Search

Objectives: Clostridioides difficile infection (CDI) is one of the leading nosocomial infections worldwide, resulting in a significantly increasing burden on the healthcare systems. However, Pan-European data about cost and resource utilization of CDI treatment do not exist. Methods: A retrospective analysis within the Combatting Bacterial Resistance in Europe CDI project was conducted based on resource costs for inpatient treatment and productivity costs. Country-specific cost values were converted to EURO referred to 1 January, 2019 values. Differences in price levels for healthcare services among the participating countries were adjusted by using an international approach of the Organisation for Economic Co-operation and Development. As the study focused on patients with recurrent CDI, the observed study population was categorized into (a) patients with CDI but without CDI recurrence (case group), (b) patients with CDI recurrence (recurrence group), and (c) patients without CDI (control group). Results: Overall, 430 hospitalized patients from 12 European countries were included into the analysis between July 2018 and November 2018. Distribution of mean hospital length of stay and mean overall costs per patient between the case group, recurrence group, and control group were as follows: 22 days (95% CI 17e27 days) vs. 55 days (95% CI 17-94 days) vs. 26 days (95% CI 22-31 days; p 0.008) and V 15 242 (95% CI 10 593-19 891) vs. V 52 024 (95% CI 715-103 334) vs. V 21 759 (95% CI 16 484-27 035; p 0.010), respectively. The CDI recurrence rate during the observational period was 18%. Change escalation in CDI medication (OR 3.735) and treatment in an intensive care unit (OR 5.454) were found to be the most important variables associated with increased overall costs of patients with CDI. Conclusions: Treatment of patients with recurrent CDI results in a significant burden. Prevention of CDI recurrences should be in focus of daily patient care to identify the most cost-effective treatment strategy. (c) 2022 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

This study examined the effect of perceived predation risk imposed by lynx (Lynx lynx) and wolf (Canis lupus) on red deer (Cervus elaphus) foraging behavior under experimental conditions. We hypothesized that in response to large carnivore scent red deer would increase their vigilance, although reducing the frequency and duration of visits to foraging sites. Consequently, browsing intensity on tree saplings was expected to decrease, whereas a higher proportion of more preferred species was expected to be browsed to compensate for higher foraging costs. We expected stronger responses towards the ambush predator lynx, compared with the cursorial predator wolf. These hypotheses were tested in a cafeteria experiment conducted within three red deer enclosures, each containing four experimental plots with olfactory cues of wolf, lynx, cow, and water as control. On each plot, a camera trap was placed and browsing intensity was measured for one consecutive week, repeated three times. Red deer reduced their visitation duration and browsing intensity on plots with large carnivore scent. Despite red deer showing a clear preference for certain tree species, the presence of large carnivore scent did not change selectivity towards different tree species. Contrary to our hypothesis, we found more pronounced effects of wolf (cursorial) compared with lynx (ambush). This study is the first to experimentally assess the perceived risk effects on the red deer foraging behavior of large carnivores differing in hunting modes. Our findings provide insights into the role of olfactory cues in predator–prey interactions and how they can modify fine-scale herbivore–plant interactions., In this study, we tested whether an ambush (lynx) and a pursuit (wolf) predator influenced behavior and food selection of a large herbivore. We experimentally showed that under perceived predation risk of both lynx and wolf, the large herbivore reduced visitation time, altered visitation duration, and reduced food intake. Differences in behavior and food intake under perceived predation risk of both predators suggests more pronounced risk effects from the pursuit predator.

The insulo-opercular network functions critically not only in encoding taste, but also in guiding behavior based on anticipated food availability. However, there remains no direct measurement of insulo-opercular activity when humans anticipate taste. Here, we collect direct, intracranial recordings during a food task that elicits anticipatory and consummatory taste responses, and during ad libitum consumption of meals. While cue-specific high-frequency broadband (70–170 Hz) activity predominant in the left posterior insula is selective for taste-neutral cues, sparse cue-specific regions in the anterior insula are selective for palatable cues. Latency analysis reveals this insular activity is preceded by non-discriminatory activity in the frontal operculum. During ad libitum meal consumption, time-locked high-frequency broadband activity at the time of food intake discriminates food types and is associated with cue-specific activity during the task. These findings reveal spatiotemporally-specific activity in the human insulo-opercular cortex that underlies anticipatory evaluation of food across both controlled and naturalistic settings., Animal studies have shown that insulo-opercular network function is critical in gustation and in behaviour based on anticipated food availability. The authors describe activities within the human insulo-opercular cortex which underlie anticipatory food evaluation in both controlled and naturalistic settings.

Although environmental variability and predictability have been proposed as the underlying ecological context in which transgenerational plasticity (TGP) arises, the adaptive significance and interaction with within-generation plasticity (WGP) in such scenarios is still poorly understood. To investigate these questions, we considered the tolerance to upper thermal limits of larvae and adults of the desert endemic Drosophila mojavensis adapted to different climatic regions (Desert vs. Mediterranean climate). Thermal plasticity was investigated by acclimating parents and offspring at 36°C (vs. at 25°C). We then used historical temperature variation data from both regions to perform individual-based simulations by modelling expected components of adaptive plasticity in multiple life stages. Our results indicated that thermal response to ramping heat shocks was more pronounced in larvae, where acclimation treatments in parents and offspring increased their heat-shock performance, while heat knockdown in adults was only increased by offspring acclimation of adults. The relative contribution of WGP and TGP was greater for the population from the more thermally variable Sonoran Desert. Similarly, individual-based simulations of evolving maternal effects indicated that variation in tolerance to upper thermal limits across life stages and climates is expected from its adaptive significance in response to environmental predictability. Our approach offers a new perspective and interpretation of adaptive plasticity, demonstrating that environmental predictability can drive thermal responses across generations and life stages in a scenario with regional climate variability. A free Plain Language Summary can be found within the Supporting Information of this article.

Acknowledgements The authors acknowledge the two anonymous reviewers for their useful comments that improved the manuscript. Financial support for the excavations in Neumark‐Nord 2 was provided by the Lausitzer Mitteldeutsche Braunkohlengesellschaft mbH, the Landesamt fur Denkmalpflege und Archaologie Sachsen‐Anhalt (Harald Meller, Susanne Friederich), the Romisch‐Germanisches Zentralmuseum Mainz, the Leids Universiteits Fonds ‘Campagne voor Leiden’ program and the Netherlands Organization for Scientific Research (N.W.O.).

Metronidazole was until recently used as a first-line treatment for potentially life-threatening Clostridioides difficile (CD) infection. Although cases of metronidazole resistance have been documented, no clear mechanism for metronidazole resistance or a role for plasmids in antimicrobial resistance has been described for CD. Here, we report genome sequences of seven susceptible and sixteen resistant CD isolates from human and animal sources, including isolates from a patient with recurrent CD infection by a PCR ribotype (RT) 020 strain, which developed resistance to metronidazole over the course of treatment (minimal inhibitory concentration [MIC] = 8 mg L−1). Metronidazole resistance correlates with the presence of a 7-kb plasmid, pCD-METRO. pCD-METRO is present in toxigenic and non-toxigenic resistant (n = 23), but not susceptible (n = 563), isolates from multiple countries. Introduction of a pCD-METRO-derived vector into a susceptible strain increases the MIC 25-fold. Our finding of plasmid-mediated resistance can impact diagnostics and treatment of CD infections., Cases of C. difficile (CD) resistant to metronidazole have been reported but the mechanism remains enigmatic. Here the authors identify a plasmid, which correlates with metronidazole resistance status in a large international collection of CD isolates, and demonstrate that the plasmid can confer metronidazole resistance.

Background Patients with multiple recurrent Clostridioides difficile infections (rCDI) are treated with fecal microbiota transplantation (FMT), using feces provided by healthy donors. Blastocystis colonization of donors is considered an exclusion criterion, whereas its pathogenicity is still under debate. Methods The introduction of molecular screening for Blastocystis sp. at our stool bank identified 2 donors with prior negative microscopies but positive polymerase chain reactions (PCRs). Potential transmission of Blastocystis sp. to patients was assessed on 16 fecal patient samples, pre- and post-FMT, by PCR and subtype (ST) analyses. In addition, clinical outcomes for the treatment of rCDI (n = 31), as well as the development of gastrointestinal symptoms, were assessed. Results There was 1 donor who carried Blastocystis ST1, and the other contained ST3. All patients tested negative for Blastocystis prior to FMT. With a median diagnosis at 20.5 days after FMT, 8 of 16 (50%) patients developed intestinal colonization with Blastocystis, with identical ST sequences as their respective donors. Blastocystis-containing fecal suspensions were used to treat 31 rCDI patients, with an FMT success rate of 84%. This success rate was not statistically different from patients transferred with Blastocystis sp.–negative donor feces (93%, 76/82). Patients transferred with Blastocystis sp.–positive donor feces did not report any significant differences in bowel complaints in the first week, after 3 weeks, or in the months following FMT. Conclusions We demonstrated the first transmission of Blastocystis ST1 and ST3 from donors to patients by FMT. This did not result in gastrointestinal symptomatology or have any significant effect on rCDI treatment outcomes.

