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Introduction The functional relevance of intra-species diversity in natural microbial communities remains largely unexplored. The guts of two closely related honey bee species, Apis cerana and A. mellifera, are colonised by a similar set of core bacterial species composed of host-specific strains, thereby providing a good model for an intra-species diversity study. Objective and method We used shotgun metagenomic sequencing to assess the functional relevance of intra-species diversity of A. cerana and A. mellifera gut microbiota. Results Comparative analysis showed that the strain composition of the core bacterial species was host-specific. These core bacterial species presented distinctive functional profiles between the hosts. However, the overall functional profiles of the A. cerana and A. mellifera gut microbiomes were similar; this was further supported by the consistency of the honey bees’ gut metabolome, as the gut microbiota of different honey bee species showed rather similar metabolic profiles in the cross-species gut bacteria colonisation assay. Moreover, this experiment also demonstrated that the gut microbiota of A. cerana and A. mellifera could cross colonise between the two honey bee species. Conclusion In summary, our findings revealed functional differences in most core gut bacteria between the guts of A. cerana and A. mellifera, which may be associated with their inter-species diversity. However, the functional profiles of the overall gut microbiomes between the two honey bee species converge, probably as a result of the overlapping ecological niches of the two species. Our findings provide critical insights into the evolution and functional roles of the mutualistic microbiota of honey bees and reveal that functional redundancy could stabilise the gene content diversity at the strain-level within the gut community.

The effect of plastic wrapping on decomposition rate and carrion fauna of rabbits (Oryctolagus cuniculus L.) was examined in spring in a semi-urban area in North Algeria. All decomposition stages were observed in all carcasses, with the same durations in the control but different durations in the wrapped carcasses. Decomposition of the carcasses in the plastic wrapping was significantly slower than that of the exposed ones. A total of 12,516 specimens, belonging to 36 families and 69 species, were morphologically identified. Thirteen species of forensic relevance were also identified at the molecular level using the cytochrome c oxidase I (COI) barcode region, and the sequences were submitted to online databases. Wrapping had a significant effect on species composition (χ2 = 569.269, df = 55, p

Wildflower areas have become a staple tool within agro-environmental schemes (AES) to counteract pollinator declines. While their role in providing food resources to resident flower-visiting insects is unambiguous, the conservation effectiveness in a landscape context is less clear. Particularly, how multiple vs. single wildflower area utilization differs between simple and complex landscapes is understudied. We examined colonisation and community dynamics of wild bees and hoverflies in 33 newly established wildflower areas across a gradient of landscape complexity (amount of semi-natural habitat) and connectivity (presence of additional wildflower areas) for seven weeks during three consecutive years (one year during and two after establishment). We recorded more than 25% of the wild bee and hoverfly species of Hesse in an area of approx. 10 ha, substantiating the general benefit of wildflower areas to pollinators. While alpha-diversity increased with landscape complexity in isolated wildflower areas, the opposite pattern was observed for connected areas. The low alpha-diversity in complex landscapes indicated a dilution effect between connected sites. The inverse relationship between alpha and beta diversity among wildflower areas within landscapes suggests interspecific trade-offs between local resource conditions and landscape context. Accordingly, the establishment of multiple wildflower areas within AES is advisable to increase connectivity of suitable habitats in simple landscapes. Moreover, adjusting local conditions (plant diversity) to landscape context likely optimizes conservation effectiveness in modern agroecosystems.

Enterohaemorrhagic Escherichia coli (EHEC) is a gastrointestinal pathogen that colonizes the colonic epithelium of humans and ruminants using a Type Three Secretion System (T3SS). This system is indispensable for disease and is regulated in response to a plethora of host and microbiota derived signals. The murine pathogen, Citrobacter rodentium, has become an instrumental tool in studying EHEC infection mechanisms in vivo, given its natural ability to infect mice and reliance on the same colonisation machinery. Here, we provide a review of the most recent advancements in EHEC infection biology, focusing on transcriptional regulation of the T3SS in response to physiologically relevant signals and how colonisation impacts on the metabolic micro-environment of the host niche. We pay particular attention to studies that have employed the C. rodentium model for elucidation of such mechanisms in vivo.

