Cross-contamination of carbapenem-resistant Gram-negative bacteria between patients and the hospital environment in the first year of a newly built surgical ward.

BACKGROUND: Transmission and outbreaks of carbapenem-resistant Gram-negative bacteria (CRGN) in hospitals are often associated with contamination of the wastewater environment. We performed a prospective observational study to investigate the colonization of the hospital wastewater environment during the first year of occupancy of the surgical intermediate and intensive care units of a newly constructed building at the University Hospital of Heidelberg, Germany. METHODS: We performed monthly screening of the wastewater system (toilets and sinks) for 12 months, starting 1 month before opening (1st October 2020 to 30th October 2021). Admission and weekly rectal screening of patients for CRGN were also performed in parallel. Bacterial isolates were characterized by whole-genome sequencing. RESULTS: Twenty-seven of 1978 (1.4%) admitted patients were colonized/infected with CRGN. A total of 29 CRGN isolates from 24 patients and 52 isolates were available for sequencing. Within the first month of occupancy, we identified seven patients colonized/infected with CRGN, while none were found in the environmental reservoirs. The first detection of CRGN isolates in the sewage system started five months after the first occupancy. Two previously non-colonized patients were colonized/infected with Pseudomonas aeruginosa strains colonizing the sewage system. The significant identity of plasmids carrying the carbapenemase gene suggests that long-term colonization of the sewage system facilitates the emergence of new carbapenem-resistant clones. CONCLUSION: Cross-contamination between patients and the hospital environment is bidirectional. Our study demonstrated that contamination of the hospital wastewater environment may lead to persistent colonization and may serve as a reservoir for nosocomial acquisition of CRGN.

The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis.

BACKGROUND: Antimicrobial resistance (AMR) is an ever-growing threat to modern medicine and, according to the latest reports, it causes nearly twice as many deaths globally as AIDS or malaria. Elucidating reservoirs and dissemination routes of antimicrobial resistance genes (ARGs) are essential in fighting AMR. Human commensals represent an important reservoir, which is underexplored for the oral microbiota. Here, we set out to investigate the resistome and phenotypic resistance of oral biofilm microbiota from 179 orally healthy (H), caries active (C), and periodontally diseased (P) individuals (TRN: DRKS00013119, Registration date: 22.10.2022). The samples were analysed using shotgun metagenomic sequencing combined, for the first time, with culture technique. A selection of 997 isolates was tested for resistance to relevant antibiotics. RESULTS: The shotgun metagenomics sequencing resulted in 2,069,295,923 reads classified into 4856 species-level OTUs. PERMANOVA analysis of beta-diversity revealed significant differences between the groups regarding their microbiota composition and their ARG profile. The samples were clustered into three ecotypes based on their microbial composition. The bacterial composition of H and C samples greatly overlapped and was based on ecotypes 1 and 2 whereas ecotype 3 was only detected in periodontitis. We found 64 ARGs conveying resistance to 36 antibiotics, particularly to tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam antibiotics, and a correspondingly high prevalence of phenotypic resistance. Based on the microbiota composition, these ARGs cluster in different resistotypes, and a higher prevalence is found in healthy and caries active than in periodontally diseased individuals. There was a significant association between the resistotypes and the ecotypes. Although numerous associations were found between specific antibiotic resistance and bacterial taxa, only a few taxa showed matching associations with both genotypic and phenotypic analyses. CONCLUSIONS: Our findings show the importance of the oral microbiota from different niches within the oral cavity as a reservoir for antibiotic resistance. Additionally, the present study showed the need for using more than one method to reveal antibiotic resistance within the total oral biofilm, as a clear mismatch between the shotgun metagenomics method and the phenotypic resistance characterization was shown.

IL-1ß knockout increases the intestinal abundancy of Akkermansia muciniphila.

