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Additional file 3: Table S3. PCR primer sequences used at Lab2, at Lab3 and in this study for the Apennine brown bear individual identification.

This study aims at presenting a reliable fast-track diagnostics for the detection of CTX-M ESBL- (CTX-M-p) and carbapenemase-producers (CA-p) directly from blood cultures (BCs) of patients with Enterobacterales (EB) bloodstream infections (BSIs) admitted in emergency and internal medicine departments and its contribution in estimation of in vitro antibiotic susceptibility. A fast-track workflow including MALDI-TOF species identification and two lateral flow immunochromatographic assays for the detection of CTX-M-p and CA-p directly from BCs was performed in parallel with conventional routine, and results were compared. A total of 236 BCs of patients suffering from EB BSI were included. Accuracy of the fast-track workflow ranged from 99.6 to 100%. Among E. coli isolates, CTX-M-p (20.5%) were susceptible to ceftolozane-tazobactam (C/T, 97%), ceftazidime-avibactam (CZA, 100%), and piperacillin-tazobactam (TZP, 84.8%), whereas CTX-M-and-main-carbapenemases-non-producer (CTX-M-CA-np, 79.5%) isolates were susceptible to all the antibiotics tested. Among K. pneumoniae isolates, CTX-M-p (23.3%) were poorly susceptible to TZP (40%) but widely susceptible to C/T (90%), CZA (100%), and amikacin (90%), whereas CTX-M-CA-np (55.8%) were also susceptible to cefepime. CA-p K. pneumoniae (20.9%) were susceptible to CZA (88.9%). All the species other than E. coli and K. pneumoniae were CTX-M-CA-np and were widely susceptible to the antibiotics tested except for isolates of the inducible and derepressed AmpC- or AmpC/ESBL-p species. Rapid identification of species and phenotype together with knowledge of local epidemiology may be crucial to determine the likelihood of deduction of in vitro antibiotic susceptibility on the same day of positive BC processing.

Additional file 4: Table S4. Putative identical genotypes that differ between labs. Genotypes ram0587 and HS374 were identified by Lab2, genotypes Gen 108 and Gen 105 were identified by Lab3. a missing data, b mismatched loci.

Additional file 7: Fig. S1. Relationship between theoretical probability of identity and number of loci assayed using four heterozygosity levels. (a) randomly sampled individuals and (b) sibs. From [37].

Rapid identification of extended-spectrum-β-lactamase (ESBL)-, serine carbapenemase-, and metallo-β-lactamase (MBL)-producing Enterobacterales directly from positive blood culture (BC) bottles is of paramount importance to early optimize antimicrobial management and infection control measures. In this study, we describe and evaluate an improved variant of direct β-lactam inactivation method, named direct ethylenediaminetetraaceticacid-modified-β-lactam inactivation method (deBLIM). The deBLIM test is designed to detect ESBL or carbapenemase activity and to differentiate serine-carbapenemases from MBLs directly from Enterobacterale-positive BCs. The deBLIM was evaluated on both aerobic and anaerobic BCs spiked with 167 characterized Enterobacterale isolates. The deBLIM showed 100% sensitivity in detecting KPC and OXA-48-like serine carbapenemase, CTX-M, SHV variants, and TEM-10 ESBLs both in aerobic and anaerobic conditions. In contrast, a significant discrepancy between aerobic and anaerobic BCs was observed in detecting MBLs. The sensitivity rate in aerobic BCs was of 100% for all metalloenzyme types, whereas only 56.1% and 80% of VIM and NDM producers were detected in anaerobic bottles, respectively. IMP-producing Escherichia coli NCTC 13476 was also not detected in the anaerobic BC. No false positive result was observed among ESBL producers and broad-spectrum-β-lactamase nonproducers, demonstrating an overall specificity of 100%. The deBLIM could be a cost-effective screening method for the identification of ESBLs, serine carbapenemases, and MBLs directly from Enterobacterale-positive BCs on the same day of bottle positivity detection. Nevertheless, it must be considered its poor performance in detecting MBLs in the anaerobic condition.

Additional file 8: Table S7. Allelic patterns in 2000–2010 (pop1 - pre-arctos) and 2011–2017 (pop2 - arctos & post arctos). Na number of different alleles, Na Freq. ≥5% number of alleles with a frequency ≥ 5%, Ne number of effective alleles, I Shannon Information Index, No. Private Alleles number of private alleles, Ho observed heterozygosity and He expected heterozygosity.

