eocene. The broad paleoceanographic objectives of drilling the sedimentary sequence anticipated at Site 1216 are as follows: (1) to help define the shift in the Intertropical Convergence Zone through the Paleogene by following the change in eolian-dust composition and flux through time (red clays) and (2) to help define the latitudinal extent, composition, and mass accumulation of plankton communities in the north equatorial Pacific region thereby constraining ocean circulation patterns and the extent of the equatorial high-productivity belt in the Eocene ocean. Results from Site 1216 will also provide important information to test whether there was significant motion of the Hawaiian hotspot with respect to the Earth's spin axis during the early Cenozoic. At 56 Ma, the backtracked location of Site 1216 based upon a hotspot reference frame (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles) is about 9°N, 108°W. If significant hotspot motion or true polar wander occurred since 57 Ma (Petronotis et al., 1994), this drill site could have been much nearer to the equator

Site 1222

Site 1222 (13°48.98´N, 143°53.35´W; 4989 meters below sea level [mbsl]; Fig. F1) forms a south-central component of the 56-Ma transect drilled during Leg 199 and is situated ~2° south of the Clarion Fracture Zone in typical abyssal hill topography. On the basis of regional magnetic anomalies, we anticipated basement age at Site 1222 to be equivalent to Chron C25r or Chron C25n (~56-57 Ma) (Cande et al., 1989), which is slightly older than at Site 1219. At the outset of drilling at Site 1222, our estimate for total sediment thickness was ~115 m (Fig. F2). Based upon a fixed hotspot model (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles) Site 1222 should have been located ~1° north of the equator at 56 Ma and ~4°N at 40 Ma. A nearby gravity core (EW9709-17GC), taken during the site survey cruise, recovered >5 m of red clay with a late-middle Miocene age on the basis of radiolarian biostratigraphy (Lyle, 2000). Deep Sea Drilling Project (DSDP) Site 42 located ~4° east of Site 1222, was not drilled to basement but contains a thin sedimentary section (~100 m thick) of upper Oligocene nannofossil ooze through middle Eocene radiolarian nannofossil ooze. In turn, DSDP Site 162 lies ~1° north of DSDP Site 42 and is situated on young crust (49 Ma) that contains ~150 m of clayey radiolarian and nannofossil oozes of early Oligocene-middle Eocene age. Site 1222 will be used to study the position of the Intertropical Convergence Zone in the late Eocene and Oligocene, to sample late Paleocene and early Eocene sediments in the central tropical Pacific Ocean, and to help determine whether or not there has been significant southward movement of the hotspots with respect to the spin axis prior to 40 Ma

Site 1217

Site 1217 (16°52.02´N, 138°06.00´W; 5342 meters below sea level [mbsl]; Fig. F1) is one of seven sites drilled to target upper Paleocene crust along a latitudinal transect during Leg 199 and will be used to investigate paleoceanographic processes in the northern tropical early Eocene Pacific Ocean. Site 1217 is situated ~1° north of the Clarion Fracture Zone on abyssal hill topography typical of the central Pacific. Based on magnetic lineations, basement age at Site 1217 should be in magnetic Anomaly C25r or ~57 Ma (Cande et al., 1989; timescale of Cande and Kent, 1995). The Cenozoic history of sedimentation in this region was poorly constrained prior to Leg 199 drilling because the nearest drill site (Deep Sea Drilling Project [DSDP] Site 162) is situated ~300 km south and west on 48-Ma crust. Based on data from this early rotary-cored hole, magnetic anomaly maps, a shallow-penetration piston core near Site 1217 (EW9709-4PC), and seismic profiling (Fig. F2), we expected the sedimentary sequence at Site 1217 to comprise a relatively thick (25 to 35 m thick) section of red clays overlying a radiolarian ooze and a basal carbonate section with possible chert near basement (estimated total depth ~125-150 meters below seafloor [mbsf]) deposited when the site was near the ridge crest in the late Paleocene and early Eocene. Site 1217 was chosen because it is anticipated to have been located just outside of the equatorial region at 56 Ma, ~5°N, 106°W based upon a fixed hotspot model (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles). On the same basis at 40 Ma, the site was located at ~8°N, 111°W. Thus, Site 1217 should help define the paleoceanography of the northern tropical Pacific, in particular locating the ancient North Equatorial Countercurrent (NECC) region. General circulation-model experiments for the early Eocene (see Huber, this volume) suggest that the NECC was a well-developed current during this time period. Other paleoceanographic and paleoclimatic objectives of drilling the sedimentary sequence anticipated at Site 1217 are as follows: (1) to help define the shift in the Intertropical Convergence Zone through the Paleogene by following the change in eolian dust composition and flux through time (red clays); (2) to help constrain the middle-late Eocene calcite compensation depth (CCD); and (3) to sample the Paleocene/Eocene (P/E) boundary, one of the most climatologically critical intervals of Cenozoic time. Recovery of deep-sea sediments from this time interval during Leg 199 is a high priority because the P/E boundary has never before been sampled in the central tropical Pacific Ocean. Results from Site 1217 will also provide important information to test whether there was significant motion of the Hawaiian hotspot, with respect to the Earth's spin axis during the early Cenozoic. At 56 Ma, the backtracked location based upon a hotspot reference frame is ~5°N, 106°W, and at 40 Ma is ~8°N, 106°W. If significant hotspot motion or true polar wander occurred since 57 Ma (Petronotis et al., 1994), this drill site could have been much nearer to the equator