The proinflammatory cytokine interleukin-1ß (IL-1ß) is known to be upregulated in patients suffering from metabolic syndrome. IL-1ß contributes to insulin resistance in obesity and type 2 diabetes, yet its influence on the intestinal microbiome is incompletely understood. The data presented here demonstrate that mice genetically deficient in IL-1ß show a specific alteration of intestinal colonisation of a small group of bacteria. Especially Akkermansia muciniphila, a bacterium reported to be inversely associated with obesity, diabetes, cardiometabolic diseases and low-grade inflammation, showed increased colonisation in IL-1ß knockout mice. In comparative microarray analysis from mucus scrapings of the colon mucosa of IL-1ß knockout and wildtype mice, angiogenin 4 mRNA was strongly reduced in IL-1ß knockout animals. Since the presence of angiogenin 4 in the culture medium showed a significant growth inhibition on A. muciniphila which was not detectable for other bacteria tested, IL-1ß induced expression of angiogenin 4 is a strong candidate to be responsible for the IL-1ß induced suppression of A. muciniphila colonisation. Thus, the data presented here indicate that IL-1ß might be the lacking link between inflammation and suppression of A. muciniphila abundance as observed in a variety of chronic inflammatory disorders.

Epidemiology and outcomes for level 1 and 2 traumas during the first wave of COVID19 in a Canadian centre.

To determine if lockdown measures imposed during the first wave of the COVID19 pandemic affected trauma patterns, volumes, and outcomes in a western Canadian level 1 trauma center, we performed a retrospective cohort study assessing level 1 and 2 trauma patients presenting to our center during the initial COVID19 "lockdown" period (March 15-June 14, 2020) compared to a similar cohort of patients presenting during a "control" period 1 year prior (March 15-June 14, 2019). Overall, we saw a 7.8% reduction in trauma volumes during the lockdown period, and this was associated with a shorter average ED length of stay (6.2 ± 4.7 h vs. 9.7 ± 11.8 h, p = 0.003), reduced time to computed tomography (88.5 ± 68.2 min vs. 105.1 ± 65.5 min, p < 0.001), a reduction in intensive care unit admissions (11.0 ± 4.9% vs. 20.0 ± 15.5%, p = 0.001), and higher injury severity score (6.5 ± 7.6 vs. 6.2 ± 9.5, p = 0.04). Our findings suggest that lockdown measures imposed during the first wave of the COVID19 pandemic had a significant impact on trauma patients.

Behavioural adjustments of predators and prey to wind speed in the boreal forest.

Wind speed can have multifaceted effects on organisms including altering thermoregulation, locomotion, and sensory reception. While forest cover can substantially reduce wind speed at ground level, it is not known if animals living in forests show any behavioural responses to changes in wind speed. Here, we explored how three boreal forest mammals, a predator and two prey, altered their behaviour in response to average daily wind speeds during winter. We collected accelerometer data to determine wind speed effects on activity patterns and kill rates of free-ranging red squirrels (n = 144), snowshoe hares (n = 101), and Canada lynx (n = 27) in Kluane, Yukon from 2015 to 2018. All 3 species responded to increasing wind speeds by changing the time they were active, but effects were strongest in hares, which reduced daily activity by 25%, and lynx, which increased daily activity by 25%. Lynx also increased the number of feeding events by 40% on windy days. These results highlight that wind speed is an important abiotic variable that can affect behaviour, even in forested environments.

Retrospective application of the HEAR score on patients evacuated for chest pain: Assessing the utility of point-of-care troponin.

INTRODUCTION: The HEART scoring system codifies the clinical gestalt used by physicians with 0-2 points assigned to 5 criteria (history, electrocardiography, age, risk factors and troponin). This scoring provides a prognostic tool that assists in disposition planning. The use of a truncated HEART score, minus the troponin data (HEAR score), was used for patients presenting with chest pain at one of four outpost nursing stations served by La Ronge Health Centre in northern Saskatchewan. These nursing stations have no onsite physician and no ability to obtain any troponin data. This study set out to determine if there was any utility in conducting point-of-care (PoC) troponins in these nursing outposts. MATERIALS AND METHODS: A retrospective analysis was conducted using the La Ronge regional electronic medical record by searching for all patients for whom an outpost nurse had called a physician regarding chest pain symptoms between 01 January 2011 and 31 December 2016. The HEAR and HEART score were then calculated for each individual presentation of patients with chest pain that met inclusion and exclusion criteria. RESULTS: By calculating both the patient's HEART score before evacuation from the outposts and after (i.e. with the troponin data), we were able to determine that, in 89.4% of cases (110/123 events), patients would require evacuation regardless of the troponin values due to a HEART score ≥4. In 10.6% (13/124 events) of cases, the patients who were evacuated had a HEART score ≤3, and in only one case did the troponin data increase this score. CONCLUSIONS: The majority of patients would continue to be evacuated regardless of the result of their PoC troponin due to an already elevated HEAR score. PoC troponin is unlikely to reduce the rate of evacuation of patients with chest pain from the nursing stations served by the La Ronge Health Centre.