The detection of carbapenemase extended-spectrum β-lactamase (ESBL)-producing Enterobacterales (EB) has become a major issue among critically ill patients, especially due to their impact on appropr...

Additional file 6: Table S6. Sampling trend of Apennine brown bear individuals over times. Genotypes were subdivided into two groups based on the years of sampling: 2000–2010 pre-arctos bears, 2011–2017 arctos and post arctos bears. Individuals sampled in both periods were eliminated from the analysis.

Objectives The aim of this study was to investigate the prevalence of ceftazidime/avibactam (CZA) resistance among carbapenemase-producing Enterobacterales (CPE) blood culture isolates as well as the performance of the main carbapenemase phenotypic detection methods to identify KPC variants associated with CZA resistance. Methods Non-duplicate CPE strains isolated from blood cultures during 2018–2020 were tested for antimicrobial susceptibility. Molecular testing was used to identify carbapenemase-producers. Strains harbouring blaKPC and with a CZA minimum inhibitory concentration (MIC) ≥8 mg/L were investigated by sequencing. Subsequentially, five phenotypic carbapenemase detection methods were evaluated on these strains, namely the modified carbapenem inactivation method (mCIM), Rapidec® Carba NP, the disk diffusion synergy test, NG-Test CARBA® 5 and RESIST-5 O.O.K.N.V. Results Overall, the CZA resistance rate was high (13.7%) and remained relevant (5.9%) excluding metallo-β-lactamases-producers. All isolates harbouringblaKPC mutants (n = 8) were associated with reduced carbapenem MICs and negative results by all detection methods based on revelation of enzyme activity. Lateral flow immunoassays failed to detect KPC-31 (n = 4) and KPC-33 (n = 2) but correctly identified KPC-14 (n = 2). Conversely, isolates harbouring wild-type KPC genes (n = 3) were associated with high-level CZA resistance and carbapenem resistance and tested positive by all of the evaluated methods. Conclusion In the era of CZA-based therapies, molecular blaKPC identification followed by a carbapenem hydrolysis-based phenotypic assay could be the most reasonable diagnostic algorithm to detect all KPC-producers and to identify mutants associated with impaired carbapenemase activity and CZA resistance.

The spread of production of Klebsiella pneumoniae carbapenemase (KPC) β-lactamase enzyme among the Enterobacterales (EB), in particularly in Klebsiella pneumoniae (KPC-Kp), has become a worldwide h...

Accurate detection of extended-spectrum-β-lactamase (ESBL)-producing Enterobacterales from bloodstream infection (BSI) is of paramount importance for both epidemiological and clinical purposes, especially for optimization of antibiotic stewardship interventions. Three phenotypic methods for the detection of ESBL phenotype in Klebsiella pneumoniae and Escherichia coli BSI were compared over a 4-month period (May–August 2021) in a main University Hospital from Northern Italy. The methods were the biochemical Rapid ESBL NP®, the immunological NG-Test CTX-M MULTI®, and the E-test technique based on ESBL E-test®. One hundred forty-two blood cultures (BCs) positive for K. pneumoniae or E. coli were included. ESBL and carbapenemase phenotype were detected in 26.1% (n = 37) and 16.9% (n = 24), respectively. The Rapid ESBL NP®, NG-Test CTX-M MULTI®, and direct ESBL E-test® positive and negative predictive values with 95% confidence intervals were 1 (0.87–1) and 0.97 (0.92–0.99), 1 (0.87–1) and 0.97 (0.92–0.99), and 1 (0.88–1) and 1 (0.96–1), respectively. The three phenotypic methods evaluated showed good performance in the detection of ESBL phenotype from K. pneumoniae– or E. coli–positive BCs. Rapid ESBL NP® and NG-test CTX-M® offer the important advantage of a turnaround time of 15 to 45 min, and the Rapid ESBL NP test in addition detects any type of ESBL producers.