Objectives The aim of this study was to compare the epidemiological and clinical characteristics of hospitalised patients colonised or infected by different types of carbapenemase-producing Enterobacterales (CPE) and to analyse the differences in their outcome. Methods This was a retrospective comparative study of all patients colonised or infected by KPC-, NDM- or OXA-48-producing CPE who were hospitalised between 1 January 2018 and 30 June 2019. Microbiological, demographic and clinical data were collected from the patients’ computerised files. Results One type of CPE was isolated in 285 patients, including 138 with KPC-CPE, 94 with NDM-CPE and 53 with OXA-48-CPE. The most common CPE types were KPC-Klebsiella pneumoniae (n = 47), OXA-48-Escherichia coli (n = 38), NDM-Enterobacter cloacae complex (n = 35) and KPC-Citrobacter freundii (n = 37). All three groups of patients were similar with respect to their risk factors, with the exception of previous exposure to antimicrobials that was more common in patients with KPC-CPE compared with OXA-48-CPE. Also, these patients were more likely to be co-infected by other multidrug-resistant bacteria. Clinical infections were more common in KPC-CPE than in OXA-48-CPE carriers (9.9% vs. 1.9%; P = 0.033). No other demographic or clinical variables were found to be correlated with clinical infections. Conclusion Our study suggests that colonisation by OXA-48-CPE might be less risky compared with KPC-CPE.

12 pages, 7 figures, 4 tables.-- Under a Creative Commons license, The introduction of non-indigenous species (NIS) induces severe impacts on marine biodiversity and ecosystems. Macaronesia is an ecologically relevant region where several NIS were detected recently. For the first time, a standard experimental approach was designed to examine biofouling assemblages and investigate NIS across the region. In this context, sessile biofouling assemblages were examined in four recreational marinas in all the Macaronesian archipelagos from 2018 to 2020: the Azores, Madeira, Canary Islands, and Cabo Verde. We hypothesised that NIS numbers, abundance, and recruitment differed in each location due to abiotic and biotic features. From the Azores (higher latitudes) to Cabo Verde (lower latitudes), NIS recruitment and percentage cover decreased following a partial latitude gradient. The present study unveiled 25 NIS, with new records for the Azores (two cryptogenic species), Canary Islands (one NIS and two cryptogenic species), and Cabo Verde (three NIS and three cryptogenic species). The present research represents a pioneer and relevant step in advancing our current understanding of marine biological invasions in Macaronesia, employing a standard and low-cost approach, NC is funded by a doctoral grant (SFRH/BD/146881/2019) awarded by Fundação para a Ciência e a Tecnologia (FCT). PR is financed by project MARE - Centro de Ciências do Mar e do Ambiente (UIDB/04292/2020). IG is supported financially by a Maria Zambrano contract UCA under the grants call for the requalification of the Spanish university system 2021–2023, funded by the European Union – NextGenerationEU. AC and MP had the support of FEDER funds through the Operational Programme for Competitiveness Factors -COMPETE and by National Funds through FCT under the UID/BIA/50027/2020 and POCI-01-0145-FEDER-006821. JCC is funded by FCT under the Scientific Employment Stimulus - Institutional Call - (CEECINST/00098/2018). This work was partially funded by MIMAR+ (MAC2/4.6.d/249) in the INTERREG MAC 2014-2020 Programme framework. This study had the support of FCT through the strategic project UIDB/04292/2020, awarded to MARE and through project LA/P/0069/2020, granted to the Associate Laboratory ARNET. This is contribution 129 from the Smithsonian's MarineGEO and Tennenbaum Marine Observatories Network

Island colonisation and adaptive responses of humans to newly colonised environments during the Pleistocene is hotly debated in archaeological discourse globally. Investigating these occurrences enables us to better understand the human condition and is a useful proxy of early human cognition. This paper reviews the evidence for Pleistocene maritime knowledge (sea crossings and adaptations) for the island of Cyprus, the palaeoclimatic and palaeonvironmental context for the arrival of early humans on the island, and the existing lithic evidence regarding a potential Pleistocene colonisation. The island of Cyprus in the Eastern Mediterranean is an important nexus for addressing these phenomena. However, its potential in elucidating early human maritime movement and adaptations has remained largely unexplored. The recent discovery of reliable evidence for the Pleistocene exploitation of other islands around the world makes the absence of Pleistocene archaeology from Cyprus, the third largest island in the Mediterranean, very puzzling and calls for systematic research on the matter. In doing so, it puts forward the need for focused multidisciplinary methodological approaches and, crucially, disentanglement from persisting outdated narratives regarding the early human past as our best means in progressing the study of Pleistocene Cyprus.

