High-resolution correlation of coastal cliff sections in the Lagos- Portimao Formation (Lower - Middle Miocene, central Algarve, Portugal)

This paper describes a high-resolution stratigraphic correlation scheme for the early to middle Miocene Lagos-Portimão Formation of central Algarve, southern Portugal. The Lagos Portimão-Formation of central Algarve is a 60 m thick package of horizontally bedded siliciclastics and carbonates. The bryozoan and mollusc dominated biofacies is typical of a shallow marine, warm-temperate climatic environment. We define four stratigraphic marker beds based on biofacies, lithology, and gamma-ray signatures. Marker bed 1 is a reddish shell bed composed predominantly of bivalve shells in various stages of fragmentation. Marker bed 2 is a fossiliferous sandstone / sandy rudstone characterized by bryozoan masses. Marker bed 3 is also a fossiliferous sandstone with abundant larger foraminifers and foliate bryozoans. Marker bed 4 is composed of three distinct layers; two fossiliferous sandstones with an intercalated shell bed. The upper sandstone unit displays thickets of the bryozoan Celleporaria palmate associated with the coral Culizia parasitica. This stratigraphic framework allows to correlate isolated outcrops within the stratigraphic context of the Lagos-Portimão Formation and to establish high resolution chronostratigraphic Sr-isotopic dating

Low Florida Coral Calcification Rates in the Plio-Pleistocene

In geological outcrops and drill cores from reef frameworks, the skeletons of scleractinian corals are usually leached and more or less completely transformed into sparry calcite because the highly porous skeletons formed of metastable aragonite (CaCO3) undergo rapid diagenetic alteration. Upon alteration, ghost structures of the distinct annual growth bands often allow for reconstructions of annual extension ( =  growth) rates, but information on skeletal density needed for reconstructions of calcification rates is invariably lost. This report presents the bulk density, extension rates and calcification rates of fossil reef corals which underwent minor diagenetic alteration only. The corals derive from unlithified shallow water carbonates of the Florida platform (south-eastern USA), which formed during four interglacial sea level highstands dated approximately 3.2, 2.9, 1.8, and 1.2 Ma in the mid-Pliocene to early Pleistocene. With regard to the preservation, the coral skeletons display smooth growth surfaces with minor volumes of marine aragonite cement within intra-skeletal porosity. Within the skeletal structures, voids are commonly present along centres of calcification which lack secondary cements. Mean extension rates were 0.44 ± 0.19 cm yr−1(range 0.16 to 0.86 cm yr−1), mean bulk density was 0.96 ± 0.36 g cm−3 (range 0.55 to 1.83 g cm−3) and calcification rates ranged from 0.18 to 0.82 g cm−2 yr−1(mean 0.38 ± 0.16 g cm−2 yr−1), values which are 50 % of modern shallow-water reef corals. To understand the possible mechanisms behind these low calcification rates, we compared the fossil calcification rates with those of modern zooxanthellate corals (z corals) from the Western Atlantic (WA) and Indo-Pacific calibrated against sea surface temperature (SST). In the fossil data, we found a widely analogous relationship with SST in z corals from the WA, i.e. density increases and extension rate decreases with increasing SST, but over a significantly larger temperature window during the Plio-Pleistocene. With regard to the environment of coral growth, stable isotope proxy data from the fossil corals and the overall structure of the ancient shallow marine communities are consistent with a well-mixed, open marine environment similar to the present-day Florida Reef Tract, but variably affected by intermittent upwelling. Upwelling along the platform may explain low rates of reef coral calcification and inorganic cementation, but is too localised to account also for low extension rates of Pliocene z corals throughout the tropical WA region. Low aragonite saturation on a more global scale in response to rapid glacial–interglacial CO2 cyclicity is also a potential factor, but Plio-Pleistocene atmospheric pCO2 is generally believed to have been broadly similar to the present day. Heat stress related to globally high interglacial SST only episodically moderated by intermittent upwelling affecting the Florida platform seems to be another likely reason for low calcification rates. From these observations we suggest some present coral reef systems to be endangered from future ocean warming

Calcitization of aragonitic bryozoans in Cenozoic tropical carbonates from East Kalimantan, Indonesia

© The Author(s) 2016. Open Access. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The file attached is the published version of the article

Whole-genome sequencing reveals two prolonged simultaneous outbreaks involving Pseudomonas aeruginosa high-risk strains ST111 and ST235 with resistance to quaternary ammonium compounds

