Antimicrobial resistance gene shuffling and a three-element mobilisation system in the monophasic Salmonella typhimurium strain ST1030

In this study we describe the genetic elements and the antimicrobial resistance units (RUs) harboured by the Salmonella Typhimurium monophasic variant 1,4,[5],12:i:- strain ST1030. Of the three identified RUs two were chromosomal, RU1 (IS26-bla_TEM-1-IS26-strAB-sul2- IS26) and RU2 (IS26-tetR(B)-tetA(B)-ΔIS26), and one, RU3 (a sul3-associated class 1 integron with cassette array dfrA12-orfF-aadA2-cmlA1-aadA1), was embedded in a Tn21-derived element harboured by the conjugative I1 plasmid pST1030-1A. IS26 elements mediated the antimicrobial resistance gene (ARG) shuffling and this gave rise to pST1030-1A derivatives with different sets of ARGs. ST1030 also harboured two ColE1-like plasmids of which one, pST1030-2A, was mobilisable and the target of an intracellular translocation of the Tn21-derived element; the second (pST1030-3) was an orphan mob-associated oriT plasmid co-transferred with pST1030-1A and pST1030-2A. pST1030-2A and pST1030-3 also carried a parA gene and a type III restriction modification system, respectively. Overall analysis of our data reinforces the role played by IS26, Tn21-derived elements and non-conjugative plasmids in the spread of ARGs and supplies the first evidence, at least in Salmonella, for the identification of a natural isolate harbouring a three-element mobilisation system in the same cell.

Atlantic and Mediterranean populations of the widespread serpulid Ficopomatus enigmaticus: Developmental responses to carbon nanotubes

Ficopomatus enigmaticus was adopted as model species for ecotoxicological bioassay, with its larval development as endpoint. Two different populations of the same species, collected in areas far from each other (Mediterranean Sea and Atlantic Ocean), were exposed to multi-walled carbon nanotubes, a class of emerging pollutants with a constantly increasing relevance in the landscape of nanomaterials production. Moreover, a molecular analysis based on Cyt b amplification and sequencing, was carried out to confirm that both populations belong to the same species. The aim of the present work was to strengthen existing results about F. enigmaticus relevance in ecotoxicological bioassays, adding the variable of population effect. For both populations the concentration-response curve of effect at different toxicant concentrations was similar and, at certain concentrations, overlapping, confirming the ecological relevance of the assay. These results posed an interesting acceptance on the introduction of this species as model in ecotoxicological bioassay scenery, underlining the relevance of a widespread wild species to compare effects of chemicals and environmental samples over large distances using the same bioassay.

Physiological Basis of Salt Stress Tolerance in a Landrace and a Commercial Variety of Sweet Pepper (Capsicum annuum L.)

Salt stress is one of the most impactful abiotic stresses that plants must cope with. Plants’ ability to tolerate salt stress relies on multiple mechanisms, which are associated with biomass and yield reductions. Sweet pepper is a salt-sensitive crop that in Mediterranean regions can be exposed to salt build-up in the root zone due to irrigation. Understanding the physiological mechanisms that plants activate to adapt to soil salinization is essential to develop breeding programs and agricultural practices that counteract this phenomenon and ultimately minimize yield reductions. With this aim, the physiological and productive performances of Quadrato D’Asti, a common commercial sweet pepper cultivar in Italy, and Cazzone Giallo, a landrace of the Campania region (Italy), were compared under different salt stress treatments. Quadrato D’Asti had higher tolerance to salt stress when compared to Cazzone Giallo in terms of yield, which was associated with higher leaf biomass vs. fruit ratio in the former. Ion accumulation and profiling between the two genoptypes revealed that Quadrato D’Asti was more efficient at excluding chloride from green tissues, allowing the maintenance of photosystem functionality under stress. In contrast, Cazzone Giallo seemed to compartmentalize most sodium in the stem. While sodium accumulation in the stems has been shown to protect shoots from sodium toxicity, in pepper and/or in the specific experimental conditions imposed, this strategy was less efficient than chloride exclusion for salt stress tolerance.