Highlights • Systematic review and meta-analysis of 18 studies and more than 6000 participants. • Adults over the age of 60 had a pooled prevalence of pneumococcal carriage of 9%. • Risk factors: contact with children, smoking and residing in a nursing home., Summary Background Colonisation with Streptococcus pneumoniae can lead to invasive pneumococcal disease and pneumonia. Pneumococcal acquisition and prevalence of colonisation are high in children. In older adults, a population susceptible to pneumococcal disease, colonisation prevalence is reported to be lower, but studies are heterogeneous. Methods This is a systematic review and meta-analysis of prevalence of, and risk factors for, pneumococcal colonisation in adults ≥ 60 years of age (PROSPERO #42016036891). We identified peer-reviewed studies reporting the prevalence of S. pneumoniae colonisation using MEDLINE and EMBASE (until April 2016), excluding studies of acute disease. Participant-level data on risk factors were sought from each study. Findings Of 2202 studies screened, 29 were analysable: 18 provided participant-level data (representing 6290 participants). Prevalence of detected pneumococcal colonisation was 0–39% by conventional culture methods and 3–23% by molecular methods. In a multivariate analysis, colonisation was higher in persons from nursing facilities compared with the community (odds ratio (OR) 2•30, 95% CI 1•26–4•21 and OR 7•72, 95% CI 1•15–51•85, respectively), in those who were currently smoking (OR 1•69, 95% CI 1•12–2•53) or those who had regular contact with children (OR 1•93, 95%CI 1•27–2•93). Persons living in urban areas had significantly lower carriage prevalence (OR 0•43, 95%CI 0•27–0•70). Interpretation Overall prevalence of pneumococcal colonisation in older adults was higher than expected but varied by risk factors. Future studies should further explore risk factors for colonisation, to highlight targets for focussed intervention such as pneumococcal vaccination of high-risk groups. Funding No funding was required.

Introduction Osteoarticular infections represent a major complication in orthopaedic surgery. The aim is to identify the percentage of suction cannulas colonised and to determine the relationship between the time they are used in surgery and the colonisation of these cannulas. Materials and methods Descriptive and prospective study that analysed 546 suction cannulas used in clean orthopaedic surgery in a trauma centre, between November 2017 and March 2018. The distal end of the cannula was cultured to determine the colonisation rate. Results 7.3% of the cultured cannulas were positive for pathogens, the most frequent being Staphylococcus epidermidis at 27.5%. In addition, an association was found between colonisation and the length of time the cannula was used. The possibility of colonisation of cannulas used for between 60 min or more, is greater than those used for less than 60 min; between 60 and 90 min the possibility is twice as high OR = 2.2 (95% CI 1.1–4.1) and in cannulas used for more than 90 min it is 8 times higher OR = 8.49 (95% CI 1.77–40.86). Conclusions The colonisation rate of cannulas is lower than reported in the literature. The longer the cannula is used in surgery increases the risk of their colonisation. Follow-up studies are being considered to determine whether suction cannula colonisation is associated with increased postoperative infection.

Objectives The intestinal microbiota develops in early infancy and is essential for health status early and later in life. In this review we focus on the effect of prenatal and intrapartum maternally administered antibiotics on the infant intestinal microbiota. Methods A systematic literature search was conducted in PubMed and EMBASE. All studies reporting effect on diversity or microbiota profiles were included. Results A total of 4.030 records were encountered. A total of 24 articles were included in the final analysis. Infants from mothers exposed to antibiotics during delivery showed a decreased microbial diversity compared to non-exposed infants. The microbiota of infants exposed to antibiotics was characterised by a decreased abundance of Bacteriodetes and Bifidobacteria, with a concurrent increase of Proteobacteria. These effects were most pronounced in term vaginally born infants. Conclusion Maternal administration of antibiotics seems to have profound effects on the infant gut microbiota colonisation. Interpretation of microbiota aberrations in specific populations, such as preterm and caesarean born infants, is complicated by multiple confounding factors and by lack of high quality studies and high heterogeneity in study design. Further research is needed to investigate the potential short- and long-term clinical consequences of these microbial alterations.