Résumé Introduction: Le système de pointage HEART codifie la gestalt clinique utilisée par les médecins avec 0­2 points attribués à 5 critères (anamnèse, ECG, âge, facteurs de risque, troponine). Ce pointage est un outil pronostique qui aide à planifier les soins aux patients. Un score HEART tronqué, c'est-à-dire moins les données de troponine (score HEAR), a été utilisé chez les patients qui se présentaient pour douleur thoracique à 1 des 4 avant-postes de soins infirmiers servis par le centre La Ronge Health Centre au nord de la Saskatchewan. Il n'y a pas de médecin sur place à ces postes de soins infirmiers, et il est impossible d'obtenir des données sur la troponine. Cette étude voulait déterminer si le dosage ciblé de troponine est utile dans ces avant-postes de soins infirmiers. Méthodes: Une analyse rétrospective a été réalisée à l'aide du dossier médical électronique de la région de La Ronge après une recherche de tous les patients pour lesquels un avant-poste de soins infirmiers avait appelé un médecin pour des symptômes de douleur thoracique entre le 1er Janvier 2011 et le 31 Décembre 2016. Les scores HEAR et HEART ont alors été calculés pour chaque cas de douleur thoracique qui répondait aux critères d'inclusion et d'exclusion. Résultats: En calculant le score HEART (c.-à-d. avec les données sur la troponine) avant et après l'évacuation du patient de l'avant-poste, nous avons pu déterminer que dans 89,4% des cas (110/123 événements), les patients devraient être évacués sans égard aux valeurs de troponine en raison d'un score HEART ≤3 et la troponine a augmenté ce score dans un seul cas. Conclusions: La majorité des patients continueraient d'être évacués, peu importe les résultats de troponine ciblée en raison d'un score HEAR déjà élevé. La troponine ciblée ne réduirait probablement pas le taux d'évacuation des patients pour douleur thoracique des postes de soins infirmiers servis par le centre La Ronge Health Centre. Mots-clés: Maladie cardiaque, médecine rurale, score HEART, troponine.

Impact of discontinuing contact precautions and enforcement of basic hygiene measures on nosocomial vancomycin-resistant Enterococcus faecium transmission.

OBJECTIVES: Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a pathogen of major concern for public health. Although definitive evidence is lacking, contact precautions have been a crucial element in infection prevention and control (IPC) strategies designed to limit nosocomial VRE transmission. This study investigated the effect of discontinuing contact precautions while enforcing basic hygiene measures, including hand hygiene, environmental cleaning and antiseptic body washing, for patients with VRE in intensive care units (ICUs) on the prevention of nosocomial VRE transmission causing bacteraemia. METHODS: Contact precautions were discontinued in January 2018. In total, 96 VREfm isolates from 61 patients with VREfm bacteraemia and/or colonization hospitalized in eight ICUs in a tertiary care hospital in 2016 and 2019 in were characterized by whole-genome sequencing. VRE transmission was investigated using patient movement data and admission screening for reliable identification of nosocomial acquisition. RESULTS: Discontinuation of contact precautions did not increase VREfm transmission events (eight in 2016 vs one in 2019). While the rate of endogenous VREfm was similar in both years (38% vs 31%), the number of non-colonized patients prior to VREfm bacteraemia was 16 (16/29, 55%) in 2019, which was significantly higher than in 2016 (8/32, 25%). The mean incidence density for VREfm bacteraemia was similar for both years (0.26 vs 0.31 per 1000 patient-days in 2016 and 2019, respectively). CONCLUSION: Discontinuation of contact precautions while enforcing basic hygiene measures did not lead to an increase in nosocomial bloodstream infection rates due to VREfm transmission in a hyperendemic ICU setting.