Unexpected Predictors of Antibiotic Resistance in Housekeeping Genes of Staphylococcus Aureus

Methicillin-resistant Staphylococcus aureus (MRSA) is currently the most commonly identified antibiotic-resistant pathogen in US hospitals. Resistance to methicillin is carried by SCCmec genetic elements. Multilocus sequence typing (MLST) covers internal fragments of seven housekeeping genes of S. aureus. In conjunction with mec typing, MLST has been used to create an international nomenclature for S. aureus. MLST sequence types with a single nucleotide polymorphism (SNP) considered distinct. In this work, relationships among MLST SNPs and methicillin/oxacillin resistance or susceptibility were studied, using a public data base, by means of cross-tabulation tests, multivariable (phylogenetic) logistic regression (LR), decision trees, rule bases, and random forests (RF). Model performances were assessed through multiple cross-validation. Hierarchical clustering of SNPs was also employed to analyze mutational covariation. The number of instances with a known methicillin (oxacillin) antibiogram result was 1526 (649), where 63% (54%) was resistant to methicillin (oxacillin). In univariable analysis, several MLST SNPs were found strongly associated with antibiotic resistance/susceptibility. A RF model predicted correctly the resistance/susceptibility to methicillin and oxacillin in 75% and 63% of cases (cross-validated). Results were similar for LR. Hierarchical clustering of the aforementioned SNPs yielded a high level of covariation both within the same and different genes; this suggests strong genetic linkage between SNPs of housekeeping genes and antibiotic resistant associated genes. This finding provides a basis for rapid identification of antibiotic resistant S. arues lineages using a small number of genomic markers. The number of sites could subsequently be increased moderately to increase the sensitivity and specificity of genotypic tests for resistance that do not rely on the direct detection of the resistance marker itself.

Effects of copper on larvae of the marbled crab Pachygrapsus marmoratus (Decapoda, Grapsidae): Toxicity test and biochemical marker responses

The importance of trace elements in ecotoxicological investigations is a well-known issue when monitoring polluted areas such as commercial harbors. Copper represents one of the most common metal contaminants, often detected in these areas as it is widely employed in various fields and has many sources of inflow in the marine environment. Pachygrapsus marmoratus is a widespread intertidal crab species that has been extensively studied in ecology, ethology and population genetics. Ecotoxicological studies have also been performed, exclusively on the adult stage. In the present study we investigated the mortality and biochemical (oxidative stress and neurotoxicity) responses of P. marmoratus larvae exposure to environmental relevant concentration of copper. Results showed dose-dependent responses in terms of larval mortality, with a calculated LC₅₀ value of 0.5 mg/L of Cu²⁺. The LC₅₀ concentration was used as the starting point for subsequent biochemical response evaluation. Results also demonstrated dose-dependent activation of antioxidant systems assuming a compensatory antioxidant activity to prevent higher cellular damage when larvae were exposed to the highest concentrations of copper. Moreover, a significant enhancement of neurotransmitter activities was observed, assuming a possible direct interaction of copper with the enzymes or an increase of free copper ion aliquot into the cells.

Ficopomatus enigmaticus larval development assay: An application for toxicity assessment of marine sediments

Ficopomatus enigmaticus is a serpulid polychaete, reef-forming, dioecious gamete spawner throughout different seasons and in different salinity conditions. Due to these characteristics, its candidacy as a model organism to monitor both marine and brackish matrices was assessed. Marine sediments collected in a polluted area near the port of Ancona (Italy) were used as case study. Besides the chemical characterization of sediments, the larval development of F. enigmaticus was adopted as an assay for ecotoxicological assessment of sediments in addition to a regulatory bioassay battery with different organisms and endpoints. The quality of sediments was classified according to the Italian Ministerial Decree for sediment management (Ministerial Decree 173, 2016) by using the SEDI-QUAL-SOFT® (ver. 109.0) software developed by the Italian Environmental Protection Agency (ISPRA). The F. enigmaticus larval development assay showed a quite similar sensitivity to C. gigas larval development assays, indicating its potential use in a regulatory battery of bioassays.