Due to the fact that arbuscular mycorrhizal fungi (AMF) provide water and elements (e.g. phosphorus) to the host, arbuscular mycorrhiza (AM) is considered to be an important plant-fungi interaction and can be helpful for plants occupying extreme habitats. Such habitats include Central European semi-natural dry feathergrass grasslands. One of the main components of feathergrass steppes in Eurasia is Stipa pennata (Poaceae). Currently, because of a lack of land use leading to the overgrowth of grasslands and consequently to habitat deterioration, this species is rare and protected in many European countries. No information regarding the simultaneous impact of vegetation, topography, soil and climatic factors on the AMF–feathergrass relationship has been published to date. Thus, the aim of our study was to investigate factors that shape AMF root colonisation and AMF community composition in different types of European semi-natural feathergrass niches occupied by S. pennata. To do that, we collected roots and soil samples along with data about topography, soil chemical and physical properties, climate and vegetation cover from three different types of edaphic niches. We found that AMF root colonisation was lower in sand than in gypsum or limestone soils and was largely explained by environmental factors. AMF root colonisation degree was predominantly influenced by soil nitrogen content, and increased along with pH. Soil physical stress disrupted relationships between AMF root colonisation degree and soil pH. The largest percentage of variance in the composition of AMF communities was explained by soil factors, followed by climate, topography and vegetation. AMF communities associated with S. pennata were composed mainly of ‘generalists’ species.

Schistosomiasis is widely distributed along the Senegal River Basin (SRB), affecting both the human population and their livestock. Damming of the Senegal River for irrigation purposes in the 1980s induced ecological changes that resulted in a large outbreak of Schistosoma mansoni, followed a few years later by an increase and spread of Schistosoma haematobium infections. The presence of hybrid crosses between the human and cattle schistosomes, S. haematobium and Schistosoma bovis, respectively, is adding complexity to the disease epidemiology in this area, and questions the strength of the species boundary between these two species. This study aimed to investigate the epidemiology of S. haematobium, S. bovis and their hybrids along the Senegal River basin using both microsatellite genetic markers and analysis of mitochondrial and nuclear DNA markers. Human schistosome populations with a S. haematobium cox1 mtDNA profile and those with a S. bovis cox1 mtDNA profile (the so-called hybrids) appear to belong to a single randomly mating population, strongly differentiated from the pure S. bovis found in cattle. These results suggest that, in northern Senegal, a strong species boundary persists between human and cattle schistosome species and there is no prolific admixing of the populations. In addition, we found that in the SRB S. haematobium was spatially more differentiated in comparison to S. mansoni. This may be related either to the presence and susceptibility of the intermediate snail hosts, or to the colonisation history of the parasite. (C) 2019 Published by Elsevier Ltd on behalf of Australian Society for Parasitology.

Corynebacterium pseudotuberculosis is an important animal pathogen with a broad host spectrum that can cause clinical diseases. Notably, this bacterium is a facultative intracellular organism that causes caseous lymphadenitis. C. pseudotuberculosis infection was reported in many animals, although there have been no reports of isolation from amphibians. In this report, an abscess on the tibiofemoral joint of a Budgett's frog (Lepidobatrachus laevis) housed in a private zoo in Istanbul, Turkey was investigated. A sample of purulent material from the abscess was cultured, and a pure growth of C. pseudotuberculosis was identified by a commercial biochemical test system (API-Coryne, BioMerieux, France) and confirmed by the BD-Phoenix Automated Microbiology System, while nucleotide sequences analysis was performed for molecular identification. As a result, the organism was confirmed as C. pseudotuberculosis. Treatment with enrofloxacin was empirically started, and the bacteria were confirmed to be sensitive to enrofloxacin. Thereafter, 0.2% nitrofurantoin pomade was injected into the wound. Complete healing was evident following treatment. This report showed, for the first time, the isolation of C. pseudotuberculosis from a frog. The possible theory for the aetiology of this disease is feeder insects, which likely spread the bacteria into the enclosure of the frog. This suggests that invertebrates may act as a reservoir of infection and that the inter-species colonisation was be able to increase over time. Due to the zoonotic characteristics of the agent, an increase in the effect of colonisation was considered important for human health.