Geochemical analysis of bulk marine sediment by Inductively Coupled Plasma–Atomic Emission Spectroscopy on board the JOIDES Resolution

Geochemical analyses on board the JOIDES Resolution have been enhanced with the addition of a Jobin-Yvon Ultrace inductively coupled plasma-atomic emission spectrometer (ICP-AES) as an upgrade from the previous X-ray fluorescence facility. During Leg 199, we sought to both challenge and utilize the capabilities of the ICP-AES in order to provide an extensive bulk-sediment geochemical database during the cruise. These near real-time analyses were then used to help characterize the recovered sedimentary sequences, calculate mass accumulation rates of the different sedimentary components, and assist with cruise and postcruise sampling requests. The general procedures, sample preparation techniques, and basic protocol for ICP-AES analyses on board ship are outlined by Murray et al. (2000) in Ocean Drilling Program Tech Note, 29. We expand on those concepts and offer suggestions for ICP-AES methodology, calibration by standard reference materials, data reduction procedures, and challenges that are specific to the analysis of bulk-sediment samples. During Leg 199, we employed an extensive bulk-sediment analytical program of ~600 samples of varying lithologies, thereby providing several opportunities for refinement of techniques. We also discuss some difficulties and challenges that were faced and suggest how to alleviate such occurrences for sedimentary chemical analyses during future legs

Using Core (mcd) to log (mbsf) depth miss-matches as a basis for interpreting core elastic rebound and re-calculating core physical properties. Results from ODP Leg 199 (abstract of paper presented at AGU Fall Meeting, San Francisco, 6-10 Dec 2002)

Leg 199 drilled a series of sites in the equatorial Pacific in order to investigate the paleoceanography of the Paleogene Pacific Ocean. The two deepest cored sites, (1218 and 1219) have provided continuous/near continuous spliced sedimentary sections and in situ wireline log data. Comparison of core to log data sets shows the familiar non-linear, increasing with depth, miss-match between the core (metres composite depth - mcd) and log (mbsf) depths and concomitant offset between core and log physical property data sets e.g. porosity, density, velocity. The depth miss-matches represent core expansion due to elastic rebound experienced by the sediments upon unloading i.e. removal of overburden stress, which is a function of the sediment void ratio and log of the effective in situ stress. The increasing depth offset observed between the 1218 core and log data is used to calculate an expansion index (C$_{r}$) for continuous discrete measurement intervals, down the core. The C$_{r}$ values are used to re-compress the core (mcd) depth scale and as expected provide a good match with the log (mbsf) depths. The C$_{r}$ values are also used to correct the core index property data, to in situ values. The quality of the corrected core index property data is good when compared with the in situ measured log data. C$_{r}$ values are dependent upon the sediment composition (especially the quantity of clay) and core light absorption spectroscopy (LAS) data collected on Leg 199, provides a continuous down-core record of sediment composition, in terms of the percent clay, carbonate and opal. A relationship between the C$_{r}$ values and the sediment LAS composition is established and is then applied to the Site 1219 core LAS data, allowing appropriate C$_{r}$ values to be assigned to continuous, discrete core intervals. These composition based C$_{r}$ values are then used to re-calculate the core (mcd) depths and correct the index property data to in situ values. The quality of the depth and index property corrections are checked by comparison with the in situ measured log data, and provide encouraging results

