Whale fall chemosymbiotic communities in a southwest Australian submarine canyon fill a distributional gap.

A whale fall community of chemosymbiotic invertebrates living on cetacean bones has been identified off southwestern Australia during a Remotely Operated Vehicle (ROV) survey at bathyal depths within the Bremer Marine Park, which is part of important marine mammal areas (IMMA) of the Albany Canyon Region. Cetacean bones on the seafloor of the Hood Canyon, consisted of isolated skulls of three species of beaked whales (family Ziphiidae): Mesoplodon cf. layardii, M. grayi, and M. hectori, a few vertebrae, and lower jaws. One of the beaked whale skulls (Mesoplodon cf. layardii) was sampled and found to be intensely colonised by hundreds of specimens of a bathymodilinae mussel ("Adipicola" s.l.). Live polychaetes (Phyllochaetopterus?), skeneimorph gastropods, and amphipods (Seba, Leptamphopus) colonised the skull bone, which represent a later stage (sulfophilic) of carcass decomposition. The reducing sediment below the skull was inhabited by lucinid (Lucinoma) and vesicomyid (Calyptogena) chemosymbiotic bivalves. Additionally, the sediment thanatocoenosis comprised shells of various other chemosymbiotic bivalves, such as Acharax, thyasirids, lucinids, vesicomyids, and limpets, representing the complex ecological turnover phases through time in this whale fall chemosynthetic habitat. With one exception, all bones recovered were colonized by bathymodiolin mussels. This is the first documented case of a chemosynthetic community and associated chemosymbiotic fauna relating to beaked whales, and the first fully documented record of a whale fall community within the Australian Southern Ocean region.

Differences in carbonate chemistry up-regulation of long-lived reef-building corals.

With climate projections questioning the future survival of stony corals and their dominance as tropical reef builders, it is critical to understand the adaptive capacity of corals to ongoing climate change. Biological mediation of the carbonate chemistry of the coral calcifying fluid is a fundamental component for assessing the response of corals to global threats. The Tara Pacific expedition (2016-2018) provided an opportunity to investigate calcification patterns in extant corals throughout the Pacific Ocean. Cores from colonies of the massive Porites and Diploastrea genera were collected from different environments to assess calcification parameters of long-lived reef-building corals. At the basin scale of the Pacific Ocean, we show that both genera systematically up-regulate their calcifying fluid pH and dissolved inorganic carbon to achieve efficient skeletal precipitation. However, while Porites corals increase the aragonite saturation state of the calcifying fluid (Ωcf) at higher temperatures to enhance their calcification capacity, Diploastrea show a steady homeostatic Ωcf across the Pacific temperature gradient. Thus, the extent to which Diploastrea responds to ocean warming and/or acidification is unclear, and it deserves further attention whether this is beneficial or detrimental to future survival of this coral genus.

First assessment of anthropogenic impacts in submarine canyon systems off southwestern Australia.

We assessed the anthropogenic impacts on southwestern Australian submarine canyons by quantifying macro-litter discovered during Remotely Operated Vehicle surveys. The study area encompasses the Bremer canyon systems and Perth Canyon. The categories of macro-litter identified by our study are plastic, metal, aluminium, glass, fabric, mixed, derelict fishing gear, and unclassified. The anthropogenic impacts in the canyons explored is minimal, especially in the Bremer canyon systems, whereas Perth Canyon has comparatively more macro-litter, presumably due to intense maritime traffic and nearby urban development. On a global scale, however, the environmental status of southwestern Australian canyons is relatively pristine. This analysis provides a baseline for the monitoring and enduring stewardship of these habitats where lush and diverse biota, including deep-sea corals, thrive.

A tri-modal tissue-equivalent anthropomorphic phantom for PET, CT and multi-parametric MRI radiomics.