Whole-genome sequencing disproves two suspected transmission events of blaNDM between Pseudomonas aeruginosa and Enterobacterales in hospitalized patients.

New Delhi metallo-ß-lactamase (blaNDM) acquisition by Gram-negative bacteria is a primary concern due to its broad-host-range distribution. This study investigated two potential in-vivo horizontal gene transfers (HGTs) of blaNDM between Enterobacterales and Pseudomonas aeruginosa, initially indicated by polymerase chain reaction. Whole-genome sequencing showed independent parallel acquisition of two different blaNDM variants (NDM-1 and NDM-5) in P. aeruginosa and Enterobacterales, respectively. The data show that short-read sequencing provides the necessary resolution to confirm or dispute HGT by the comparison of genetic elements surrounding the gene of interest, and thus provide a timely response to potential outbreaks.

Optimisation of energetic and reproductive gains explains behavioural responses to environmental variation across seasons and years.

Animals switch between inactive and active states, simultaneously impacting their energy intake, energy expenditure and predation risk, and collectively defining how they engage with environmental variation and trophic interactions. We assess daily activity responses to long-term variation in temperature, resources and mating opportunities to examine whether individuals choose to be active or inactive according to an optimisation of the relative energetic and reproductive gains each state offers. We show that this simplified behavioural decision approach predicts most activity variation (R2  = 0.83) expressed by free-ranging red squirrels over 4 years, as quantified through accelerometer recordings (489 deployments; 5066 squirrel-days). Recognising activity as a determinant of energetic status, the predictability of activity variation aggregated at a daily scale, and the clear signal that behaviour is environmentally forced through optimisation of gain, provides an integrated approach to examine behavioural variation as an intermediary between environmental variation and energetic, life-history and ecological outcomes.

Alteration of antibiotic regimen as an additional control measure in suspected multi-drug-resistant Enterobacter cloacae outbreak in a neonatal intensive care unit.

BACKGROUND: Increased occurrence of a particular species of Gram-negative bacteria (GNB), especially when multi-drug-resistant (MDR), in routine screening surveillance in neonatal intensive care units (NICUs) can be evoked by selection pressure. AIM: To evaluate adaptation of the empiric antibiotic regimen for its usefulness as a control measure in suspected outbreaks in the NICU. METHODS: In a retrospective outbreak analysis, cases between 1st December 2017 and 31st March 2018 were identified through microbiology and hygiene surveillance records. Furthermore, risk factors for MDR-GNB colonization were collected. Whole-genome sequencing (WGS) was performed on all isolates. Control measure documentations and interviews were employed to define interventions. As well as infection control measures, administration of third-generation cephalosporins was avoided and replaced whenever clinically acceptable as part of the intervention bundle. FINDINGS: In total, nine patients were found to have rectal colonization with third-generation cephalosporin-resistant Enterobacter cloacae in routine screening surveillance in the pre-intervention period. After implementation of an infection control bundle, the incidence declined rapidly. WGS analysis revealed that two MDR E. cloacae were transmitted, and the majority were new cases. The incidence density of MDR-GNB colonization was 7.94/1000 patient-days (PD) before the intervention and 1.68/1000 PD during the altered antibiotic regimen. No infections with MDR-GNB occurred during the study. CONCLUSIONS: Altering the antibiotic regimen with regard to selection pressure may be considered as part of an intervention bundle to rapidly control the emergence of MDR-GNB in suspected outbreak situations in the NICU.

Comparative genomic analysis reveals a high prevalence of inter-species in vivo transfer of carbapenem-resistance plasmids in patients with haematological malignancies.