Whole-genome sequencing reveals host factors underlying critical COVID-19

Critical COVID-19 is caused by immune-mediated inflammatory lung injury. Host genetic variation influences the development of illness requiring critical care1 or hospitalization2,3,4 after infection with SARS-CoV-2. The GenOMICC (Genetics of Mortality in Critical Care) study enables the comparison of genomes from individuals who are critically ill with those of population controls to find underlying disease mechanisms. Here we use whole-genome sequencing in 7,491 critically ill individuals compared with 48,400 controls to discover and replicate 23 independent variants that significantly predispose to critical COVID-19. We identify 16 new independent associations, including variants within genes that are involved in interferon signalling (IL10RB and PLSCR1), leucocyte differentiation (BCL11A) and blood-type antigen secretor status (FUT2). Using transcriptome-wide association and colocalization to infer the effect of gene expression on disease severity, we find evidence that implicates multiple genes—including reduced expression of a membrane flippase (ATP11A), and increased expression of a mucin (MUC1)—in critical disease. Mendelian randomization provides evidence in support of causal roles for myeloid cell adhesion molecules (SELE, ICAM5 and CD209) and the coagulation factor F8, all of which are potentially druggable targets. Our results are broadly consistent with a multi-component model of COVID-19 pathophysiology, in which at least two distinct mechanisms can predispose to life-threatening disease: failure to control viral replication; or an enhanced tendency towards pulmonary inflammation and intravascular coagulation. We show that comparison between cases of critical illness and population controls is highly efficient for the detection of therapeutically relevant mechanisms of disease

Site 1215

Site 1215 (26°01.77´N, 147°55.99´W, 5396 meters below sea level [mbsl]; Fig. F1) is the northernmost of seven sites drilled on the 56-Ma-crust transect during Ocean Drilling Program (ODP) Leg 199. It will be used to investigate paleoceanographic processes in the northern subtropical early Eocene Pacific Ocean. Site 1215 is situated north of the Molokai Fracture Zone on typical abyssal hill topography in an area of thin but continuous sediment cover (Fig. F2). Based on magnetic lineations, basement age at Site 1215 should be in the youngest part of Anomaly An26R, or ~58 Ma (Cande et al., 1989; timescale of Cande and Kent, 1995). The Cenozoic history of sedimentation in this region was poorly constrained prior to Leg 199 drilling because the nearest Deep Sea Drilling Project (DSDP) or ODP drill site (DSDP Leg 5) is >1000 km away. Based on data from these early rotary coring activities (together with magnetic anomaly maps, a program of shallow-penetration piston coring, and seismic profiling), we expected the sedimentary sequence at Site 1215 to comprise red clays (a mixture of wind-blown dust and authigenic precipitates) overlying a basal carbonate section deposited when the site was near the ridge crest in the late Paleocene and early Eocene. The broad paleoceanographic objectives of drilling the sedimentary sequence anticipated at Site 1215 are as follows: (1) to help define the shift in the Intertropical Convergence Zone through the Paleogene by following the change in eolian-dust composition and flux through time (red clays); (2) to help define the North Equatorial Current and North Pacific subtropical gyre processes (basal carbonates); and (3) sampling of the Paleocene/Eocene (P/E) boundary, one of the most climatologically critical intervals of Cenozoic time. Recovery of deep-sea sediments from this time interval was a high priority because the P/E boundary has never been sampled in the central tropical Pacific Ocean. Results from Site 1215 will also provide important information to test whether there was significant motion of the Hawaiian hotspot, with respect to the Earth's spin axis, during the early Cenozoic. At 56 Ma, the backtracked location based upon a hotspot reference frame (Gripp and Gordon, 1990, for 0- to 5-Ma Pacific hotspot rotation pole; Engebretson et al., 1985, for older poles) is ~11°N, 117°W. If significant hotspot motion or true polar wander occurred since 57 Ma (Petronotis et al., 1994), this drill site could have been much closer to the equator