PURPOSE: Radiomics has emerged as an advanced image processing methodology to define quantitative imaging biomarkers for prognosis and prediction of treatment response and outcome. The development of quantitative imaging biomarkers requires careful analysis to define their accuracy, stability and reproducibility through phantom measurements. Few efforts were devoted to develop realistic anthropomorphic phantoms. In this work, we developed a multimodality image phantom suitable for PET, CT and multiparametric MRI imaging. METHODS: A tissue-equivalent gel-based mixture was designed and tested for compatibility with different imaging modalities. Calibration measurements allowed to assess gel composition to simulate PET, CT and MRI contrasts of oncological lesions. The characterized gel mixture was used to create realistic synthetic lesions (e.g. lesions with irregular shape and non-uniform image contrast), to be inserted in a standard anthropomorphic phantom. In order to show phantom usefulness, issues related to accuracy, stability and reproducibility of radiomic biomarkers were addressed as proofs-of-concept. RESULTS: The procedure for gel preparation was straightforward and the characterized gel mixture allowed to mime simultaneously oncological lesion contrast in CT, PET and MRI imaging. Proofs-of-concept studies suggested that phantom measurements can be customized for specific clinical situations and radiomic protocols. CONCLUSIONS: We developed a strategy to manufacture an anthropomorphic, tissue-equivalent, multimodal phantom to be customized on specific radiomics protocols, for addressing specific methodological issues both in mono and multicentric studies.

Plutonium in coral archives: A good primary marker for an Anthropocene type section.

While we officially live in the Holocene epoch, global warming and many other impacts of global change have led to the proposal and wide adoption of the Anthropocene to define the present geological epoch. The Anthropocene Working Group (AWG) established that it should be treated as a formal stratigraphic unit, demonstrated by a reference level commonly known as "golden spike", still under discussion. Here we show that the onset of bomb-derived plutonium recorded in two banded massive corals from the Caribbean Sea is consistent (1955-1956 CE), so sites far from nuclear testing grounds are potentially suitable to host a type section of the Anthropocene. Coastal coral demonstration sites are feasible, could foster economic development, and may serve as focal points for scientific dissemination and environmental education.

Human respiratory viruses, including SARS-CoV-2, circulating in the winter season 2019-2020 in Parma, Northern Italy.

OBJECTIVES: The aim of this study was to determine the prevalence of respiratory virus infections, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), during the winter period December 2019 to March 2020, via a tertiary care hospital-based survey in Parma, Northern Italy. METHODS: A total of 906 biological samples from the respiratory tract were analysed by both conventional assays (including culture) and molecular assays targeting nucleic acids of SARS-CoV-2 and other respiratory viruses. RESULTS: Overall, 474 samples (52.3%) were positive for at least one virus, with a total of 583 viruses detected. Single infections were detected in 380 (80.2%) samples and mixed infections were detected in 94 (19.8%). Respiratory syncytial virus (138/583, 23.7%) and rhinovirus (130/583, 22.3%) were the most commonly identified viruses, followed by SARS-CoV-2 (82/583, 14.1%). Respiratory syncytial virus predominated until February, with 129 detections; it then decreased drastically in March to only nine detections. SARS-CoV-2 was absent in the study area until February 26, 2020 and then reached 82 detections in just over a month. SARS-CoV-2 was found in mixed infections in only three cases, all observed in children younger than 1 year old. CONCLUSIONS: This study showed a completely different trend between SARS-CoV-2 and the 'common' respiratory viruses: the common viruses mostly affected children, without any distinction according to sex, while SARS-CoV-2 mostly affected adult males.

SARS-CoV-2 infection diagnosed only by cell culture isolation before the local outbreak in an Italian seven-week-old suckling baby.

SARS-CoV-2 emerged in China in December 2019 and has now been declared a pandemic by the World Health Organization. This paper described the case of a 7-week-old suckling baby from Italy who was SARS-CoV-2-positive only by the cell culture method, with no clinical suspicion of and/or risk factors for SARS-CoV-2 infection. The baby was referred to hospital, with signs and symptoms of upper respiratory tract infection, before the virus had spread to the province. Nasal and pharyngeal swabs and a nasopharyngeal aspirate were used for conventional and molecular diagnostic assays not including the SARS-CoV-2 virus. Bacteria referred to the resident population were revealed in nasal and pharyngeal swabs. No viruses were detected using both immunofluorescence assay and nucleic acid amplification assays in the nasopharyngeal aspirate. The baby was discharged in good condition after 3 days of hospitalisation. Later, a cytopathic effect on the cell monolayers currently used for respiratory viruses was observed and the viral particles were identified as Coronaviridae by transmission electron microscopy. SARS-CoV-2 was identified by RT-PCR performed both on cell culture and on the stored aliquot of the original sample. The virus isolate was named SARS-Cov-2/human/Parma/1/2020. Cell culture still remains the only reference diagnostic method also for emerging viruses, allowing it to reveal cytopathogenic viruses and demonstrate their infectivity.