Peptoniphilus asaccharolyticus are gram-positive anaerobic cocci (GPAC) usually found as commensals of the skin or in the setting of polymicrobial colonisation of chronic wounds and ulcers. However, its pathogenic potential in more severe, invasive infections such as bone, joint or blood stream infections remains unclear, with studies on underlying virulence factors still pending. In this case report we present two cases of P. asaccharolyticus-associated infections of the bone and joint as well as a review of the literature. The cases cast a new light on possible synergistic interactions between P. asaccharolyticus and more virulent aerobic bacteria as well as on its role as pathogen in severe mono-infection.

Graphical abstract, Highlights • The physicochemistry of leaves is unique and is a major driver of leaf colonisation. • Competition and cooperation may be major drivers of bacterial colonisation. • Leaves respond to bacterial colonisation locally and systemically. • How leaf responses shape bacterial colonisation patterns is unclear. • Plant-microbe interaction should be studied at the micrometer resolution., Bacteria establish complex, compositionally consistent communities on healthy leaves. Ecological processes such as dispersal, diversification, ecological drift, and selection as well as leaf surface physicochemistry and topology impact community assembly. Since the leaf surface is an oligotrophic environment, species interactions such as competition and cooperation may be major contributors to shape community structure. Furthermore, the plant immune system impacts on microbial community composition, as plant cells respond to bacterial molecules and shape their responses according to the mixture of molecules present. Such tunability of the plant immune network likely enables the plant host to differentiate between pathogenic and non-pathogenic colonisers, avoiding costly immune responses to non-pathogenic colonisers. Plant immune responses are either systemically distributed or locally confined, which in turn affects the colonisation pattern of the associated microbiota. However, how each of these factors impacts the bacterial community is unclear. To better understand this impact, bacterial communities need to be studied at a micrometre resolution, which is the scale that is relevant to the members of the community. Here, current insights into the driving factors influencing the assembly of leaf surface-colonising bacterial communities are discussed, with a special focus on plant host immunity as an emerging factor contributing to bacterial leaf colonisation.

International audience; Non-albicans Candida (NAC) species have emerged as potent pathogenic yeasts among HIV-infected patients. Authors evaluated the epidemiology and antifungal susceptibility testing of non-albicansCandida species colonizing Yaoundé (capital of the Republic of Cameroon, Central Africa) HIV-infected patients. The mucosal specimens were collected and submitted to the mycological diagnosis. Yeast isolates were identified by the Matrix Assisted Laser Desorption Ionisation - Time of Flight Mass Spectrometry (MALDI-TOF MS). The antifungal susceptibility testing was achieved by the CLSI-M27 protocols, and the interpretation of clinical break points (CBPs) and epidemiological cutoff values were in accordance with the CLSI-M60 and M59 recommendations. Four hundred and two patients were recruited and 1218 samples collected. The colonisation frequency was 24.1% and 304 yeasts isolated. Yeast isolates were 113 (37.2%) C. albicans, 2 (0.7%) C. africana and 172 (56.6%) NAC isolates. The NAC isolates were grouped into 13 species including C. krusei (18.1%), C. glabrata (10.9%), C. tropicalis (8.5%) and C. parapsilosis (5.9%) as the major ones. All the isolates appeared to be wild-type for amphotericin B and itraconazole. One (1/33) isolate of C. glabrata was resistant to fluconazole. C. arapsilosis isolates appeared all susceptible to fluconazole. C. tropicalis isolates presented 50% (13/26) resistance to fluconazole. The achieved results bring out new insights about epidemiology of NAC species in Cameroon. The results also highlight the resistance of NAC species to current antifungal drugs.