Purpose of review Antimicrobial resistance is a rising threat to global health and is associated with increased mortality. Intestinal colonisation with multidrug-resistant organisms (MDRO) can precede invasive infection and facilitates spread within communities and hospitals. Novel decolonisation strategies, such as faecal microbiota transplantation (FMT), are being explored. The purpose of this review is to provide an update on how the field of FMT for MDRO decolonisation has developed during the past year and to assess the efficacy of FMT for intestinal MDRO decolonisation. Recent findings Since 2020, seven highly heterogenous, small, nonrandomised cohort studies and five case reports have been published. In line with previous literature, decolonisation rates ranged from 20 to 90% between studies and were slightly higher for carbapenem-resistant Enterobacteriaceae than vancomycin-resistant Enterococcus. Despite moderate decolonisation rates in two studies, a reduction in MDRO bloodstream and urinary tract infections was observed. Summary and implications Although a number of smaller cohort studies show some effect of FMT for MDRO decolonisation, questions remain regarding the true efficacy of FMT (taking spontaneous decolonisation into account), the optimal route of administration, the role of antibiotics pre and post-FMT and the efficacy in different patient populations. The observed decrease in MDRO infections post-FMT warrants further research.

BACKGROUND & AIMS: Patients with multiple recurrent Clostridioides difficile infection (rCDI) have a disturbed gut microbiota that can be restored by fecal microbiota trans-plantation (FMT). Despite extensive screening, healthy feces donors may carry bacteria in their intestinal tract that could have long-term health effects, such as potentially procarci-nogenic polyketide synthase-positive (pks+) Escherichia coli. Here, we aim to determine whether the pks abundance and persistence of pks+ E coli is influenced by pks status of the donor feces. METHODS: In a cohort of 49 patients with rCDI treated with FMT and matching donor samples-the largest cohort of its kind, to our knowledge-we retrospectively screened fecal metagenomes for pks+ E coli and compared the presence of pks in patients before and after treatment and to their respective donors. RESULTS: The pks island was more prevalent (P = .026) and abundant (P < .001) in patients with rCDI (pre-FMT, 27 of 49 [55%]; median, 0.46 reads per kilobase per million [RPKM] pks) than in healthy donors (3 of 8 donors [37.5%], 11 of 38 samples [29%]; median, 0.01 RPKM pks). The pks status of patients post-FMT depended on the pks status of the donor suspension with which the patient was treated (P = .046). Particularly, persistence (8 of 9 cases) or clearance (13 of 18) of pks+ E coli in pks+ patients was correlated to pks in the donor (P = .004). CONCLUSIONS: We conclude that FMT contrib-utes to pks+ E coli persistence or eradication in patients with rCDI but that donor-to-patient transmission of pks+ E coli is unlikely.

Monika Kaba&lstrok;a,1,&ast; Zygmunt Gofron,1,&ast; Ma&lstrok;gorzata Aptekorz,1 Krzysztof Sacha,1 Celine Harmanus,2 Ed Kuijper,2 Gayane Martirosian1 1Department of Medical Microbiology Medical University of Silesia in Katowice, Katowice, Poland; 2Department of Medical Microbiology Leiden University Medical Center, Leiden, the Netherlands&ast;These authors contributed equally to this workCorrespondence: Gayane MartirosianDepartment of Medical Microbiology Medical University of Silesia in Katowice, 18 Medyków str, Katowice, 40-752, PolandEmail gmartir@sum.edu.plObjective: The aim of this study was Clostridioides difficile outbreak investigation due to the emergence of rifampicin resistant ribotype 027 (RT 027) fecal isolates from patients of Polish tertiary care hospital between X. 2017 and II. 2018 using multilocus variable tandem repeat analysis (MLVA).Materials and Methods: Twenty-nine C. difficile fecal isolates from patients of tertiary care hospital in Southern Poland were ribotyped and analyzed by MLVA. Multiplex PCR (mPCR) for genes encoding GDH (gluD), toxins A (tcdA)/ B (tcdB), 16S rDNA and binary toxin genes (ctdA and ctdB) was performed. The antibiotic susceptibility profile was determined by E-test.Results: The A, B and binary toxins encoding genes were detected in all 29 C. difficile strains which were sensitive to metronidazole, vancomycin and were resistant to erythromycin, clindamycin, and moxifloxacin; resistance to imipenem demonstrated 97%, to rifampicin – 45% isolates. C. difficile strains could be grouped by MLVA into 5 distinct clusters, and the largest cluster II contains 16 strains. The comparison of rifampicin GM MIC of cluster II (n=16 strains) with all others (n=13) showed that strains from clusters I, III, IV and V possessed significantly (p < 0.005) higher GM MIC and were more resistant to rifampicin.Conclusion: MLVA analysis proved transmission and recognized outbreak due to multidrug-resistant RT 027 C. difficile among patients of tertiary care hospital in Southern Poland. The reason for this is probably the widespread occurrence of spores in the hospital environment, which includes, among others, neglect of hygienic procedures and epidemic supervision. High resistance to imipenem (97%) and to rifampicin (45%) among C. difficile RT 027 Silesian isolates is threatening and requires further studies to elucidate this phenomenon.Keywords: Clostridioides difficile, epidemiology, MLVA, RT 027, rifampicin resistance

Clostridioides difficileis the most common cause of antibiotic-associated gastrointestinal infections. Capillary-electrophoresis (CE)-PCR ribotyping is currently the gold standard forC. difficiletyping but lacks discriminatory power to study transmission and outbreaks in detail. New molecular methods have the capacity to differentiate better, but backward compatibility with CE-PCR ribotyping must be assessed. Using a well-characterized collection of diverse strains (N=630; 100 unique ribotypes [RTs]), we aimed to investigate PCR ribotyping prediction from core genome multilocus sequence typing (cgMLST). Additionally, we compared the discriminatory power of cgMLST (SeqSphere & EnteroBase) and whole genome MLST (wgMLST) (EnteroBase) with single nucleotide polymorphism (SNP) analysis). A unique cgMLST profile (>6 allele differences) was observed in 82/100 ribotypes, indicating sufficient backward compatibility. Intra-RT allele difference varied per ribotype and MLST clade. Application of cg/wgMLST and SNP analysis in two outbreak settings with ribotypes RT078 and RT181 (known with a low intra-ribotype allele difference) showed no distinction between outbreak- and non-outbreak strains, in contrast to wgMLST and SNP analysis. We conclude that cgMLST has the potential to be an alternative to CE-PCR ribotyping. The method is reproducible, easy to standardize and offers higher discrimination. However, in some ribotype complexes adjusted cut-off thresholds and epidemiological data are necessary to recognize outbreaks. We propose to decrease the current threshold of 6 to 3 alleles to better identify outbreaks.

Background Until recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Objectives To identify factors that contribute to plasmid-independent metronidazole resistance of C. difficile. Methods Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile using a combination of antimicrobial susceptibility testing on different solid agar media and WGS of selected isolates. Results We find that nearly all isolates demonstrate a haem-dependent increase in the MIC of metronidazole, which in some cases leads to isolates qualifying as resistant (MIC >2 mg/L). Moreover, we find an SNP in the haem-responsive gene hsmA, which defines a metronidazole-resistant lineage of PCR ribotype 010/MLST ST15 isolates that also includes pCD-METRO-containing strains. Conclusions Our data demonstrate that haem is crucial for medium-dependent metronidazole resistance in C. difficile.

Treatment of bacterial infections with broad-spectrum antibiotics is a strategy severely limited by the decreased ability of the perturbed resident microbiota to control expansion of antibiotic-resistant pathogens. Live biotherapeutic products (LBPs) could provide an alternative to antibiotics in infection control by restoring gut colonization resistance and controlling expansion of resistant strains, an important therapeutic need not being addressed with existing anti-infective drug modalities. We review opportunities and challenges in developing LBPs for multidrug-resistant organisms colonization and infection control, with a focus on commercial fecal microbiota transplantation-like products and defined bacterial consortia, and spanning considerations related to availability of models for rational drug candidate selection and dose regimen selection, good manufacturing practice, intellectual property, and commercial viability.