Ecotourism gives tourists the opportunity to improve knowledge and awareness of environmental issues while on vacation. Recreational environmental education has been proven an effective method to raise perception of human impact on ecosystems. “Glocal Education” is an education project aimed at developing environmental interest in tourists on vacation. The present study assessed the effectiveness of Glocal Education in improving tourist environmental interest. Using specific questionnaires, we evaluated project impact on tourists, tourist satisfaction regarding the project and customer loyalty towards the tour operator hosting the project. The study took place at three mass touristic facilities, where tourists were asked to fill a questionnaire before and after participating in educational activities (e.g., biology lessons, excursions). The average score of both questionnaires was then compared to evaluate possible improvement of tourist knowledge, attitude and awareness. Results showed that such activities had a significantly positive impact on tourist knowledge, attitude and awareness at all localities. High levels of satisfaction and loyalty towards the host tour operator were observed at all sites, which indicate that once a person is briefed about the correct approach to natural systems, they can become increasingly interested in taking action, developing an “advocate” role. This study shows how informal education activities can act as trigger for environmental awareness and behavior among tourists, providing them with the tools, knowledge, and motivation to critically discern what is and isn't environmentally friendly, not only in terms of products and services in their everyday life, but also when choosing their vacation spots.

Hybridization is a natural or anthropogenic process that can deeply affect the genetic make-up of populations, possibly decreasing individual fitness but sometimes favoring local adaptations. The population of Italian wolves (Canis lupus), after protracted demographic declines and isolation, is currently expanding in anthropic areas, with documented cases of hybridization with stray domestic dogs. However, identifying admixture patterns in deeply introgressed populations is far from trivial. In this study, we used a panel of 170,000 SNPs analyzed with multivariate, Bayesian and local ancestry reconstruction methods to identify hybrids, estimate their ancestry proportions and timing since admixture. Moreover, we carried out preliminary genotype–phenotype association analyses to identify the genetic bases of three phenotypic traits (black coat, white claws, and spur on the hind legs) putative indicators of hybridization. Results showed no sharp subdivisions between nonadmixed wolves and hybrids, indicating that recurrent hybridization and deep introgression might have started mostly at the beginning of the population reexpansion. In hybrids, we identified a number of genomic regions with excess of ancestry in one of the parental populations, and regions with excess or resistance to introgression compared with neutral expectations. The three morphological traits showed significant genotype–phenotype associations, with a single genomic region for black coats and white claws, and with multiple genomic regions for the spur. In all cases the associated haplotypes were likely derived from dogs. In conclusion, we show that the use of multiple genome-wide ancestry reconstructions allows clarifying the admixture dynamics even in highly introgressed populations, and supports their conservation management.

Dear Sir,The global epidemic caused by carbapenem-resistant Enterobacterales is constantly rising, with KPC-producing Klebsiella pneumoniae (KPC-Kp) representing a tough challenge for both clinicia...

Paternity testing using genetic markers has shown that extra-pair paternity (EPP) is common in many pair-bonded species [1, 2]. Evolutionary theory and empirical data show that extra-pair copulations can increase the fitness of males as well as females [3, 4]. This can carry a significant fitness cost for the social father, who then invests in rearing offspring that biologically are not his own [5]. In human populations, the incidence and correlates of extra-pair paternity remain highly contentious [2, 6, 7]. Here, we use a population-level genetic genealogy approach [6, 8] to reconstruct spatiotemporal patterns in human EPP rates. Using patrilineal genealogies from the Low Countries spanning a period of over 500 years and Y chromosome genotyping of living descendants, our analysis reveals that historical EPP rates, while low overall, were strongly impacted by socioeconomic and demographic factors. Specifically, we observe that estimated EPP rates among married couples varied by more than an order of magnitude, from 0.4% to 5.9%, and peaked among families with a low socioeconomic background living in densely populated cities of the late 19 century. Our results support theoretical predictions that social context can strongly affect the outcomes of sexual conflict in human populations by modulating the incentives and opportunities for engaging in extra-pair relationships [9–11]. These findings show how contemporary genetic data combined with in-depth genealogies open up a new window on the sexual behavior of our ancestors. Larmuseau et al. combine genetic data with family trees to reconstruct historical patterns of human extra-pair paternity (EPP). They show that EPP rates in Western society were low overall (∼1%) but varied in function of social context, peaking at ∼6% among families with low socioeconomic status in densely populated cities of the 19 century., Funding was provided by KU Leuven (BOF-C1 grant C12/15/013) and the Fund for Scientific Research – Flanders (Research grant number 1503216N and postdoc grants of M.H.D.L. and P.v.d.B.). F.C. was supported by Agencia Estatal de Investigación and Fondo Europeo de Desarollo Regional (FEDER) (grant CGL2016-75389-P), Agència de Gestió d’Ajuts Universitaris i de la Recerca (Generalitat de Catalunya) grant 2017 SGR00702, and “Unidad de Excelencia María de Maeztu,” funded by the MINECO (ref: MDM-2014-0370).