Immune biomarkers of response to immune-checkpoint inhibitors in head and neck squamous cell carcinoma

Anti-programmed cell death protein 1 (PD-1) agents have become the standard of care for platinum-refractory recurrent/metastatic head and neck squamous cell carcinoma (HNSCC) and are currently being evaluated in various disease settings. However, despite the gain in overall survival seen in some of the clinical trials, the majority of patients display primary resistance and do not benefit from these agents. Taking into consideration the potentially severe immune-related toxicities and their high cost, the search for predictive biomarkers of response is crucial. Besides Programmed death ligand-1 (PD-L1) expression, other biomarkers such as immune infiltration, tumor mutational burden or immune-gene expression profiling have been explored, but none of them has been validated in this disease. Among these, the microbiota has recently garnered tremendous interest since it has proven to influence the efficacy of PD-1 blockade in some tumor types. With the accumulating evidence on the effect of the microbiota in HNSCC tumorigenesis and progression, the study of its potential role as a predictive immune biomarker is warranted. This review examines the available evidence on emerging immune predictive biomarkers of response to anti-PD-1/PD-L1 therapy in HNSCC, introducing the microbiota and its potential use as a predictive immune biomarker in this disease.

Late Quaternary environmental dynamics in Lenin Peak area (Pamir Mountains, Kyrgyzstan)

The Pamir Mountains include peaks exceeding 7000 m, such as Lenin Peak (7134 m) in the northern Zaalai Range. Here, we examine the distribution of soils and geomorphological processes and landforms in its northern slope, from the highest glaciated environments until Alai valley floor. We present the first geomorphological map of the study area as well as an accurate description the main geomorphological units in order to reconstruct landscape dynamics in the area from Quaternary cold stages until present-day. Five main units are distributed: (1) valley floor (2900-3040 m), an area that must have been ice-free during Quaternary glaciations and is currently being reshaped by glaciofluvial processes, with a large alluvial fan reworked by aeolian activity; (2) hummocky terrain (3040-3500 m) including two moraine systems left by a piedmont glacier during the Last Glaciation as well as hilly deposits originated by a catastrophic rockfall event; (3) U-shaped glacial valley (3500-3800 m), including some moraine ridges as well as a sedimentary cover composed of glacial till that is being eroded by fluvial and mass-wasting processes; (4) high mountain valleys (up to 4600-4800 m) adjacent to the main valley floor with small cirque and alpine glaciers and widespread periglacial processes in ice-free environments; (5) glaciers flowing from the Lenin Peak summit until the foot of the mountain, where they form a debris-covered (surge-type) glacier. The existence of abundant glacial, periglacial and rockfall deposits (moraines, till, erratic boulders) allows inferring five different environmental stages since the Last Glaciation. The latest glacial advances took place during the 20th century and the Little Ice Age and deposited two moraine systems near the glacial front. The occurrence of active rock glaciers and protalus lobes indicates that the limit of permafrost conditions is now located at 3400-3500 m, with seasonal frozen ground in lower areas.

Physiological, biochemical and molecular responses to water stress and rehydration in Mediterranean adapted tomato landraces

Mediterranean tomato landraces adapted to arid environments represent an option to counteract drought, and to address the complexity of responses to water deficit and recovery, which is a crucial component of plant adaptation mechanisms. We investigated physiological, biochemical and molecular responses of two Mediterranean tomato landraces, 'Locale di Salina' (Lc) and 'Pizzutello di Sciacca' (Pz) under two dehydration periods and intermediate rehydration in greenhouse pot experiments. Relationship between CO₂ assimilation (A) and stomatal conductance under severe water stress (g_s  < 0.05 mol·m^-2 ·s^-1 ) indicated the occurrence of stomatal and non-stomatal limitations of photosynthesis. Gas exchange promptly recovered within 2-3 days of rehydration. ABA and g_s showed a strict exponential relationship. Both leaf ABA and proline peaked under severe water stress. Lc showed higher accumulation of ABA and higher induction of the expression of both NCED and P5CS genes than Pz. Poly(ADP-ribose) polymerase increased during imposition of stress, mainly in Lc, and decreased under severe water stress. The two landraces hardly differed in their physiological performance. Under severe water stress, g_s showed low sensitivity to ABA, which instead controlled stomatal closure under moderate water stress (g_s  > 0.15 mol·m^-2 ·s^-1 ). The prompt recovery after rehydration of both landraces confirmed their drought-tolerant behaviour. Differences between the two landraces were instead observed at biochemical and molecular levels.

Early-drug development in the era of immuno-oncology: are we ready to face the challenges?