Red blood cell transfusions (RBCT) remain the cornerstone of supportive care in lower-risk myelodysplastic syndrome (LRMDS) [1]. Transfusion dependency in LRMDS patients is associated with inferior outcomes, mainly attributed to severe bone marrow failure [2]. However, iron toxicity, due to frequent RBCT or ineffective erythropoiesis, may be an additional negative prognostic factor [3,4,5,6]. Recently, much progress has been made in unraveling the iron metabolism. The peptide hormone hepcidin is the key regulator by inhibiting iron uptake through degradation of ferroportin, a cellular iron exporter [7]. Erythroferrone and GDF15, produced by erythroblasts, inhibit hepcidin production, which leads to increased uptake and cellular release of iron for the purpose of erythropoiesis [8]. The pathophysiology of iron metabolism in MDS is still not completely understood. Exceedingly high reactive oxygen species (ROS) levels are associated with iron toxicity, disease development, and progression in MDS patients [9,10,11,12]. Malondialdehyde (MDA), resulting from lipid peroxidation of polyunsaturated fatty acids, is a biomarker of oxidative stress [10, 12]. Currently, little is known about the prognostic impact of ROS in MDS patients. The aim of this study is twofold: (1) describe iron and oxidative stress parameters over time in LRMDS patients and (2) to assess their effect on overall and progression-free survival. The EUMDS registry prospectively collects observational data on newly diagnosed LRMDS patients from 148 centers in 16 countries in Europe and Israel as of January 2008. All patients provided informed consent. Clinical data were collected at baseline and at each six-monthly follow-up visit. Serum samples were collected prospectively at each visit from 256 patients included in six participating countries. Conventional iron parameters were measured with routine assays. We additionally analyzed hepcidin, growth differentiation factor 15 (GDF15), soluble transferrin receptor (sTfR), non-transferrin bound iron (NTBI), labile plasma iron (LPI), and MDA. Subjects were prospectively followed until death, loss to follow-up, or withdrawal of consent. All iron parameters were measured centrally at the department of Laboratory Medicine of the Radboudumc, Nijmegen, The Netherlands. Serum samples were collected just prior to transfusion in transfusion-dependent patients and stored at −80 °C. Details on the assays and reference ranges of hepcidin, GDF15, sTfR, NTBI, LPI, and MDA are provided in the supplement. The Spearman rank test was used to evaluate correlations between iron parameters. We stratified the results by transfusion dependency per visit and the presence of ring sideroblasts. When evaluating temporal changes in iron parameters, with linear quantile mixed models, we excluded patients from the timepoint they received iron chelation therapy. Overall survival (OS) was defined as the time from MDS diagnosis to death or, in case of progression-free survival, to date of progression or death; patients still alive at the end of follow-up were censored. Time-dependent Kaplan–Meier curves and cox proportional hazards models were used. In total, 256 consecutive patients, were included in this study. Over five six-monthly visits, 1040 samples were collected. Table 1 describes the patient characteristics. Most patients without ring sideroblasts were transfusion-independent at diagnosis (nonRS-TI; 55.9%), 18.8% with ring sideroblasts were transfusion-independent (RS-TI), 18.4% without ring sideroblasts were transfusion-dependent (nonRS-TD), and 7% with ring sideroblasts were transfusion-dependent patients (RS-TD). The median follow-up time was 6.6 years (95% CI 5.9–7.0). LPI was positively correlated with transferrin saturation (TSAT) (r = 0.15, p < 0.001, Fig. S1). LPI values increased exponentially at TSAT values above 80%. This effect was most pronounced in the transfusion-dependent groups, but also observed in the RS-TI group. MDA was weakly correlated with NTBI (r = 0.09, p = 0.069) and negatively correlated with hemoglobin level (r = −0.1, p = 0.033). GDF15 and hepcidin were negatively correlated in the RS-TI and nonRS-TD group and significantly negatively correlated in the RS-TD group (r = −0.34, p = 0.007, Fig. S2). Serum ferritin levels were elevated in all subgroups with a mean value of 858 µg/L at visit 5. The highest serum ferritin levels were observed in the RS-TD group (mean value at visit 5: 2092 µg/L, Table S1). Serum ferritin increased significantly per visit in the RS-TD group (beta 454.46 µg/L; 95% CI 334.65–574.27), but not in the other groups (Table S2). All subgroups, except for the nonRS-TI, had elevated TSAT levels. TSAT levels were most markedly increased in the RS-TD group with a mean TSAT of 88% at visit 5 (Table S1). In both transfusion-dependent groups the median increase per visit was significant (Table S2). LPI was elevated in the RS-TD group exclusively with a mean value of 0.59 µmol/L at visit 5 (Table S1). NTBI was elevated in all subgroups, with the highest values in the RS-TD group (Table S1). The increase in median NTBI level was significant in both transfusion-dependent groups (Table S2). Hepcidin levels were markedly elevated in the nonRS-TD group. Interestingly, hepcidin levels were lower in the RS-TD group, probably reflecting ineffective erythropoiesis, likewise supported by lower hepcidin/ferritin ratios in RS groups (Table S1). Median hepcidin levels increased over time in the transfusion-dependent subgroups only (Table S2). GDF15 levels, analyzed in the light of its potential role in hepcidin suppression, were increased in all subgroups (Table S1). The RS subgroups had higher GDF15 levels compared to the nonRS groups, reflecting increased erythropoiesis. Mean sTfR levels were within the reference range in all subgroups except for the RS-TI group, which showed elevated levels, reflecting...

Background Carbapenemases produced by Enterobacterales are often encoded by genes on transferable plasmids and represent a major healthcare problem, especially if the plasmids contain additional antibiotic resistance genes. As part of Dutch national surveillance, 50 medical microbiological laboratories submit their Enterobacterales isolates suspected of carbapenemase production to the National Institute for Public Health and the Environment for characterization. All isolates for which carbapenemase production is confirmed are subjected to next-generation sequencing. Objectives To study the molecular characteristics of a genetic cluster of Enterobacter cloacae complex isolates collected in Dutch national surveillance in the period 2015–20 in the Netherlands. Methods Short- and long-read genome sequencing was used in combination with MLST and pan-genome MLST (pgMLST) analyses. Automated antimicrobial susceptibility testing (AST), the Etest for meropenem and the broth microdilution test for colistin were performed. The carbapenem inactivation method was used to assess carbapenemase production. Results pgMLST revealed that nine E. cloacae complex isolates from three different hospitals in the Netherlands differed by Conclusions The EclCluster-013 reported here represents an MDR E. cloacae complex ST78 strain containing an IncH12 plasmid carrying both the blaVIM-1 carbapenemase and the mcr-9 colistin resistance gene.

BackgroundGut colonization by antibiotic resistant E. coli strains, including extended-spectrum beta-lactamase (ESBL)-producing E. coli is a risk factor for developing overt infection. The gut microbiome can provide colonization resistance against enteropathogens, but it remains unclear whether it confers resistance against potentially pathogenic ESBL-producing E. coli.MaterialsFrom a Dutch cross-sectional population study (PIENTER-3), feces from 2751 individuals were used to culture ESBL-producing bacteria. Of these, we selected 49 samples which were positive for an ESBL-producing Escherichia coli (ESBL+), and negative for a variety of variables known to affect microbiome composition. These were matched in a 1:1 ratio to ESBL− samples based on age, sex, having been abroad in the past six months and ethnicity. Shotgun metagenomic sequencing was performed and taxonomic species composition and functional annotations (microbial metabolism and carbohydrate-active enzymes) were determined. Targeted quantitative metabolic profiling (1H NMR-spectroscopy) was performed to investigate metabolomic profiles.ResultsNo differences in alpha or beta diversity were observed, nor in relative abundance, between ESBL+ and ESBL− individuals based on bacterial species level composition. Machine learning approaches based on microbiota composition did not accurately predict ESBL status (area under the receiver operating characteristic curve (AUROC)=0.53), neither when based on functional profiles. The metabolome did also not convincingly differ between ESBL groups as assessed by a variety of approaches, including machine learning through random forest (AUROC=0.61).ConclusionUsing a combination of multi-omics and machine learning approaches, we conclude that asymptomatic gut carriage of ESBL-producing E. coli is not associated with an altered microbiome composition or function. This may suggest that microbiome-mediated colonization resistance against ESBL-producing E. coli is not as relevant as it is against other enteropathogens.