A number of studies carried out since the early ‘70s has investigated the effects of isolation on genetic variation within and among human populations in diverse geographical contexts. However, no extensive analysis has been carried out on the heterogeneity among genomes within isolated populations. This issue is worth exploring since events of recent admixture and/or subdivision could potentially disrupt the genetic homogeneity which is to be expected when isolation is prolonged and constant over time. Here, we analyze literature data relative to 87,818 autosomal single-nucleotide polymorphisms, which were obtained from a total of 28 European populations. Our results challenge the traditional paradigm of population isolates as genetically (and genomically) uniform entities. In fact, focusing on the distribution of variance of intra-population diversity measures across individuals, we show that the inter-individual heterogeneity of isolated populations is at least comparable to the open ones. More in particular, three small and highly inbred isolates (Sappada, Sauris and Timau in Northeastern Italy) were found to be characterized by levels of this parameter largely exceeding that of all other populations, possibly due to relatively recent events of genetic introgression. Finally, we propose a way to monitor the effects of inter-individual heterogeneity in disease-gene association studies.

Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer’s disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved.

Extensive European and African admixture coupled with loss of Amerindian lineages makes the reconstruction of pre-Columbian history of Native Americans based on present-day genomes extremely challenging. Still open questions remain about the dispersals that occurred throughout the continent after the initial peopling from the Beringia, especially concerning the number and dynamics of diffusions into South America. Indeed, if environmental and historical factors contributed to shape distinct gene pools in the Andes and Amazonia, the origins of this East-West genetic structure and the extension of further interactions between populations residing along this divide are still not well understood. To this end, we generated new high-resolution genome-wide data for 229 individuals representative of one Central and ten South Amerindian ethnic groups from Mexico, Peru, Bolivia, and Argentina. Low levels of European and African admixture in the sampled individuals allowed the application of fine-scale haplotype-based methods and demographic modeling approaches. These analyses revealed highly specific Native American genetic ancestries and great intragroup homogeneity, along with limited traces of gene flow mainly from the Andes into Peruvian Amazonians. Substantial amount of genetic drift differentially experienced by the considered populations underlined distinct patterns of recent inbreeding or prolonged isolation. Overall, our results support the hypothesis that all non-Andean South Americans are compatible with descending from a common lineage, while we found low support for common Mesoamerican ancestors of both Andeans and other South American groups. These findings suggest extensive back-migrations into Central America from non-Andean sources or conceal distinct peopling events into the Southern Continent.

Simple models for spherical particles with a soft shell have been shown to self-assemble into numerous crystal phases and even quasicrystals. However, most of these models rely on a simple pairwise interaction, which is usually a valid approximation only in the limit of small deformations, i.e. low densities. In this work, we consider a many-body yet simple model for the evaluation of the elastic energy associated with the deformation of a spherical shell. The resulting energy evaluation, however, is relatively expensive for direct use in simulations. We significantly reduce the associated numerical cost by fitting the potential using a set of symmetry functions. We propose a method for selecting a suitable set of symmetry functions that capture the most relevant features of the particle environment in a systematic manner. The fitted interaction potential is then used in Monte Carlo simulations to draw the phase diagram of the system in two dimensions. The system is found to form both a fluid and a hexagonal crystal phase., Comment: 10 pages, 9 figures

The authors report the case of an 86-year-old woman presenting with recurrent Klebsiella pneumoniae bacteraemia. She had severe aortic stenosis submitted to a recent transcatheter aortic valve implantation (TAVI). Initially, Klebsiella pneumoniae bacteraemia from a urinary source was diagnosed. Following another 4 episodes of bacteraemia with the same agent, the source was ultimately found to be a periprosthetic abscess. Considering the patient’s unsuitability for surgery, a decision was made for life-long antimicrobial therapy. This approach has been successful in preventing recurrences or complications. Endocarditis is one of the most severe complications seen following TAVI, often carrying a poor prognosis. Even though Klebsiella spp. are common pathogens for healthcare-associated infections among the elderly, they are seldom the causative agent for endocarditis. Being the first reported case of TAVI-related Klebsiella endocarditis, it was successfully managed using a medical approach. LEARNING POINTS Non-HACEK Gram-negative bacilli are organisms infrequently found to cause infective endocarditis (IE). This is the first reported case of transcatheter aortic valve implantation (TAVI)-related Klebsiella IE. Diagnosing an infectious complication associated with procedural or prosthetic material is not always straightforward; a high level of suspicion and a systematic approach are essential. Most cases of TAVI-related IE are ineligible for surgery due to a prohibitive procedural risk. Long-term antibiotic therapy may be a suitable alternative for patients with uncontrolled infection considered unfit for surgery.