Gram-negative bacterial endophytes have attracted research interest caused by their advantageous over epiphytic bacteria in plant nutrition and protection. However, research on these typically Gram-negative endophytes has deficiencies concerning the role of cultivation and pre-formulation strategies on further plant colonisation capabilities. Besides, the influence of cultivation conditions and osmotic stress within bacterial endophytes on their phosphate solubilising ability has not yet been addressed. By pre-conditioning cells with an osmoadaptation and a hydroxyectoine accumulation approach, this research aimed at enhancing the capability of the plant growth promoting bacterium Kosakonia radicincitans strain DSM 16656T to both solubilise phosphate and colonise plant seedlings. The results showed that halotolerant bacterial phenotypes increased the root-colonising capability by approximately 3-fold and presented growth-promoting effects in radish plants. Interestingly, findings also demonstrated that salt stress in the culture media along with the accumulation of hydroxyectoine led to an increase in the in vitro phosphate-solubilising ability by affecting the production of acid phosphatases, from 1.24 to 3.34 U mg-1 for non-salt stressed cells and hydroxyectoine-added cells respectively. Thus, this approach provides a useful knowledge upon which the salt stress and compatible solutes in bacteria endophytes can confer phenotypic adaptations to support the eco-physiological performance concerning phosphate-solubilising abilities and endosphere establishment. Keywords: Bacterial endophytes, Osmoadaptation, Hydroxyectoine, Compatible solutes, Phosphate solubilisation, Plant tissue colonisation

Here we describe an outbreak due to NDM-1+CTX-M-15+DHA-1-producing Klebsiella pneumoniae (NDM-1-Kp) in Spain related to a patient previously admitted to a healthcare centre in an endemic area (Pakistan). Nine colonised patients were detected in the Neurosurgery ward between September 2015 and February 2016 during the R-GNOSIS European Project. NDM-1-Kp isolates from clinical samples were also recovered in three of these patients. Surveillance culture at admission was negative in the index case, but NDM-1-Kp colonisation was detected 27 days later after receiving antibiotic treatment. Co-colonisation with a second NDM-1-Kp isolate was identified in this patient 61 days post-admission. Overall length of stay (LOS = 75 days) (P0.01) and LOS until carbapenemase detection (LOS-1 = 36 days) was longer in NDM-1-Kp carriers than in patients with other carbapenemase-producing Enterobacterales. Intervention strategies were implemented after the outbreak declaration and NDM-1-Kp transmission was contained. Among the NDM-1-Kp isolates, two clones [ST437 (index case and Patient 2) and ST101 (index case and Patients 3-9)] with different IncFIB NDM-1-containing plasmids were identified. Whole-genome sequencing revealed a high content of antimicrobial resistance genes in both isolates in addition to a large number of virulence factors. Colonisation with other epidemic (OXA-48-ST11-K. pneumoniae and VIM-1-ST54-K. pneumoniae) and non-epidemic (VIM-1-ST908-K. pneumoniae and VIM-ST431-Escherichia coli) clones was also detected in two NDM-1 carriers. Implementation of adequate infection control measures and uninterrupted active surveillance programmes for detecting patients with a low colonisation status are crucial to prevent the introduction and dissemination of NDM-type enzymes in our region.

Widespread use of Pneumococcal Conjugate Vaccines (PCV) has reduced vaccine-type nasopharyngeal colonisation and invasive pneumococcal disease. In a double-blind, randomised controlled trial using the Experimental Human Pneumococcal Challenge (EHPC) model, PCV-13 (Prevenar-13) conferred 78% protection against colonisation acquisition and reduced bacterial intensity (AUC) as measured by classical culture. We used a multiplex qPCR assay targeting lytA and pneumococcal serotype 6A/B cpsA genes to re-assess the colonisation status of the same volunteers. Increase in detection of low-density colonisation resulted in reduced PCV efficacy against colonisation acquisition (29%), compared to classical culture (83%). For experimentally colonised volunteers, PCV had a pronounced effect on decreasing colonisation density. These results obtained in adults suggest that the success of PCV vaccination could primarily be mediated by the control of colonisation density. Studies assessing the impact of pneumococcal vaccines should allow for density measurements in their design.