Contains fulltext : 220210.pdf (Publisher’s version ) (Open Access) We investigated the prevalence of azole resistance of Aspergillus fumigatus isolates in the Netherlands by screening clinical A. fumigatus isolates for azole resistance during 2013-2018. We analyzed azole-resistant isolates phenotypically by in vitro susceptibility testing and for the presence of resistance mutations in the Cyp51A gene. Over the 6-year period, 508 (11%) of 4,496 culture-positive patients harbored an azole-resistant isolate. Resistance frequency increased from 7.6% (95% CI 5.9%-9.8%) in 2013 (58/760 patients) to 14.7% (95% CI 12.3%-17.4%) in 2018 (112/764 patients) (p = 0.0001). TR(34)/L98H (69%) and TR(46)/Y121F/T289A (17%) accounted for 86% of Cyp51A mutations. However, the mean voriconazole MIC of TR(34)/L98H isolates decreased from 8 mg/L (2013) to 2 mg/L (2018), and the voriconazole-resistance frequency was 34% lower in 2018 than in 2013 (p = 0.0001). Our survey showed changing azole phenotypes in TR(34)/L98H isolates, which hampers the use of current PCR-based resistance tests. 01 juli 2020

Landscapes of fear have become widely studied in the northern hemisphere, but are still largely understudied in the more complex, diverse carnivore-prey communities of Africa. Habitat changes brought about by a megaherbivore, the African elephant (Loxodonta africana), can modify the perceived landscape of fear by predation vulnerable prey species (impala Aepyceros melampus and warthog Phacochoerus africanus) in contrast with non-prey species (white rhinoceros Ceratotherium simum). We hypothesized that by opening up woody vegetation, elephants may modify perceived risk at a landscape-scale, but also at a fine scale by depositing escape impediments in the form of coarse woody debris. We experimentally tested this in Hluhluwe-iMfolozi Park, South Africa, by simulating elephant-induced habitat changes on patch scale (opening up woody vegetation) and within-patch scale (deposition of coarse woody debris) and monitoring the herbivore visitation using camera traps. We compared visitation on the edge of grazing lawns (in proximity of dense vegetation) and the centre (open, highly visible patches), either with or without coarse woody debris and with or without fresh predator scat. We found that mesoherbivore prey species showed contrasting responses, with warthog avoiding plots close to dense vegetation and plots with coarse woody debris. Impala reduced their visitation to dense vegetation patches only during risky times, at night, especially in the presence of predator scat, but did not clearly avoid plots with coarse woody debris. Our study indicates that, in African savannas, the perceived landscape of fear is a highly dynamic phenomenon varying in both space and time and being species-specific. Elephant induced habitat changes may shape landscapes of fear in complex and contrasting ways.

The long-term influence of persistent small herbivores on successional plant community configuration is rarely studied. We used a herbivore exclusion experiment along the successional gradient in a salt-marsh system, to investigate the effects of hares and geese, and hares alone, on plant diversity at five successional stages (the earliest, two early, the intermediate and the late successional stages) in the short and long term, i.e. 7 and 22 years, respectively. Plant diversity declined over time at all successional stages except for the earliest one. Small herbivores slowed down species decline, but only at one early successional stage. Small herbivores slowed down species decline via decreasing dominance of preferred grass Festuca rubra in the short term, and less preferred Elytrigia atherica in the long term. The effects of hares and geese were more pronounced than hares alone, indicating an important additive role of geese, especially in the long term. Synthesis. Small herbivores can have a strong and long-lasting impact on plant diversity, but it highly depends on the abundance of small herbivores, which in turn depends on the quality and abundance of forage plants. A diverse herbivore community may have more positive effects on regulating plant communities. Fil: Chen, Qingqing. University Of Groningen; Países Bajos Fil: Howison, Ruth A.. University Of Groningen; Países Bajos Fil: Bakker, Jan P.. University Of Groningen; Países Bajos Fil: Alberti, Juan. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mar del Plata. Instituto de Investigaciones Marinas y Costeras. Universidad Nacional de Mar del Plata. Facultad de Ciencias Exactas y Naturales. Instituto de Investigaciones Marinas y Costeras; Argentina Fil: Kuijper, Dries P. J.. Mammal Research Institute Of The Polish Academy Of Sciences; Polonia Fil: Olff, Han. University Of Groningen; Países Bajos Fil: Smit, Christian. University Of Groningen; Países Bajos

The recolonization of wolves in European human-dominated landscapes poses a conservation challenge to protect this species and manage conflicts. The question of how humans can co-exist with large carnivores often triggers strong emotions. Here we provide an objective, science-based discussion on possible management approaches. Using existing knowledge on large carnivore management from Europe and other parts of the globe, we develop four potential wolf management scenarios; 1) population control, 2) protection and compensation, 3) fencing, 4) managing behaviour of wolf and man. For each scenario, we discuss its impact on wolf ecology, its prospects of reducing wolf-human conflicts and how it relates to current European legislation. Population control and fencing of local wolf populations are problematic because of their ecological impacts and conflicts with European legislation. In contrast, a no-interference approach does not have these problems but will likely increase human-wolf conflicts. Despite the large challenges in European, human-dominated landscapes, we argue that wolf management must focus on strengthening the separation between humans and wolves by influencing behaviour of wolves and humans on a fine spatio-temporal scale to prevent and reduce conflicts. As separation also demands a sufficiently large wild prey base, we urge restoring natural ungulate populations, to reduce human-wolf conflicts. Mutual avoidance provides the key to success, and is critical to avoid creating the conditions for reinstating wolf persecution as the default policy in Europe.

Spatial variation in habitat riskiness has a major influence on the predator–prey space race. However, the outcome of this race can be modulated if prey shares enemies with fellow prey (i.e., another prey species). Sharing of natural enemies may result in apparent competition, and its implications for prey space use remain poorly studied. Our objective was to test how prey species spend time among habitats that differ in riskiness, and how shared predation modulates the space use by prey species. We studied a one‐predator, two‐prey system in a coastal dune landscape in the Netherlands with the European hare (Lepus europaeus) and European rabbit (Oryctolagus cuniculus) as sympatric prey species and red fox (Vulpes vulpes) as their main predator. The fine‐scale space use by each species was quantified using camera traps. We quantified residence time as an index of space use. Hares and rabbits spent time differently among habitats that differ in riskiness. Space use by predators and habitat riskiness affected space use by hares more strongly than space use by rabbits. Residence time of hare was shorter in habitats in which the predator was efficient in searching or capturing prey species. However, hares spent more time in edge habitat when foxes were present, even though foxes are considered ambush predators. Shared predation affected the predator–prey space race for hares positively, and more strongly than the predator–prey space race for rabbits, which were not affected. Shared predation reversed the predator–prey space race between foxes and hares, whereas shared predation possibly also released a negative association and promoted a positive association between our two sympatric prey species. Habitat riskiness, species presence, and prey species’ escape mode and foraging mode (i.e., central‐place vs. noncentral‐place forager) affected the prey space race under shared predation.

Large carnivores can reduce ungulate numbers by predation and via induced risk effects alter ungulate behavior, indirectly affecting lower trophic levels. However, predator-induced risk effects probably act at different spatial scales, which have often been ignored in trophic cascade studies. We studied how a fine-scale risk factor (distance from tree logs) affects ungulate browsing intensity and how this is modified over a landscape-scale risk gradient (distance from human settlements to wolf core) in the Białowieża forest, Poland. We found that landscape-and fine-scale risk factors strongly interacted in determining the strength and magnitude of carnivore-induced risk effects on lower trophic levels. In low-risk areas, tree logs reduced browsing intensity in small patches (approx. 4–6 m from logs), whereas in high-risk areas browsing intensity was reduced up to at least 16 m from tree logs. Moreover, the magnitude of these effects changed, with the strongest reduction in browsing intensity around tree logs in high-risk areas (up to 37%) and the smallest in low-risk areas (< 20%). Overall, the results of this study indicate that perceived risk factors act at different spatial scales, where impediments (objects blocking view and escape routes) act as a risk factor at a fine scale and carnivore distribution shapes perceived risk at the landscape scale. Moreover, these risk factors strongly interact, thereby determining the functional role of large carnivores in affecting ecosystem processes. These interactive effects should be incorporated in predator-induced trophic cascade studies to understand patterns of tree regeneration in ecosystems where large carnivores and herbivores live together.