A unique and threatened deep water coral-bivalve biotope new to the Mediterranean Sea offshore the Naples megalopolis.

The Gulf of Naples is an example of the most beautiful and biodiverse marine regions of the Mediterranean Sea and of the most impacted areas in terms of industrial activities, large contaminated areas, resource exploitation, infrastructures at sea and maritime transportation. We conducted Remotely Operated Vehicle surveys in the Dohrn Canyon in the Tyrrhenian Sea at approximately 12 NM off Naples metropolitan area, and revealed a hotspot of deep-sea benthic biodiversity of sessile fauna at ca. 400 m depth. The hard bottoms are characterized by a high abundance of charismatic species, such as the habitat forming cold-water corals (CWC) Madrepora oculata, Lophelia pertusa, Desmophyllum dianthus in association with the large size bivalves Acesta excavata and Neopycnodonte zibrowii. This CWC-bivalve co-occurrence represents a novel biotope for the Mediterranean Sea, which coexists with the evidence of severe anthropogenic threats, such as illegal dumping and fishery malpractices that were visually documented during the survey. We recommend the adoption of specific protection measures to preserve these unique deep-sea assemblages showing the uncommon co-existence of such a number of deep-sea species in a single habitat.

Uncertainty and variability of extension rate, density and calcification rate of a hermatypic coral (Orbicella faveolata).

Skeleton growth variables of hermatypic corals, such as extension rate, density and calcification rate, are widely used to study coral response to environmental stressors, establish chronological age models and reconstruct the evolution of key climate variables. In this work, we addressed methodological aspects of the measurement of coral growth variables and the implications of their variability. A core of Orbicella faveolata was collected from the Puerto Morelos coral reef, in the Mexican Caribbean, and we measured and analysed 10 parallel transects of a core slab, covering 30 years. Density calibration was performed by measuring a high-quality and well-characterised wedge of Tridacna maxima, and the interval of interest was adjusted to the measured coral optical densities. The measurement uncertainties of extension rate, density and calcification rate were 0.011%, 1.1% and 1.6%, respectively. However, for density and calcification rate, overall variability was 29% and 33%, respectively, of which about half was attributed to intra-band growth variability. The intra-band variability of extension rate was only 0.68%, indicating the suitability of extension rate as a precise environmental proxy. These results likely differ by coral species, environments and experimental conditions, such as the exact location of the core within the colony and the method used to determine density. Uncertainties of coral growth variables should be carefully considered when reconstructing past environmental conditions.

Contribution of the FilmArray® Gastrointestinal Panel in the laboratory diagnosis of gastroenteritis in a cohort of children: a two-year prospective study.

This study represents a 2-year picture of the epidemiology of enteric pathogens in children suffering from gastroenteritis using the FilmArray® Gastrointestinal Panel (FA-GP), a multiplex molecular assay that allows to simultaneously detect a large panel of pathogens independently of the etiological suspicion and to evaluate its potential contribution to the diagnosis compared to the conventional methods. A total of 1716 stool samples, collected from children with clinical suspicion of bacterial and/or viral gastroenteritis attending the University Hospital of Parma, was submitted to the FA-GP and, when an adequate aliquot was available, to electron microscopy (n = 1163) for virus detection and to an enterovirus-targeting real-time PCR (n = 1703). Specimens with positive results for Salmonella, Yersinia enterocolitica, Vibrio, diarrheagenic Escherichia coli/Shigella, Campylobacter, Plesiomonas shigelloides and/or parasites by the FA-GP were also submitted to conventional diagnostic methods. The FA-GP gave positive results in 958 (55.8%) cases, 64.8% from inpatients: 647 (67.5%) contained a single agent and 311 (32.5%) multiple agents, for a total of 1374 pathogens. Enteropathogenic E. coli, rotavirus, norovirus, toxigenic Clostridioides difficile, and sapovirus were the most commonly detected pathogens. A total of 812 additional agents (344 of which as single pathogen) was detected by the FA-GP and not included in the clinical suspicion. The overall recovery rate of the conventional methods from stools that resulted positive by the FA-GP was 38.6% for bacteria, 50% and 84.2% for Giardia intestinalis and Cryptosporidium, respectively, and ranged from 3.7% to 64.6% for viruses, if excluding all electron microscopy-negative astroviruses. Enterovirus, an agent not targeted by the FA-GP, was revealed in 9.6% (164/1703) of the examined samples, and in 52 cases it was the only agent detected. The results of this study allowed to extend the range of detectable pathogens independently of the clinical suspicion, to detect co-infections in almost one third of children positive for at least one agent and to show that conventional methods would have missed more than half of the enteric agents detected by the FA-GP.