Cadmium (Cd) is one of the most toxic heavy metals found in soil. Arbuscular mycorrhiza (AM) is known to reduce Cd translocation in plants by immobilising Cd in the root system. The effect of mycorrhiza on plant Cd uptake is usually studied in simple systems with single strains of mycorrhizal fungi and few levels of Cd. Here we studied how a wide range of soil Cd concentrations affected plant AM colonisation, and how the species-specific differences in AM colonisation affected uptake, translocation, and toxicity of Cd in plants in a system with naturally occurring mycorrhizal fungi. Six plant species were grown in pots in a greenhouse across seven levels of Cd, which made it possible to model dose-response curves, and calculate EC50 for each plant species. We found a remarkable trend where Cd at moderate levels stimulated mycorrhizal colonisation until a certain threshold where the symbiosis breaks down. Our results support the existence of a protective effect of AM fungi against Cd, as the symbiosis reduces Cd translocation to shoots, especially in plants with very high AM colonisation. Thus, we conclude that it is the combination of plant species and AM colonisation that determines Cd uptake in plants. AM is therefore an essential trait to consider when growing plants in Cd-polluted soil.

The ancient Egyptians believed in an afterlife where the body of a dead person would be needed by the spirit. In order to preserve the deceased in as lifelike condition as possible they developed artificial mummification to a high level of sophistication. It is widely believed that natron was the main desiccation agent in the preparation of Egyptian mummified bodies in the 18th Dynasty. Natron is a natural mixture of sodium chloride, sodium sulphate, sodium carbonate and sodium bicarbonate found in the Nile Delta which has significant desiccation properties, but it is currently unclear if natron has further beneficial properties for the mummification process. Previous work indicates that it does not deter insect colonisation in general, although it has been found to act as a killing agent of blow flies. In particular, we are aware of no studies investigating the antibacterial activity of natron nor the wider investigation of the insect repellent nature of ancient Egyptian mummification resins. This study investigated the properties of ancient Egyptian embalming fluids alongside their application in an artificial mummification of a human body at the Medico-legal Centre in Sheffield, UK. Antibacterial assays were used to compare the activity of a modern day antibiotic (Chloramphenicol) to those of key embalming ingredients used in ancient Egypt (natron, palm wine and pine resin). In addition, a field study using rabbit carcasses investigated whether pine resin has insect repellent properties. Results demonstrated that palm wine and natron had higher antibacterial activity than Chlorophemical against the Gram-positive bacteria, Staphylococcus aureus, and that natron had higher antibacterial activity than Chloramphenicol against the Gram-negative bacteria, Escherichia coli. The field study showed a delay in the colonisation of necrophagous insects and a temporal shift in the families of insects present on the carcasses treated with pine resin compared to control carcasses (no pine resin). We found no insect mortality on any of the carcasses during the study, indicating that the pine resin was acting as a repellent only and not as an insecticide. Although this is a preliminary study, the clear results strongly suggest that the embalming fluids used in mummification procedures during the 18th Dynasty had a number of properties which could affect the development of associated bacterial and insect communities.

Azole-resistant Aspergillus fumigatus (ARAF) has been reported in the domestic environment of patients at risk for aspergillosis. Here, we assessed the mother's and father's homes of an 18-year-old cystic fibrosis patient harbouring chronic colonisation with H285Y CYP51A azole-resistant isolate, in order to explore the link between environmental exposure and ARAF infection. In one dwelling, a very high overall contamination level was found (710–7.240 CFU/m3), with a predominance of A. fumigatus (640–6.490 CFU/m3), and ARAF showing the TR34/L98H mutation was isolated. Mycological follow-up of the patient showed the persistence of H285Y isolates, but no acquisition of TR34/L98H isolates was observed. This could be due to the low proportion of TR34/L98H isolates (