We analyzed intestinal contents of two late-glacial mastodons preserved in lake sediments in Ohio (Burning Tree mastodon) and Michigan (Heisler mastodon). A multi-proxy suite of macrofossils and microfossils provided unique insights into what these individuals had eaten just before they died and added significantly to knowledge of mastodon diets. We reconstructed the mastodons’ habitats with similar multi-proxy analyses of the embedding lake sediments. Non-pollen palynomorphs, especially spores of coprophilous fungi differentiated intestinal and environmental samples. The Burning Tree mastodon gut sample originates from the small intestine. The Heisler mastodon sample is part of the large intestine to which humans had added clastic material to anchor parts of the carcass under water to cache the meat. Both carcasses had been dismembered, suggesting that the mastodons had been hunted or scavenged, in line with other contemporaneous mastodon finds and the timing of early human incursion into the Midwest. Both mastodons lived in mixed coniferous-deciduous late-glacial forests. They browsed tree leaves and twigs, especiallyPicea. They also ate sedge-swamp plants and drank the lake water. Our multi-proxy estimates for a spring/summer season of death contrast with autumn estimates derived from prior tusk analyses. We document the recovered fossil remains with photographs.

Background Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs. Methods We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016–April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study. Results Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents. Conclusions Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation.

Background A high prevalence of COVID‐19 associated pulmonary aspergillosis (CAPA) has been reported, though histopathological evidence is frequently lacking. To assess the clinical significance of Aspergillus species in respiratory samples of mechanically ventilated COVID‐19 patients, we implemented routine screening for Aspergillus in tracheal aspirate (TA). Patients/methods From all adult COVID‐19 patients admitted to the intensive care unit (ICU), TA samples were collected twice a week for Aspergillus screening by PCR and or culture. Bronchoalveolar lavage (BAL) sampling was performed in patients with a positive screening result if possible. Clinical information was obtained from the electronic patient record and patients were categorised according to the recently published consensus case definition for CAPA. Results Our study population consisted of 63 predominantly (73%) male patients, with a median age of 62 years and total median ICU stay of 18 days. Aspergillus species were present in TA screening samples from 15 patients (24%), and probable CAPA was diagnosed in 11 (17%) patients. Triazole resistance was detected in one patient (14%). Concordance between TA and BAL was 86%, and all TA culture positives were confirmed in BAL. We were able to withhold treatment in three of fifteen patients with positive screening (20%) but negative BAL results. Conclusions Positive culture, molecular detection and or antigen detection of Aspergillus species do not equal infection. Until we understand the clinical relevance of Aspergillus species detected in respiratory samples of COVID‐19 patients, minimal‐invasive screening by TA is a feasible method to monitor patients. Positive screening results should be an indication to perform a BAL to rule out upper airway colonisation.

Impediments, such as tree logs, can prevent access to saplings for deer, and can increase perceived predation risk by blocking view and escape possibilities for deer in areas with large carnivores. Therefore, impediments can influence deer foraging decisions and the trade-off between safety and food of different quality indirectly influencing tree regeneration. The aim of our study was to test how the presence of an impediment affects deer foraging behavior and tree sapling performance of eight species that differ in preference by deer. We planted saplings without, nearby and inside impediments and followed their fate for three consecutive years in Bialowieza forest, Poland. We constructed 1 m high impediments of 5 × 5 m that would still allow deer to enter the impediment and forage from the saplings planted inside. However, we never recorded deer inside the impediments. Near the impediments deer visitation rate and cumulative visitation time was reduced. As a result, browsing intensity of all tree species was lower nearby and especially inside the impediment. Deer did not select different tree species without, near or inside the impediment. Due to the overall lower browsing intensity, tree saplings increased in height near the impediment and heights increased significantly within the impediment. The palatable, but browsing intolerant, Acer platanoides benefited most from the impediment as this species was highly selected and heavily browsed without an impediment. Followed by the palatable, but more browse tolerant Tilia cordata and Pyrus pyraster. In comparison, the presence of an impediment had a smaller effect on the less preferred Alnus glutinosa, Picea abies and Pinus sylvestris which survived well without an impediment. Our study showed that impediments modified deer behavior as they visited these plots less frequently and thereby indirectly reduced the browsing impact on the preferred tree species. Therefore, the potential for successful recruitment of preferred tree species is higher near an impediment, and especially when surrounded by impediment structures. In the long-term, the presence of natural impediments like tree logs allows browsing intolerant tree species to escape browsing, ultimately leading to a more diverse forest composition.

We analyzed the effect of forest management and wolf (Canis lupus) space-use on diet composition of red deer (Cervus elaphus) and European bison (Bison bonasus) in Bialowieza Primeval Forest (BPF), Poland. The red deer is the main prey species for the wolf, whereas the European bison is rarely preyed upon. As both species behave as intermediate feeders in BPF, we expected a large overlap in their diet composition. The red deer perceives the risk of wolf predation; thus, we hypothesized that its diet would change in relation to the intensity of wolf space-use, whereas bison’s would not. We compared diet composition between two contrasting management regimes: a national park managed as a protected area (no hunting, no forestry activities, restricted tourism), and an adjacent production forest managed for timber growth and extraction, where hunting on ungulates (but not wolves) does occur. We collected dung pellets of bison and red deer along transects in low and high wolf-use areas (with distance to settlements as proxy for wolf space-use) in both management types and analyzed diet composition using DNA-metabarcoding. In the national park both the bison and red deer had higher proportions of broadleaved tree species in their diet (bison 39%, red deer 42%) than in the managed forest (bison 26%, red deer 28%). The bison diet contained a higher proportion of shrubs, and specifically Rubus in the managed forest (shrubs 29%, Rubus 31%), compared to the national park (shrubs 21%, Rubus 8%). Only in the national park, red deer ate relatively more broadleaved tree species (51%) and fewer forbs (23%) in the high wolf-use area than in the low wolf-use area (33% broadleaved trees versus 37% forbs). Bison showed a qualitatively similar shift in diet composition as red deer, but the shift was not significant and also much smaller in extent. Our results indicate that forest management shapes the diet composition of both ungulate species. In addition, red deer showed larger shifts in diet composition than bison in high versus low wolf-use areas. This suggests that in addition to habitat differences, predation risk also plays a role in shaping the red deer diet. While earlier studies in BPF illustrated that wolves affect fine-scale deer foraging behavior, this study suggests this could potentially lead to changes in diet composition. We present alternative explanations for these diet shifts and urge others to look further into predation risk as a possible driver of dietary shifts in red deer.

We describe four secondary fungal infections caused by Mucorales species in COVID-19 patients. Three COVID-19 associated mucormycosis (CAM) occurred in ICU, one outside ICU. All were men aged > 50 years, three died. Clinical presentations included pulmonary, rhino-orbital cerebral and disseminated infection. Infections occurred in patients with and without diabetes mellitus. CAM is an emerging disease and our observations underscore the need to be aware of invasive mucormycosis, including in COVID-19 patients without (poorly controlled) diabetes mellitus and outside ICU.

OBJECTIVES Cocaine is the second most frequently used illicit drug worldwide (after cannabis), and cocaine use disorder (CUD) related deaths increased globally by 80% from 1990 to 2013. There is yet to be a regulatory-approved treatment. Emerging preclinical evidence indicates that deep brain stimulation (DBS) of the nucleus accumbens may be a therapeutic option. Prior to expanding the costly investigation of DBS for treatment of CUD, it is important to ensure societal cost-effectiveness. AIMS We conducted a threshold and cost-effectiveness analysis to determine the success rate at which DBS would be equivalent to contingency management (CM), recently identified as the most efficacious therapy for treatments of CUDs. MATERIALS AND METHODS Quality of life, efficacy, and safety parameters for CM were obtained from previous literature. Costs were calculated from a societal perspective. Our model predicted the utility benefit based on quality-adjusted-life-years (QALYs) and incremental-cost-effectiveness-ratio resulting from two treatments on a one-, two-, and five-year timeline. RESULTS On a one-year timeline, DBS would need to impart a success rate (i.e., cocaine free) of 70% for it to yield the same utility benefit (0.492 QALYs per year) as CM. At no success rate would DBS be more cost-effective (incremental-cost-effectiveness-ratio

Until recently, metronidazole was the first-line treatment for Clostridioides difficile infection and it is still commonly used. Though resistance has been reported due to the plasmid pCD-METRO, this does not explain all cases. Here, we investigate resistance to metronidazole in a collection of clinical isolates of C. difficile. We find that nearly all isolates demonstrate a heme-dependent increase in the minimal inhibitory concentration for metronidazole, which in some cases leads to isolates being qualified as resistant (MIC > 2 mg/L). Moreover, whole genome sequence analysis reveals a single nucleotide polymorphism in the heme responsive gene hsmA, which defines a metronidazole resistant lineage of PCR ribotype 010 / multilocus sequence type 15 isolates that also includes pCD-METRO containing strains. Together our data demonstrate that heme is crucial for medium-dependent metronidazole resistance in C. difficile.