The classical development of drugs has progressively faded away, and we are currently in an era of seamless drug-development, where first-in-human trials include unusually big expansion cohorts in the search for early signs of activity and rapid regulatory approval. The fierce competition between different pharmaceutical companies and the hype for immune combinations obliges us to question the current way in which we are evaluating these drugs. In this review, we discuss critical issues and caveats in immunotherapy development. A particular emphasis is put on the limitations of pre-clinical toxicology studies, where both murine models and cynomolgus monkeys have underpredicted toxicity in humans. Moreover, relevant issues surrounding dose determination during phase I trials, such as dose-escalation methods or flat versus body-weight dosing, are discussed. A proposal of how to face these different challenges is offered, in order to achieve maximum efficacy with minimum toxicity for our patients.

Bloodstream infection in patients with head and neck cancer: a major challenge in the cetuximab era

PURPOSE

To assess the impact of bloodstream infection (BSI) in patients with head and neck cancer (HNC) in the cetuximab era.

METHODS

We prospectively analysed the epidemiology, microbiology and outcomes of 51 BSI episodes occurring in 48 patients with HNC (2006-2017). We performed a retrospective matched-cohort study (1:2) to determine the risk factors for BSI. Finally, we compared patients who died with those who survived to identify risk factors for mortality.

RESULTS

The most frequent HNC localization was the oropharynx (43%), and pneumonia was the most frequent source (25%). Gram-positive BSI occurred in 55% cases, mainly due to Streptococcus pneumoniae (21%), and among Gram-negatives, Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae were the most frequent. Hypoalbuminemia (OR 8.4; 95% CI, 3.5-19.9), previous chemotherapy (OR, 3.2; 95% CI, 1.3-7.4) and cetuximab therapy (OR, 2.8; 95% CI, 1.6-6.7) were significant risk factors for BSI. Patients with BSI had a higher overall case-fatality rate than patients without BSI (OR, 4.4; 95% CI, 1.7-11.8). Hypoalbuminemia was an independent risk factor for the early (7 day) and overall (30 day) case-fatalities, with ORs of 0.8 (95% CI, 0.6-0.9) and 0.8 (95% CI, 0.7-0.97), respectively. The presence of comorbidities (OR, 7; 95% CI, 1.4-34) was also an independent risk factor for overall case-fatality.

CONCLUSIONS

BSI causes high mortality in patients with HNC and is most often secondary to pneumonia. It occurs mainly among patients with hypoalbuminemia who receive treatment with cetuximab or chemotherapy. The development of BSI in patients with HNC impairs their outcome, especially in the presence of hypoalbuminemia and comorbidities.

Spatial characterization of glacial and periglacial landforms in the highlands of Sierra Nevada (Spain)

Sierra Nevada constitutes the southernmost and highest massif in the Iberian Peninsula, with elevations exceeding 3000m. Two large glacial advances were recorded during the Last Glaciation and several minor advances occurred until the Early Holocene. Since then, periglacial activity has prevailed above 2500m. Here, we present a new and more accurate geomorphological map of the highlands of Sierra Nevada, integrating in a GIS environment i) high resolution satellite imagery, ii) topographic data, and iii) field observations. This approach has allowed a better characterization of the spatial extent of cold-climate morphogenic processes and associated landforms formed during the Last Glaciation and subsequent deglaciation. Despite its extension and high altitude, the steep relief of Sierra Nevada and its southern location conditioned a significantly lower glaciated surface (104.6km²) with respect to other Iberian massifs. We have also inferred the paleoclimatic conditions of the study area through the calculation of Equilibrium Line Altitudes (ELAs). The distribution of the lowest moraines suggests an ELA for the maximum glacial extent at 2525m in the northern slope and 2650m in the southern side, increasing towards the east. Local ELA differences are related to: (i) the influence of the warmer Mediterranean Sea in contrast to the cooler Atlantic Ocean, (ii) the climate with more continental characteristics on the northern slope, and (iii) the microscale control of the local topography. Mean annual air temperatures in the ice-free summit plateaus were between -4/-6°C during the maximum local glacial extent, determining permafrost conditions with intense periglacial dynamics. Rock glaciers and protalus lobes developed until 2500m, the lowest boundary for permafrost regime. The distribution of other glacial and periglacial landforms within the limits of the maximum ice extent provides evidence to better understand the extent of subsequent glacial stages and post-glacial landscape evolution in Sierra Nevada.