Paleochannel and beach-bar palimpsest topography as initial substrate for coralligenous buildups offshore Venice, Italy.

We provide a model for the genesis of Holocene coralligenous buildups occurring in the northwestern Adriatic Sea offshore Venice at 17-24 m depth. High-resolution geophysical surveys and underwater SCUBA diving reconnaissance revealed meandering shaped morphologies underneath bio-concretionned rocky buildups. These morphologies are inferred to have been inherited from Pleistocene fluvial systems reactivated as tidal channels during the post- Last Glacial Maximum transgression, when the study area was a lagoon protected by a sandy barrier. The lithification of the sandy fossil channel-levee systems is estimated to have occurred at ca. 7 cal. ka BP, likely due to the interaction between marine and less saline fluids related to onshore freshwater discharge at sea through a sealed water-table. The carbonate-cemented sandy layers served as nucleus for subsequent coralligenous buildups growth.

Calcification is not the Achilles' heel of cold-water corals in an acidifying ocean.

Ocean acidification is thought to be a major threat to coral reefs: laboratory evidence and CO2 seep research has shown adverse effects on many coral species, although a few are resilient. There are concerns that cold-water corals are even more vulnerable as they live in areas where aragonite saturation (Ωara ) is lower than in the tropics and is falling rapidly due to CO2 emissions. Here, we provide laboratory evidence that net (gross calcification minus dissolution) and gross calcification rates of three common cold-water corals, Caryophyllia smithii, Dendrophyllia cornigera, and Desmophyllum dianthus, are not affected by pCO2 levels expected for 2100 (pCO2  1058 µatm, Ωara 1.29), and nor are the rates of skeletal dissolution in D. dianthus. We transplanted D. dianthus to 350 m depth (pHT 8.02; pCO2  448 µatm, Ωara 2.58) and to a 3 m depth CO2 seep in oligotrophic waters (pHT 7.35; pCO2  2879 µatm, Ωara 0.76) and found that the transplants calcified at the same rates regardless of the pCO2 confirming their resilience to acidification, but at significantly lower rates than corals that were fed in aquaria. Our combination of field and laboratory evidence suggests that ocean acidification will not disrupt cold-water coral calcification although falling aragonite levels may affect other organismal physiological and/or reef community processes.

Prevalence and antimicrobial susceptibility of Ureaplasma urealyticum and Mycoplasma hominis in a population of Italian and immigrant outpatients.

Ureaplasma urealyticum and Mycoplasma hominis are associated with non-gonococcal urethritis, increased risk of recurrent miscarriage, infertility and pelvic inflammatory disease. Migration flows from other countries change the local epidemiological profile of infectious diseases of patients treated by general practitioners and hospital doctors. Few studies have evaluated this ever-changing issue in the Italian population. The aim of this study was to assess possible differences in prevalence and antimicrobial susceptibility of U. urealyticum and M. hominis in a population of 433 Italian and immigrant outpatients by means of the commercially available MYCOFAST(®) Screening EvolutioN 3 Kit. Prevalence of positive samples was 44.5% in Italian patients and 53.4% in immigrants. Samples positive for U. urealyticum and total isolates were more frequent in African patients: U. urealyticum, 51.5% vs 33.3%; Yates-corrected chi-square=3.98; p=0.046; total isolates, 54.5% vs 34.3%; Yates-corrected chi-square=4.45; p=0.035. Among samples positive for U. urealyticum, 66.4% were resistant to ciprofloxacin, whereas 27.6% to ofloxacin. In M. hominis isolates, 66.7% were resistant to both azythromycin and roxythromycin. Our study showed how prevalence of genital mycoplasmas and antibiotic resistance profiles change in relation to the country of origin. Therefore, surveillance is critical for the early cure and prevention of the occurrence of resistant strains.