Hookworms are soil-transmitted helminths that use immune-evasive strategies to persist in the human duodenum where they are responsible for anemia and protein loss. Given their location and immune regulatory effects, hookworms likely impact the bacterial microbiota. However, microbiota studies struggle to deconvolute the effect of hookworms from confounders such as coinfections and malnutrition. We thus used an experimental human hookworm infection model to explore temporal changes in the gut microbiota before and during hookworm infection. Volunteers were dermally exposed to cumulative dosages of 50, 100 or 150 L3 Necator americanus larvae. Fecal samples were collected for microbiota profiling through 16S rRNA gene amplicon sequencing at weeks zero, four, eight, fourteen and twenty. During the acute infection phase (trial week zero to eight) no changes in bacterial diversity were detected. During the established infection phase (trial week eight to twenty), bacterial richness (Chao1, p = .0174) increased significantly over all volunteers. No relation was found between larval dosage and diversity, stability or relative abundance of individual bacterial taxa. GI symptoms were associated with an unstable microbiota during the first eight weeks and rapid recovery at week twenty. Barnesiella, amongst other taxa, was more abundant in volunteers with more GI symptoms throughout the study. In conclusion, this study showed that clinical GI symptoms following N. americanus infection are associated with temporary microbiota instability and relative abundance of specific bacterial taxa. These results suggest a possible role of hookworm-induced enteritis on microbiota stability.

Wild ungulates are a major consumer of agricultural crops in human dominated landscapes. Across Europe, ungulate populations are leading to intensified human-wildlife conflicts. At the same time, ungulates play a vital role in the structuring and functioning of ecosystems, and are also highly appreciated for recreational hunting. Thus, managers often face the challenge of maintaining the benefits of having thriving ungulate populations while simultaneously minimizing their negative impacts. Broadcasting playbacks of predator vocalizations (e.g. dogs barking, wolves howling or humans talking) could potentially be used to induce fear and thereby displace or steer behavior of ungulates from conflict-prone sites resulting in reduced visitation and foraging time and consumption. Predator playback experiments in wilderness areas have repeatedly been demonstrated to reduce the preys´ resource use and impacts on the surrounding landscape, but this has not been tested in agricultural fields where human-ungulate conflicts are most pronounced.. We responded to this need by conducting a predator playback experiment in multiple crop fields in southern Sweden, where multiple ungulate species (fallow deer, roe deer, red deer, moose, wild boar) coexist, using a novel integrated camera trap – speaker system (ABRs) that broadcasts sounds of choice when a camera is triggered by an ungulate. Predator playbacks (wolf, dog, human) reduced deer patch use and crop damage on wheat fields more than playbacks of control sounds (owl, goose, raven). Our results confirm findings from previous studies in wilderness areas, and demonstrate that broadcasting predator playbacks using ABRs may provide an effective tool to reduce crop damage at the scale and duration of our study.

116 environmental samples from a 504 bed clinical hospital obtained in 2017/19 were inoculated into C diff Banana Broth (TM). Six C. difficile and 12 C. pefringens strains were isolated. Antibiotic-resistant Clostridium spp. dominated in hospital environment. To determine Clostridium spp. in hospital environment suitable medium like C diff Banana Broth (TM) should be used. (C) 2021 Published by Elsevier Ltd.

Bacterial vaginosis (BV) is perceived as a condition of disrupted vaginal microbiota, but remains of unknown aetiology. In this study, vaginal microbiota composition was determined in twenty-one women with BV, before and after treatment with metronidazole or clindamycin. Microbiota composition varied greatly between women and defining a (un)healthy vaginal microbiota state remains elusive, challenging BV diagnosis and treatment. While relative abundance of Lactobacillus increased after antibiotic treatment in two-third of women, its abundance was not associated with treatment outcome. Instead, remaining complaints of abnormal vaginal discharge were more common after metronidazole treatment and associated with increased relative abundance of Ureaplasma.

African swine fever (ASF) has been spreading in the Eurasian continent for more than 10 years now. Although the course of ASF in domestic pigs and its negative economic impact on the pork industry are well-known, we still lack a quantitative assessment of the impact of ASF on wild boar (Sus scrofa) populations under natural conditions. Wild boar is not only a reservoir for ASF; it is also one of the key wildlife species affecting structure and functioning of ecosystems. Therefore, knowledge on how ASF affects wild boar populations is crucial to better predict ecosystem response and for the design of scientific-based wild boar management to control ASF. We used a long-term camera trap survey (2012-2017) from the Białowieza Primeval Forest (BPF, Poland), where an ASF outbreak occurred in 2015, to investigate the impact of the disease on wild boar population dynamics under two contrasting management regimes (hunted vs. non-hunted). In the hunted part of BPF ("managed area"), hunting was drastically increased prior and after the first ASF case occurred (March 2015), whereas inside the National Park, hunting was not permitted ("unmanaged area," first detected case in June 2015). Using a random encounter model (REM), we showed that the density and abundance of wild boar dropped by 84 and 95% within 1 year following ASF outbreak in the unmanaged and managed area, respectively. In the managed area, we showed that 11-22% additional mortality could be attributed to hunting. Our study suggests that ASF-induced mortality, by far, outweighs hunting-induced mortality in causing wild boar population decline and shows that intensified hunting in newly ASF-infected areas does not achieve much greater reduction of population size than what is already caused by the ASF virus. published

Diet and body mass index (BMI) have been shown to affect the gut microbiota of children, but studies are largely performed in developed countries. Here, we conducted a cross-sectional investigation on the differences in the bacterial gut microbiota between normal-weight and overweight urban Filipino children, and determined the relationship between their energy, macronutrient and dietary fiber intakes, and their gut microbiota composition and diversity. Forty-three children (normal-weight, n = 32, overweight, n = 11) participated in the study. Energy and fiber intakes were collected using a semi-quantitative Food Frequency Questionnaire (FFQ). The gut microbiota was profiled using 16S rRNA gene amplicon sequencing of the V3&ndash, V4 region. The diet of the children was a mixture of traditional and Western patterns. There were no significant differences in energy, macronutrients and energy-adjusted fiber intakes between the normal-weight and overweight groups, but there were significantly more children meeting the recommended fiber intake in the overweight group. Alpha and beta bacterial diversities did not significantly differ between weight groups. Relative abundance of Bifidobacterium, Turicibacter and Clostridiaceae 1 were higher in the normal-weight than overweight children, and Lachnospira was higher in overweight children.

Clostridioides difficile is one of the most important healthcare-associated pathogens. Recently, several new 027-like types have been found that all belong to the multilocus sequence typing (MLST) Clade 2. We report a rapidly spreading outbreak of C. difficile infections (CDI) due to a newly identified PCR ribotype (RT) 181 in a Rehabilitation Centre (RC). Genomic analysis revealed the outbreak strain, not previously identified in Greece, belonged to clade 2, sequence type (ST) 1 and had a 18bp deletion in tcdC at position 311 together with a single nucleotide deletion at position 117, similarly to RT 027. The presence of a clonal outbreak was confirmed by whole genome sequencing, yet the source of this ribotype remained unclear. The emergence and rapid spread of new C. difficile ribotypes highlights the need for ongoing C. difficile surveillance and better understanding of overall Clade 2 phylogeny. (C) 2020 Elsevier Ltd. All rights reserved.

To understand the relationship between the gut microbiota and the health profile of Indonesians, it is important to elucidate the characteristics of the bacterial communities that prevail in this population. To this end, we profiled the faecal bacterial community of 140 Indonesian schoolchildren in urban Makassar. The core microbiota of Indonesian schoolchildren consisted of Bifidobacterium, Collinsella, and multiple members of the Lachnospiraceae and Ruminicoccaceae families, but the relative abundance of these taxa varied greatly among children. Socioeconomic status (SES) was the main driver for differences in microbiota composition. Multiple bacterial genera were differentially abundant between high and low SES children, including Bifidobacterium, Lactobacillus, Prevotella, and Escherichia-Shigella. In addition, the microbiota of high SES children was less diverse and strongly associated with body mass index (BMI). In low SES children, helminth infection was prevalent and positively associated with Olsenella, Enterohabdus, Lactobacillus, and Mogibacterium abundance, while negatively associated with relative abundance of Prevotella. Protozoa infection was also prevalent, and positively associated with Rikenellaceae, while it was negatively associated with the relative abundance of Romboutsia and Prevotella. In conclusion, Indonesian schoolchildren living in urban Makassar share a core microbiota, but their microbiota varies in diversity and relative abundance of specific bacterial taxa depending on socioeconomic status, nutritional status, and intestinal parasites infection.