Glacial stages and post-glacial environmental evolution in the Upper Garonne valley, Central Pyrenees

The maximum glacial extent in the Central Pyrenees during the Last Glaciation is known to have occurred before the global Last Glacial Maximum, but the succession of cold events afterwards and their impact on the landscape are still relatively unknown. This study focuses on the environmental evolution in the upper valley of the Garonne River since the Last Glaciation. Geomorphological mapping allows analysis of the spatial distribution of inherited and current processes and landforms in the study area. The distribution of glacial records (moraines, till, erratic boulders, glacial thresholds) suggests the existence of four glacial stages, from the maximum expansion to the end of the glaciation. GIS modeling allows quantification of the Equilibrium Line Altitude, extent, thickness and volume of ice in each glacial stage. During the first stage, the Garonne glacier reached 460m in the Loures-Barousse-Barbazan basin, where it formed a piedmont glacier 88km from the head and extended over 960km². At a second stage of glacier stabilization during the deglaciation process, the valley glaciers were 12-23km from the head until elevations of 1000-1850m, covering an area of 157km². Glaciers during stage three remained isolated in the upper parts of the valley, at heights of 2050-2200m and 2.6-4.5km from the head, with a glacial surface of 16km². In stage four, cirque glaciers were formed between 2260m and 2590m, with a length of 0.4-2km and a glacial area of 5.7km². Also, the wide range of periglacial, slope, nival and alluvial landforms existing in the formerly glaciated environments allows reconstruction of the post-glacial environmental dynamics in the upper Garonne basin. Today, the highest lands are organized following three elevation belts: subnival (1500-1900m), nival (1900-2300m) and periglacial/cryonival (2300-2800m).

Recent regional climate cooling on the Antarctic Peninsula and associated impacts on the cryosphere

The Antarctic Peninsula (AP) is often described as a region with one of the largest warming trends on Earth since the 1950s, based on the temperature trend of 0.54°C/decade during 1951-2011 recorded at Faraday/Vernadsky station. Accordingly, most works describing the evolution of the natural systems in the AP region cite this extreme trend as the underlying cause of their observed changes. However, a recent analysis (Turner et al., 2016) has shown that the regionally stacked temperature record for the last three decades has shifted from a warming trend of 0.32°C/decade during 1979-1997 to a cooling trend of -0.47°C/decade during 1999-2014. While that study focuses on the period 1979-2014, averaging the data over the entire AP region, we here update and re-assess the spatially-distributed temperature trends and inter-decadal variability from 1950 to 2015, using data from ten stations distributed across the AP region. We show that Faraday/Vernadsky warming trend is an extreme case, circa twice those of the long-term records from other parts of the northern AP. Our results also indicate that the cooling initiated in 1998/1999 has been most significant in the N and NE of the AP and the South Shetland Islands (>0.5°C between the two last decades), modest in the Orkney Islands, and absent in the SW of the AP. This recent cooling has already impacted the cryosphere in the northern AP, including slow-down of glacier recession, a shift to surface mass gains of the peripheral glacier and a thinning of the active layer of permafrost in northern AP islands.

On the outside looking in: rethinking the molecular mechanism of 1,3-dipolar cycloadditions from the perspective of bonding evolution theory. The reaction between cyclic nitrones and ethyl acrylate

Understanding the molecular mechanism of 1,3-dipolar cycloadditions using the bonding evolution theory.

A novel group of IncQ1 plasmids conferring multidrug resistance

The IncQ is a group of non-conjugative but mobilisable plasmids that are found and stably maintained in a wide range of bacteria contributing to the spread of antimicrobial resistance genes and to the insurgence of multidrug resistant bacteria. Here we report the identification, in clinical Salmonella Typhimurium strains, of an IncQ1 plasmid (pNUC) which confers resistance to sulfamethoxazole, streptomycin and tetracycline through the presence of sul2, strAB and tetA genes, respectively. pNUC was detected in five multidrug resistant S. Typhimurium strains collected in Southern Italy from various hospitals and years of isolation. Bioinformatics analyses highlighted the presence of pNUC-like plasmids in pathogenic bacteria of various Enterobacteriaceae genera or species. Taken as a whole, these plasmids constitute a novel group of IncQ1 plasmids that might have originated through recombination events between a tetR-tetA gene cluster (possibly derived from a Tn1721) and a recipient IncQ1 plasmid related to RSF1010. Our findings raise concerns regarding the possible contribution of the newly identified group of IncQ1 plasmids to the spread of tetracycline resistance.