Diagnostic performance of a multiple real-time PCR assay in patients with suspected sepsis hospitalized in an internal medicine ward.

Early identification of causative pathogen in sepsis patients is pivotal to improve clinical outcome. SeptiFast (SF), a commercially available system for molecular diagnosis of sepsis based on PCR, has been mostly used in patients hospitalized in hematology and intensive care units. We evaluated the diagnostic accuracy and clinical usefulness of SF, compared to blood culture (BC), in 391 patients with suspected sepsis, hospitalized in a department of internal medicine. A causative pathogen was identified in 85 patients (22%). Sixty pathogens were detected by SF and 57 by BC. No significant differences were found between the two methods in the rates of pathogen detection (P = 0.74), even after excluding 9 pathogens which were isolated by BC and were not included in the SF master list (P = 0.096). The combination of SF and BC significantly improved the diagnostic yield in comparison to BC alone (P < 0.001). Compared to BC, SF showed a significantly lower contamination rate (0 versus 19 cases; P < 0.001) with a higher specificity for pathogen identification (1.00, 95% confidence interval [CI] of 0.99 to 1.00, versus 0.94, 95% CI of 0.90 to 0.96; P = 0.005) and a higher positive predictive value (1.00, 95% CI of 1.00 to 0.92%, versus 0.75, 95% CI of 0.63 to 0.83; P = 0.005). In the subgroup of patients (n = 191) who had been receiving antibiotic treatment for ≥24 h, SF identified more pathogens (16 versus 6; P = 0.049) compared to BC. These results suggest that, in patients with suspected sepsis, hospitalized in an internal medicine ward, SF could be a highly valuable adjunct to conventional BC, particularly in patients under antibiotic treatment.

Comparison of conventional culture with SeptiFast real-time PCR for microbial pathogen detection in clinical specimens other than blood.

Early detection of aetiological agents is pivotal for adequate therapy for bacterial infections. Although culture is still considered the mainstay for laboratory diagnosis, it often lacks sensitivity, especially in patients already treated with antibiotics. The present study investigated the potential clinical utility of the commercial real-time-PCR-based system SeptiFast (SF), originally intended for diagnosis of sepsis from blood specimens, in the aetiological diagnosis of other bacterial infections, in patients undergoing antibiotic therapy. A total of 53 non-blood specimens were analysed for microbial pathogen detection by conventional culture and with SF real-time PCR: 19 (35.8%) synovial fluids, 9 (17.0%) cardiac valve tissues and 25 (47.2%) purulent exudates from various body sites. Overall, the number of specimens positive for a pathogen by SF (26/53; 49.1%) was significantly greater (P=0.001) than that of specimens positive by culture (10/53; 18.9%). In particular, SF was superior to culture for pathogen detection in cardiac valve tissues and synovial fluids. The analysis of concordance showed a fair agreement between the two methods (kappa value=0.314; 95% confidence interval=0.531-0.097). Even with the limitation of the low number of specimens, this study confirmed the great potential of diagnosing bacterial infections by a molecular approach, and indicates that the real-time PCR SF system can be used for specimens other than blood, from patients undergoing antibiotic treatment.

Phosphorus in cold-water corals as a proxy for seawater nutrient chemistry.

Phosphorus is a key macronutrient being strongly enriched in the deep ocean as a result of continuous export and remineralization of biomass from primary production. We show that phosphorus incorporated within the skeletons of the cosmopolitan cold-water coral Desmophyllum dianthus is directly proportional to the ambient seawater phosphorus concentration and thus may serve as a paleo-oceanographic proxy for variations in ocean productivity as well as changes in the residence times and sources of deep-water masses. The application of this tool to fossil specimens from the Mediterranean reveals phosphorus-enriched bottom waters at the end of the Younger Dryas period.