Gut microbiota composition in patients with Clostridioides difficile colonization is not well investigated. We aimed to identify bacterial signatures associated with resistance and susceptibility to C. difficile colonization (CDC) and infection (CDI). Therefore, gut microbiota composition from patients with CDC (n = 41), with CDI (n = 41), and without CDC (controls, n = 43) was determined through 16S rRNA gene amplicon sequencing. Bacterial diversity was decreased in CDC and CDI patients (p&lt, 0.01). Overall microbiota composition was significantly different between control, CDC, and CDI patients (p = 0.001). Relative abundance of Clostridioides (most likely C. difficile) increased stepwise from controls to CDC and CDI patients. In addition, differential abundance analysis revealed that CDI patients&rsquo, gut microbiota was characterized by significantly higher relative abundance of Bacteroides and Veillonella than CDC patients and controls. Control patients had significantly higher Eubacterium hallii and Fusicatenibacter abundance than colonized patients. Network analysis indicated that Fusicatenibacter was negatively associated with Clostridioides in CDI patients, while Veillonella was positively associated with Clostridioides in CDC patients. Bacterial microbiota diversity decreased in both CDC and CDI patients, but harbored a distinct microbiota. Eubacterium hallii and Fusicatenibacter may indicate resistance against C. difficile colonization and subsequent infection, while Veillonella may indicate susceptibility to colonization and infection by C. difficile.

Two hundred and fifty-three non-duplicate toxigenic Clostridium difficile isolates, collected from February 2012 to December 2014, were evaluated for phenotypic resistance to ten antimicrobial drugs with the E-test gradient diffusion method. All strains of C. difficile were susceptible to metronidazole, vancomycin, and tigecycline. The metronidazole MIC values of the hyperepidemic PCR-ribotypes RT027 and RT176 were higher than those of non-epidemic PCR-ribotypes (p < 0.05, as evidenced by Mann-Whitney U test). In contrast, vancomycin susceptibility did not differ between hyperepidemic and non-epidemic strains, although the difference was almost significant (p = 0.065). Clostridium difficile RT027 and RT176 isolates could be assessed to five and four different susceptibility patterns, respectively, representing various combinations of resistance to different antimicrobial classes. A single point mutation (Thr82Ile) in the gyrA gene was detected in 11 (78.6%) of 14 isolates with high level of resistance to ciprofloxacin and moxifloxacin and four different types of single point mutations (Arg447Lys, Ser416Ala, Asp426Val, Asp426Asn) in the gyrB gene were detected in 4 strains, also with high level of resistance to ciprofloxacin and moxifloxacin. Four different point mutations were detected in the rpoB gene in 21 rifampicin-resistant strains of which one has not been reported previously, GIn489Leu. This study demonstrates the presence of multidrug-resistant C. difficile strains in Polish hospitals over the study period, irrespective of geographical location or reference level of the hospital. (C) 2020 Elsevier Ltd. All rights reserved.

All organisms have a stress response system to cope with environmental threats, yet its precise form varies hugely within and across individuals, populations, and species. While the physiological mechanisms are increasingly understood, how stress responses have evolved remains elusive. Here, we show that important insights can be gained from models that incorporate physiological mechanisms within an evolutionary optimality analysis (the 'evo-mecho' approach). Our approach reveals environmental predictability and physiological constraints as key factors shaping stress response evolution, generating testable predictions about variation across species and contexts. We call for an integrated research programme combining theory, experimental evolution, and comparative analysis to advance scientific understanding of how this core physiological system has evolved.

Clostridium difficile is a leading causative agent of hospital-acquired and community-acquired diarrhea in human. This study aims to characterize the predominant C. difficile strains, RT001 and 126, circulating in Iranian hospitals in relation to resistant phenotypes, the antibiotic resistance genes, and their genetic relatedness. A total number of 735 faecal specimens were collected from patients suspected of CDI in Tehran hospitals. Typing and subtyping of the strains were performed using CE-PCR ribotyping and MLVA, respectively, followed by PCR assays for ARGs and indicators of Tns. Minimum inhibitory concentrations (MICs) of five antibiotics were determined by MIC Test Strips. Among 65 strains recovered from CDI patients, RT001 (32.3%) and RT126 (9.2%) were found as the most frequent ribotypes, and 64 MLVA types were identified. Using MLVA, RT001 and RT126 were subtyped into 6 and 4 groups, respectively. The vanA, nim, tetM, gyrA, gyrB genes were detected in 24.6%, 0%, 89.2%, 95.3%, and 92.3% of the strains, respectively. The indicators of Tns including vanHAX, tndX, and int were found in 0%, 3% and 29.2% of the strains, respectively. The most common amino acid (AA) alterations of GyrA and GyrB were related to substitutions of Thr82 → Val and Ser366 → Val, respectively. Resistance rate to metronidazole, vancomycin, tetracycline, ciprofloxacin, and moxifloxacin was 81.5%, 30.7%, 85%, 79%, and 74%, respectively. This study, for the first time revealed the subtypes of circulating RT001 and RT126 in Iran. It is of importance that the majority of the strains belonging to RT001 were multidrug resistant (MDR). This study also pointed to the intra-hospital dissemination of the strains belonging to RT001 and RT126 for short and long periods, respectively, using MLVA. The most important resistance phenotypes observed in this study was vancomycin-resistant phenotypes. Resistance to metronidazole was also high and highlights the need to determine its resistance mechanisms in the future studies.

Glioblastoma is the most aggressive brain malignancy, for which immunotherapy has failed to prolong survival. Glioblastoma-associated immune infiltrates are dominated by tumor-associated macrophages and microglia (TAMs), which are key mediators of immune suppression and resistance to immunotherapy. We and others demonstrated aberrant expression of glycans in different cancer types. These tumor-associated glycans trigger inhibitory signaling in TAMs through glycan-binding receptors. We investigated the glioblastoma glycocalyx as a tumor-intrinsic immune suppressor. We detected increased expression of both tumor-associated truncated O-linked glycans and their receptor, macrophage galactose-type lectin (MGL), on CD163+ TAMs in glioblastoma patient-derived tumor tissues. In an immunocompetent orthotopic glioma mouse model overexpressing truncated O-linked glycans (MGL ligands), high-dimensional mass cytometry revealed a wide heterogeneity of infiltrating myeloid cells with increased infiltration of PD-L1+ TAMs as well as distant alterations in the bone marrow (BM). Our results demonstrate that glioblastomas exploit cell surface O-linked glycans for local and distant immune modulation. Fil: Dusoswa, Sophie A.. Vrije Universiteit Amsterdam; Países Bajos Fil: Verhoeff, Jan. Vrije Universiteit Amsterdam; Países Bajos Fil: Abels, Erik. Vrije Universiteit Amsterdam; Países Bajos Fil: Mendez Huergo, Santiago Patricio. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: Croci Russo, Diego Omar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos. Universidad Nacional de Cuyo. Facultad de Ciencias Médicas. Instituto de Histología y Embriología de Mendoza Dr. Mario H. Burgos; Argentina Fil: Kuijper, Lisan H.. Vrije Universiteit Amsterdam; Países Bajos Fil: de Miguel, Elena. Vrije Universiteit Amsterdam; Países Bajos Fil: Wouters, Valerie M. C. J.. Vrije Universiteit Amsterdam; Países Bajos Fil: Best, Myron G.. Vrije Universiteit Amsterdam; Países Bajos Fil: Rodriguez, Ernesto. Vrije Universiteit Amsterdam; Países Bajos Fil: Cornelissen, Lenneke A.M.. Vrije Universiteit Amsterdam; Países Bajos Fil: van Vliet, Sandra J.. Vrije Universiteit Amsterdam; Países Bajos Fil: Wesseling, Pieter. Vrije Universiteit Amsterdam; Países Bajos Fil: Breakefield, Xandra O.. Vrije Universiteit Amsterdam; Países Bajos Fil: Noske, David P.. Vrije Universiteit Amsterdam; Países Bajos Fil: Würdinger, Thomas. Harvard Medical School; Estados Unidos Fil: Broekman, Marike L.D.. Harvard Medical School; Estados Unidos Fil: Rabinovich, Gabriel Adrián. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Biología y Medicina Experimental. Fundación de Instituto de Biología y Medicina Experimental. Instituto de Biología y Medicina Experimental; Argentina Fil: van Kooyk, Yvette. Vrije Universiteit Amsterdam; Países Bajos Fil: Garcia Vallejo, Juan J.. Vrije Universiteit Amsterdam; Países Bajos

Background The elderly (≥65 years) are one of the populations most at risk for respiratory tract infections (RTIs). The aim of this study was to determine whether nasal and/or oropharyngeal microbiota profiles are associated with age and RTIs. Methods Nasal and oropharyngeal swabs of 152 controls and 152 patients with an RTI were included. The latter group consisted of 72 patients with an upper respiratory tract infection (URTI) and 80 with a lower respiratory tract infection (LRTI). Both nasal and oropharyngeal swabs were subjected to microbiota profiling using amplicon sequencing of the 16S rRNA gene. Moraxella species were determined using quantitative real-time PCR and culture. Results Based on the microbiota profiles of the controls and the patients with an RTI, eight nasal and nine oropharyngeal microbiota clusters were defined. Nasal microbiota dominated by either Moraxella catarrhalis or Moraxella nonliquefaciens was significantly more prevalent in elderly compared to mid-aged adults in the control group (p = 0.002). Dominance by M. catarrhalis/nonliquefaciens was significantly less prevalent in elderly with an LRTI (p = 0.001) compared to controls with similar age. Conclusions Nasal microbiota dominated by M. catarrhalis/nonliquefaciens is associated with respiratory health in the elderly population.