Objective Water-bearing systems are known as frequent Pseudomonas aeruginosa (PA) outbreak sources. However, many older buildings continue to have sanitary facilities in high-risk departments such as the ICU. We present two simultaneous prolonged multi-drug-resistant (MDR) PA outbreaks detected at the ICU of a pulmonology hospital, which were resolved by whole-genome sequencing (WGS). Methods Outbreak management and investigations were initiated in August 2019 after detecting two patients with nosocomial VIM-2-positive MDR PA. The investigations involved weekly patient screenings for four months and extensive environmental sampling for 15 months. All patient and environmental isolates were collected and analysed by WGS. Results From April to September 2019, we identified 10 patients with nosocomial MDR PA, including five VIM-2-positive strains. VIM-2-positive strains were also detected in nine sink drains, two toilets, and a cleaning bucket. WGS revealed that of 16 VIM-2-positive isolates, 14 were ST111 that carried qacE, or qacEΔ1 genes, whereas 13 isolates clustered (difference of ≤11 alleles by cgMLST). OXA-2 (two toilets), and OXA-2, OXA-74, PER-1 (two patients, three toilets) qacEΔ1-positive ST235 isolates dominated among VIM-2-negative isolates. The remaining seven PA strains were ST17, ST233, ST273, ST309 and ST446. Outbreak containment was achieved by replacing U-bends, and cleaning buckets, and switching from quaternary ammonium compounds (QUATs) to oxygen-releasing disinfectant products. Conclusion Comprehension and management of two simultaneous MDR PA outbreaks involving the high-risk strains ST111 and ST235 were facilitated by precise control due to identification of different outbreak sources per strain, and by the in-silico detection of high-level QUATs resistance in all isolates

Nanosilver/DCOIT-containing surface coating effectively and constantly reduces microbial load in emergency room surfaces

Background Colonization of near-patient surfaces in hospitals plays an important role as a source of healthcare-associated infections. Routine disinfection methods only result in short-term elimination of pathogens. Aim To investigate the efficiency of a newly developed antimicrobial coating containing nanosilver in long-term reduction of bacterial burden in hospital surfaces to close the gap between routine disinfection cycles. Methods In this prospective, double-blinded trial, frequently touched surfaces of a routinely used treatment room in an emergency unit of a level-I hospital were treated with a surface coating (nanosilver/DCOIT-coated surface, NCS) containing nanosilver particles and another organic biocidal agent (4,5-dichloro-2-octyl-4-isothiazolin-3-one, DCOIT), whereas surfaces of another room were treated with a coating missing both the nanosilver- and DCOIT-containing ingredient and served as control. Bacterial contamination of the surfaces was examined using contact plates and liquid-based swabs daily for a total trial duration of 90 days. After incubation, total microbial counts and species were assessed. Findings In a total of 2880 antimicrobial samples, a significant reduction of the overall bacterial load was observed in the NCS room (median: 0.31 cfu/cm2; interquartile range: 0.00–1.13) compared with the control coated surfaces (0.69 cfu/cm2; 0.06–2.00; P 5 cfu/cm2) by 60% (odds ratio 0.38, P < 0.001). No significant difference in species distribution was detected between NCS and control group. Conclusion Nanosilver-/DCOIT-containing surface coating has shown efficiency for sustainable reduction of bacterial load of frequently touched surfaces in a clinical setting

An epidemic CC1-MRSA-IV clone yields false-negative test results in molecular MRSA identification assays: a note of caution, Austria, Germany, Ireland, 2020

We investigated why a clinical meticillin-resistant Staphylococcus aureus (MRSA) isolate yielded false-negative results with some commercial PCR tests for MRSA detection. We found that an epidemic European CC1-MRSA-IV clone generally exhibits this behaviour. The failure of the assays was attributable to a large insertion in the orfX/SCCmec integration site. To ensure the reliability of molecular MRSA tests, it is vital to monitor emergence of new SCCmec types and junction sites

Genetic Analysis of a Novel Human Adenovirus with a Serologically Unique Hexon and a Recombinant Fiber Gene

In February of 1996 a human adenovirus (formerly known as Ad-Cor-96-487) was isolated from the stool of an AIDS patient who presented with severe chronic diarrhea. To characterize this apparently novel pathogen of potential public health significance, the complete genome of this adenovirus was sequenced to elucidate its origin. Bioinformatic and phylogenetic analyses of this genome demonstrate that this virus, heretofore referred to as HAdV-D58, contains a novel hexon gene as well as a recombinant fiber gene. In addition, serological analysis demonstrated that HAdV-D58 has a different neutralization profile than all previously characterized HAdVs. Bootscan analysis of the HAdV-D58 fiber gene strongly suggests one recombination event

Signal transduction controls heterogeneous NF-κB dynamics and target gene expression through cytokine-specific refractory states

Cells respond dynamically to pulsatile cytokine stimulation. Here we report that single, or well-spaced pulses of TNFα (>100 min apart) give a high probability of NF-κB activation. However, fewer cells respond to shorter pulse intervals (<100 min) suggesting a heterogeneous refractory state. This refractory state is established in the signal transduction network downstream of TNFR and upstream of IKK, and depends on the level of the NF-κB system negative feedback protein A20. If a second pulse within the refractory phase is IL-1β instead of TNFα, all of the cells respond. This suggests a mechanism by which two cytokines can synergistically activate an inflammatory response. Gene expression analyses show strong correlation between the cellular dynamic response and NF-κB-dependent target gene activation. These data suggest that refractory states in the NF-κB system constitute an inherent design motif of the inflammatory response and we suggest that this may avoid harmful homogenous cellular activation