OBJECTIVES: Conjugative gene transfer has been considered as one of the driving factors in the transmission and dissemination of multidrug resistance in bacteria. The abundance of antimicrobial resistance genes and bacteria in the gut microbiome may provide the ideal platform for plasmid exchange. Systematic data on in vivo horizontal gene transfer (HGT) and its frequency are scarce. MATERIALS AND METHODS: One hundred and ninety-six carbapenem-resistant gram-negative bacilli (CRGNBs) from 179 patients (158 inpatients and 21 outpatients) between January 2016 and April 2017 were analysed retrospectively. Alignment of plasmid content for 32 isolates from 16 patients with multiple CRGNB species was performed from whole-genome sequencing (WGS) data. RESULTS: Sixteen of the 179 patients (8.9%) were colonized and/or infected with more than one CRGNB species; 11/179 (6.1%) were colonized by multiple carbapenem-resistant Enterobacteriaceae (CREs) and 5/179 (2.8%) by carbapenem-resistant non-fermenters (CRNFs) and CREs. WGS suggested interspecies transfer as the predominant mechanism rather than independent acquisition in 8/10 patients (80%, one non-recoverable isolate) with multiple CREs but not in CRNF-CRE combinations; 30/158 inpatients (20%) had underlying haematological malignancies, and they are more likely to exhibit multiple CRGNB strains (OR 3.0, 95%CI 0.98-8.89, p 0.05) and CRE strains (OR 3.9, 95%CI 1.02-14.58, p 0.04) during hospital stay compared to other patient groups. CONCLUSION: Our data give insight into the occurrence of natural in vivo HGT in a clinical setting. Better understanding of HGT will help optimize containment measures and may guide antibiotic stewardship programmes.

Induction of tumor-specific CTL responses using the C-terminal fragment of Viral protein R as cell penetrating peptide.

The discovery of tumor-associated antigens recognized by T lymphocytes opens the possibility of vaccinating cancer patients with defined antigens. However, one of the major limitation of peptide-based vaccines is the low immunogenicity of antigenic peptides. Interestingly, if these epitopes are directly delivered into the cytoplasm of antigen presenting cells, they can be efficiently presented via the direct MHC class I presentation pathway. To improve antigen entry, one promising approach is the use of cell penetrating peptides (CPPs). However, most studies use a covalent binding of the CPP with the antigen. In the present study, we focused on the C-terminal domain of Vpr which was previously demonstrated to efficiently deliver plasmid DNA into cells. We provide evidence that the peptides Vpr55-91 and Vpr55-82 possess the capacity of delivering proteins and epitopes into cell lines as well as into human primary dendritic cells, without the necessicity for a chemical linkage. Moreover, immunization of HLA-A2 transgenic mice with Vpr55-91 as the sole adjuvant is able to induce antigen-specific cytotoxic T lymphocytes against multiple tumor epitopes.

Import of community-associated, methicillin-resistant Staphylococcus aureus to Europe through skin and soft-tissue infection in intercontinental travellers, 2011-2016.

OBJECTIVES: Recently, following import by travel and migration, epidemic community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has caused nosocomial outbreaks in Europe, sometimes with a fatal outcome. We describe clinico-epidemiological characteristics of CA-MRSA detected by the European Network for the Surveillance of imported S. aureus (www.staphtrav.eu) from May 2011 to November 2016. METHODS: Sentinel surveillance at 13 travel clinics enrolling patients with travel-associated skin and soft-tissue infection (SSTI) and analysing lesion and nose swabs at one central laboratory. RESULTS: A total of 564 independent case-patients with SSTI were enrolled and had 374 (67%) S. aureus-positive lesions, of which 14% (51/374) were MRSA. The majority of CA-MRSA isolates from SSTI were Panton-Valentine leucocidin (PVL) -positive (43/51, 84%). The risk of methicillin-resistance in imported S. aureus varied by travel region (p <0.001) and was highest in Latin America (16/57, 28%, 95% CI 17.0-41.5) and lowest in Sub-Saharan Africa (4/121, 3%, 95% CI 0.9-8.3). Major epidemic clones (USA300 / USA300 Latin-American Variant, Bengal Bay, South Pacific) accounted for more than one-third (19/51, 37%) of CA-MRSA imports. CA-MRSA SSTI in returnees was complicated (31/51 multiple lesions, 61%; 22/50 recurrences, 44%), led to health-care contact (22/51 surgical drainage, 43%; 7/50 hospitalization, 14%), was transmissible (13/47 reported similar SSTI in non-travelling contacts, 28%), and associated with S. aureus nasal colonization (28 of 51 CA-MRSA cases, 55%; 24 of 28 colonized with identical spa-type in nose and lesion, 85%). CONCLUSIONS: Travel-associated CA-MRSA SSTI is a transmissible condition that leads to medical consultations and colonization of the infected host.