Dear Sir,Bloodstream infection (BSI) is a serious clinical condition which can lead to sepsis, thereby increasing the burden of morbidity and mortality. Especially among patients suffering from hea...

We prospectively compared the performance of RESIST-5 O.O.K.N.V. and NG-Test Carba 5 assays directly from blood cultures spiked with 130 characterized Enterobacterales isolates. Overall, both assays yielded 100% sensitivity to detect KPC-type carbapenemases and OXA-48-like carbapenemases. Both assays failed to detect KPC-31 and KPC-33, D179Y point mutation variants of KPC-3 and KPC-2, that are deprived of carbapenemase activity and confer resistance to ceftazidime-avibactam. On blood culture bacterial pellets, NDMand VIM-type carbapenemases were detected in 50.0% and 52.2%, respectively, by RESIST5 O.O.K.N.V. vs 100% by NG-Test Carba 5. The sensitivity of RESIST-5 O.O.K.N.V. improved to 100% and 95.6%, respectively, by performing the assay on 4-h early subculture. (C) 2020 Published by Elsevier Ltd on behalf of The Healthcare Infection Society.

Introduction: Bacterial lower respiratory tract infections (BLRTI) may represent serious clinical conditions which can lead to respiratory failure, intensive care unit admission and high hospital costs. The detection of carbapenemase- and extended-spectrum β-lactamase (ESBL)-producing Enterobacterales, as well as meticillin-resistant Staphylococcus aureus (MRSA), has become a major issue, especially in healthcare-associated infections. This study aimed to determine whether molecular assays could detect genes encoding carbapenemases, ESBL and MRSA directly from respiratory samples in order to expedite appropriate therapy and infection control for patients with BLRTI. Methods: The carbapenem-resistant enterobacterales (CRE), ESBL and MRSA/SA ELITe MGB assays were performed directly on 354 respiratory specimens sampled from 318 patients admitted with BLRTI. Molecular results were compared with routine culture-based diagnostics results. Results: Positive (PPV) and negative (NPV) predictive values of the CRE ELITe MGB kit were 75.9% [95% confidence interval (CI) 60.3-86.7] and 100%, respectively. PPV and NPV of the ESBL ELITe MGB kit were 80.8% (95% CI 63.6-91.0) and 99.1% (95% CI 96.6-99.8), respectively. PPV and NPV of the MRSA/SA ELITe MGB kit were 91.7% (95% CI 73.7-97.7)/100% and 98.3% (95% CI 89.8-99.3)/96.8% (95% CI 81.6-99.5), respectively. Discussion: Validity assessment of molecular assays detecting the main antibiotic resistance genes directly from respiratory samples showed high accuracy compared with culture-based results. Molecular assays detecting the main carbapenemase, ESBL, S. aureus and meticillin resistance encoding genes provide an interesting tool with potential to expedite optimization of antibiotic therapy and infection control practices in patients with BLRTI. info:eu-repo/semantics/publishedVersion

Few questions in condensed matter science have proven as difficult to unravel as the interplay between structure and dynamics in supercooled liquids. To explore this link, much research has been devoted to pinpointing local structures and order parameters that correlate strongly with dynamics. Here we use an unsupervised machine learning algorithm to identify structural heterogeneities in three archetypical glass formers—without using any dynamical information. In each system, the unsupervised machine learning approach autonomously designs a purely structural order parameter within a single snapshot. Comparing the structural order parameter with the dynamics, we find strong correlations with the dynamical heterogeneities. Moreover, the structural characteristics linked to slow particles disappear further away from the glass transition. Our results demonstrate the power of machine learning techniques to detect structural patterns even in disordered systems, and provide a new way forward for unraveling the structural origins of the slow dynamics of glassy materials., The origin of dynamical slowdown in disordered materials remains elusive, especially in the absence of obvious structural changes. Boattini et al. use unsupervised machine learning to reveal correlations between structural and dynamical heterogeneity in supercooled liquids.