Method choice throughout the workflow of a microbiome study, from sample collection to DNA extraction and sequencing procedures, can greatly affect results. This study evaluated three different DNA extraction methods and two bioinformatic pipelines by including positive and negative controls and various biological specimens. By identifying an optimal combination of DNA extraction method and bioinformatic pipeline use, we hope to contribute to increased methodological consistency in microbiota studies. Our methods were applied not only to commonly studied samples for microbiota analysis, e.g., feces, but also to more rarely studied, low-biomass samples. Microbiota composition profiles of low-biomass samples (e.g., urine and tumor biopsy specimens) were not always distinguishable from negative controls, or showed partial overlap, confirming the importance of including negative controls in microbiota studies, especially when low bacterial biomass is expected., When studying the microbiome using next-generation sequencing, the DNA extraction method, sequencing procedures, and bioinformatic processing are crucial to obtain reliable data. Method choice has been demonstrated to strongly affect the final biological interpretation. We assessed the performance of three DNA extraction methods and two bioinformatic pipelines for bacterial microbiota profiling through 16S rRNA gene amplicon sequencing, using positive and negative controls for DNA extraction and sequencing and eight different types of high- or low-biomass samples. Performance was evaluated based on quality control passing, DNA yield, richness, diversity, and compositional profiles. All DNA extraction methods retrieved the theoretical relative bacterial abundance with a maximum 3-fold change, although differences were seen between methods, and library preparation and sequencing induced little variation. Bioinformatic pipelines showed different results for observed richness, but diversity and compositional profiles were comparable. DNA extraction methods were successful for feces and oral swabs, and variation induced by DNA extraction methods was lower than intersubject (biological) variation. For low-biomass samples, a mixture of genera present in negative controls and sample-specific genera, possibly representing biological signal, were observed. We conclude that the tested bioinformatic pipelines perform equally, with pipeline-specific advantages and disadvantages. Two out of three extraction methods performed equally well, while one method was less accurate regarding retrieval of compositional profiles. Lastly, we again demonstrate the importance of including negative controls when analyzing low-bacterial-biomass samples. IMPORTANCE Method choice throughout the workflow of a microbiome study, from sample collection to DNA extraction and sequencing procedures, can greatly affect results. This study evaluated three different DNA extraction methods and two bioinformatic pipelines by including positive and negative controls and various biological specimens. By identifying an optimal combination of DNA extraction method and bioinformatic pipeline use, we hope to contribute to increased methodological consistency in microbiota studies. Our methods were applied not only to commonly studied samples for microbiota analysis, e.g., feces, but also to more rarely studied, low-biomass samples. Microbiota composition profiles of low-biomass samples (e.g., urine and tumor biopsy specimens) were not always distinguishable from negative controls, or showed partial overlap, confirming the importance of including negative controls in microbiota studies, especially when low bacterial biomass is expected.

Este artículo se encuentra disponible en la siguiente URL: https://onlinelibrary.wiley.com/doi/10.1111/tbed.13470 This is the peer reviewed version of the following article: Sevilla, E., Marín, C., Delgado-Blas, JF., González-Zorn, B., Vega, S., Kuijper, E., Bolea, R. & Mainar-Jaime, RC. Wild griffon vultures (Gyps fulvus) fed at supplementary feeding stations: Potential carriers of pig pathogens and pig-derived antimicrobial resistance?. Transbounddary and Emergency Diseases, vol. 67, i. 3 (may 2020), pp. 1295-1305, which has been published in final form at https://doi.org/10.1111/tbed.13470. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. Este es el post-print del siguiente artículo: Sevilla, E., Marín, C., Delgado-Blas, JF., González-Zorn, B., Vega, S., Kuijper, E., Bolea, R. & Mainar-Jaime, RC. Wild griffon vultures (Gyps fulvus) fed at supplementary feeding stations: Potential carriers of pig pathogens and pig-derived antimicrobial resistance?. Transbounddary and Emergency Diseases, vol. 67, i. 3 (may 2020), pp. 1295-1305, que se ha publicado de forma definitiva en https://doi.org/10.1111/tbed.13470 The carriage of two important pathogens of pigs, i.e. enterotoxigenic E. coli (ETEC) and Clostridioides difficile, was investigated in 104 cloacal samples from wild griffon vultures (Gyps fulvus) fed on pig carcasses at supplementary feeding stations (SFS), along with their level of antimicrobial resistance (AMR). E. coli was isolated from 90 (86.5%) samples but no ETEC was detected, likely because ETEC fimbriae confer the species specificity of the pathogen. Resistance to at least one antimicrobial agent was detected in 89.9% of E. coli isolates, being AMR levels extremely high (>70%) for tetracycline and streptomycin, and very high (>50%) for ampicillin and sulfamethoxazole-trimethoprim. Resistance to other critically important antimicrobials such as colistin and extended-spectrum cephalosporins was 2.2%, and 1.1%, respectively, and was encoded by the mcr-1 and blaSHV-12 genes. Multidrug resistance was displayed by 80% of the resistant E. coli and blaSHV-12 gene shared plasmid with other AMR genes. In general, resistance patterns in E. coli from vultures mirrored those found in pigs. C. difficile was detected in three samples (2.9%), two of them belonged to PCR-ribotype 078 and one to PCR-ribotype 126, both commonly found in pigs. All C. difficile isolates were characterized by a moderate to high level of resistance to fluoroquinolones and macrolides but susceptible to metronidazole or vancomycin, similar to what is usually found in C. difficile isolates from pigs. Thus, vultures may contribute somewhat to the environmental dissemination of some pig pathogens through their acquisition from pig carcasses and, more importantly, of AMR for antibiotics of critical importance for humans. However, the role of vultures would likely be much lesser than that of disposing pig carcasses at the SFS. The monitoring of AMR, and particularly of colistin resistant and ESLB-producing E. coli, should be considered in pig farms used as sources of carcasses for SFS.

Fecal microbiota transplantation (FMT) is a well-established treatment for recurrent Clostridioides difficile infection. FMT has become a more readily available and useful new treatment option as a result of stool banks. The current state of knowledge indicates that dysbiosis of the gut microbiota is implicated in several disorders in addition to C. difficile infection. Randomized controlled studies have shown FMT to be somewhat effective in treating ulcerative colitis, irritable bowel syndrome, and hepatic encephalopathy. In addition, FMT has been beneficial in treating several other conditions, such as the eradication of multidrug-resistant organisms and graft-versus-host disease. We expect that FMT will soon be implemented as a treatment strategy for several new indications, although further studies are needed.

Large carnivores are recolonizing many regions in Europe, where their ungulate prey have lived without them for >150 years. Whether the returning large carnivores will modify ungulate behavior and indirectly affect lower trophic levels, depends on the ability of ungulates to recognize risk based on past encounters and cues indicating carnivore presence. In two case studies, we tested, by means of camera trapping, the behavioral response of deer to wolf urine. The first case study was in the Netherlands where deer (still) live in absence of wolves, and the second in Poland with long-term wolf presence. As controls we used water (no scent) and all-purpose soap (unfamiliar scent). Deer vigilance level on control plots was 20% in both case studies indicating that wolf occupancy per se does not lead to a consistent difference in behavior. Placing wolf urine did not significantly affect deer behavior in either the wolf-absent or the wolf-present area. More intense cues, or a combination of cues, are likely needed to affect deer behavior. Moreover, we found an unexpected reaction of deer towards all-purpose soap of reduced foraging (and tendency for increased vigilance) in the wolf-present area, whereas it did not affect deer behavior in the wolf-absent area. We hypothesize that deer associate all-purpose soap with human presence, causing no response in human-dominated landscapes (the Netherlands), but triggering a behavioral reaction in more remote areas (Poland). This illustrates attention should be paid to controls used in scent experiments as they may be associated differently than intended.