Improving the assessment of predator functional responses by considering alternate prey and predator interactions.

To improve understanding of the complex and variable patterns of predator foraging behavior in natural systems, it is critical to determine how density-dependent predation and predator hunting success are mediated by alternate prey or predator interference. Despite considerable theory and debate seeking to place predator-prey interactions in a more realistic context, few empirical studies have quantified the role of alternate prey or intraspecific interactions on predator-prey dynamics. We assessed functional responses of two similarly sized, sympatric carnivores, lynx (Lynx canadensis) and coyotes (Canis latrans), foraging on common primary (snowshoe hares; Lepus americanus) and alternate (red squirrels; Tamiasciurus hudsonicus) prey in a natural system. Lynx exhibited a hyperbolic prey-dependent response to changes in hare density, which is characteristic of predators relying primarily on a single prey species. In contrast, the lynx-squirrel response was found to be linear ratio dependent, or inversely dependent on hare density. The coyote-hare and coyote-squirrel interactions also were linear and influenced by predator density. We explain these novel results by apparent use of spatial and temporal refuges by prey, and the likelihood that predators commonly experience interference and lack of satiation when foraging. Our study provides empirical support from a natural predator-prey system that (1) predation rate may not be limited at high prey densities when prey are small or rarely captured; (2) interference competition may influence the predator functional response; and (3) predator interference has a variable role across different prey types. Ultimately, distinct functional responses of predators to different prey types illustrates the complexity associated with predator-prey interactions in natural systems and highlights the need to investigate predator behavior and predation rate in relation to the broader ecological community.

Post-weaning parental care increases fitness but is not heritable in North American red squirrels.

Most empirical attempts to explain the evolution of parental care have focused on its costs and benefits (i.e. fitness consequences). In contrast, few investigations have been made of the other necessary prerequisite for evolutionary change, inheritance. Here, we examine the fitness consequences and heritability (h(2)) of a post-weaning parental care behaviour (territory bequeathal) in a wild population of North American red squirrels. Each year, a subset (average across all years = 19%) of reproductive females bequeathed their territory to a dependent offspring. Bequeathing females experienced higher annual reproductive success and did not suffer a survival cost to themselves relative to those females retaining their territory. Bequeathing females thus realized higher relative annual fitness [ω = 1.18 ± 0.03 (SE)] than nonbequeathing females [ω = 0.96 ± 0.02 (SE)]. Additive genetic influences on bequeathal behaviour, however, were not significantly different from 0 (h(2) = 1.9 × 10(-3); 95% highest posterior density interval = 3.04 × 10(-8) to 0.37) and, in fact, bequeathal behaviour was not significantly repeatable (R = 2.0 × 10(-3); 95% HPD interval = 0-0.27). In contrast, directional environmental influences were apparent. Females were more likely to bequeath in years following low food abundance and when food availability in the upcoming autumn was high. Despite an evident fitness benefit, a lack of heritable genetic variance will constrain evolution of this trait.

Selection on female behaviour fluctuates with offspring environment.

Temporal variation in selection has long been proposed as a mechanism by which genetic variation could be maintained despite short-term strong directional selection and has been invoked to explain the maintenance of consistent individual differences in behaviour. We tested the hypothesis that ecological changes through time lead to fluctuating selection, which could promote the maintenance of variation in female behavioural traits in a wild population of North American red squirrels. As predicted, linear selection gradients on female aggression and activity significantly fluctuated across years depending on the level of competition among juveniles for vacant territories. This selection acted primarily through juvenile overwinter survival rather than maternal fecundity. Incorporating uncertainty in individual measures of behaviour reduced the magnitude of annual selection gradients and increased uncertainty in these estimates, but did not affect the overall pattern of temporal fluctuations in natural selection that coincided with the intensity of competition for vacant territories. These temporal fluctuations in selection might, therefore, promote the maintenance of heritable individual differences in behaviour in this wild red squirrel population.

Microbiome investigation in the ecological speciation context of lake whitefish (Coregonus clupeaformis) using next-generation sequencing.

Few studies have applied NGS methods to investigate the microbiome of vertebrates in their natural environment and in freshwater fishes in particularly. Here, we used pyrosequencing of the 16S gene rRNA to (i) test for differences in kidney bacterial communities (i.e. microbiota) of dwarf and normal whitefish found as sympatric pairs, (ii) test the hypothesis of higher bacterial diversity in normal compared with dwarf whitefish and (iii) test for the occurrence of parallelism with the presence and composition of bacterial communities across species pairs inhabiting different lakes. The kidney microbiota of 253 dwarf and normal whitefish from five lakes was analysed combining a double-nested PCR approach with 454 pyrosequencing. Bacteria were detected in 52.6% of the analysed whitefish. There was no overall significant difference among lakes and forms, although the lake × form interaction was found significant. We identified 579 bacterial genera, which is substantially more than previous descriptions using less sensitive techniques of fish bacterial diversity in kidney, pathogenic or not. Ten of these genera contained eighteen pathogenic species. Differences in bacteria composition between whitefish forms were not parallel among lakes. In accordance with the higher diversity of prey types, normal whitefish kidney tissue consistently had a more diverse bacterial community and this pattern was parallel among lakes. These results add to building evidence from previous studies on this system that the adaptive divergence of dwarf, and normal whitefish has been driven by both parallel and nonparallel ecological conditions across lakes.

Measurement-induced qubit state mixing in circuit QED from up-converted dephasing noise.

We observe measurement-induced qubit state mixing in a transmon qubit dispersively coupled to a planar readout cavity. Our results indicate that dephasing noise at the qubit-readout detuning frequency is up-converted by readout photons to cause spurious qubit state transitions, thus limiting the nondemolition character of the readout. Furthermore, we use the qubit transition rate as a tool to extract an equivalent flux noise spectral density at f~1 GHz and find agreement with values extrapolated from a 1/f(α) fit to the measured flux noise spectral density below 1 Hz.

Regional boreal biodiversity peaks at intermediate human disturbance.

The worldwide biodiversity crisis has intensified the need to better understand how biodiversity and human disturbance are related. The 'intermediate disturbance hypothesis' suggests that disturbance regimes generate predictable non-linear patterns in species richness. Evidence often contradicts intermediate disturbance hypothesis at small scales, and is generally lacking at large regional scales. Here, we present the largest extent study of human impacts on boreal plant biodiversity to date. Disturbance extent ranged from 0 to 100% disturbed in vascular plant communities, varying from intact forest to agricultural fields, forestry cut blocks and oil sands. We show for the first time that across a broad region species richness peaked in communities with intermediate anthropogenic disturbance, as predicted by intermediate disturbance hypothesis, even when accounting for many environmental covariates. Intermediate disturbance hypothesis was consistently supported across trees, shrubs, forbs and grasses, with temporary and perpetual disturbances. However, only native species fit this pattern; exotic species richness increased linearly with disturbance.

Low heritabilities, but genetic and maternal correlations between red squirrel behaviours.

Consistent individual differences in behaviour, and behavioural correlations within and across contexts, are referred to as animal personalities. These patterns of variation have been identified in many animal taxa and are likely to have important ecological and evolutionary consequences. Despite their importance, genetic and environmental sources of variation in personalities have rarely been characterized in wild populations. We used a Bayesian animal model approach to estimate genetic parameters for aggression, activity and docility in North American red squirrels (Tamiasciurus hudsonicus). We found support for low heritabilities (0.08-0.12), and cohort effects (0.07-0.09), as well as low to moderate maternal effects (0.07-0.15) and permanent environmental effects (0.08-0.16). Finally, we found evidence of a substantial positive genetic correlation (0.68) and maternal effects correlation (0.58) between activity and aggression providing evidence of genetically based behavioural correlations in red squirrels. These results provide evidence for the presence of heritable variation in red squirrel behaviour, but also emphasize the role of other sources of variation, including maternal effects, in shaping patterns of variation and covariation in behavioural traits.