Like any constructed ecosystem, the vegetation of extensive green roofs (EGRs) will change over time. Although this may influence the desired function and performance, little work has examined the floristic dynamism of EGRs over the long-term. Variations in species composition may be associated with original species (persistent or lost), colonisers (gained), or the effects of spatial heterogeneity. This paper reports on floristic variation of two unmanaged German EGRs twenty years after installation. To evaluate floristic change, the analyses focused on functional composition and plant strategies sensu Grime's CSR theory, referring to the basic adaptive strategies of competition, stress-tolerance and ruderality, and their derivatives. With reference to original documentation, less than half the original species persisted. In spite of the losses, both roofs had entire cover, or nearly so, thanks to colonising species. The generalist strategy (CSR strategists) was the most important functional trait in the observed vegetation, followed by stress-tolerance and then by variations in stress-tolerant ruderality. The functional composition of colonising species was chiefly ruderals, followed by stress tolerators and generalists. The drivers behind these changes relate to the pressures of stress, disturbance and competition, as well as spatial heterogeneity and strategies for dispersal and regeneration, seedbank and propagule sources. This study suggests that long-term floristic diversity may be facilitated by ensuring a diversity of traits and species from the start, by providing spatial heterogeneity, and by considering the mechanisms that support persistence and those which determine colonisation.

The presence of Lactobacillus strains in dairy products and the intestinal tracts of humans and animals is frequently considered to have beneficial effects on gut health. In this study, five L. plantarum and five L. casei strains from fermented food origin were isolated and compared to characterise their functional properties, including generation time, survival in the gastrointestinal environmental conditions and carbohydrate utilisation. The growth rate of L. plantarum CGMCC12436 was the same level with that of L. plantarum strain ST-III. The L. plantarum CCFM605 and CGMCC12436 maintained the similar levels of cell numbers under the simulated gastrointestinal tract, which were comparable to the cell numbers of L. plantarum strain ST-III. The L. casei CCFM236 and CGMCC12435 exhibited significant higher survival rates than CCFM5 in the duodenal juice. The evaluation of their colonisation in the mouse gut indicated that the L. plantarum strain ST-III, CCFM595 and CGMCC12436 could colonise relatively longer than other tested strains. Furthermore, two strains were selected for characterisation of whole genome sequences. Among the identified key genes responsible for the functional properties, we found that the cpsD gene cluster in L. plantarum CGMCC12436 may be closely associated with its colonisation ability in the mouse gut during and after discontinuing the strain administration. In conclusion, we revealed the functional properties of Lactobacillus strains in vitro assays and colonisation properties in the mouse gut, and elucidated the relevant genes involved in the tolerance or colonisation in gut using comparative genome analysis.

The diversity of Australia's mammalian fauna has decreased markedly since European colonisation. Species in the small-to-medium body size range have been particularly badly affected. Feral cats and foxes have played a central role in this decline and consequently strategies for reducing their numbers are being evaluated. One such strategy is the reintroduction to the mainland of the Tasmanian devil, Sarcophilus harrisii. Here, we provide a palaeontological perspective on this proposal. We begin by collating published records of devil remains in Quaternary deposits. These data show that the range of devils once spanned all the main ecological zones in Australia. This indicates that they are capable of coping with a wide range of climatic and environmental conditions, and suggests that they could conceivably be reintroduced much more widely than has been thought possible hitherto. Subsequently, we examine fossils and coprolites from two sites in the Willandra Lakes Region World Heritage Area. These specimens not only support the suggestion that devils have wide ecological tolerances, but also suggest that devils can coexist with native small-to-medium species over long periods of time, which addresses one of the major concerns about the proposed reintroduction. We believe these two sets of palaeontological observations add substantial weight to the idea of reintroducing devils to the mainland as a way of suppressing cat and fox numbers.

There is much interest in supporting biodiversity through eye-catching low maintenance requiring herbaceous vegetation types in urban environments. Community development of forb vegetation is not well understood, and experimental studies investigating the potentials and limitations of establishing such vegetation are needed. We performed a field experiment including three mixtures of 19 forb species (three annuals, three biennials, 13 perennials) and analysed the development of the community over 3 years. In spring 2010 a total of 3630 seedling plug plants were transplanted in a randomized block experiment with 30 plots; non-planted control plots were monitored as reference. Management was limited to removal of dead plant material in February. We documented transplant survivorship, gap colonisation and soil seed bank composition. Standing biomass was harvested in a subset of plots in August 2012, and in all plots in July 2013. After four growing seasons, 1592 transplants were still alive. Fifteen experimental species had spread to gaps, but grasses, Achillea millefolium and Trifolium pratense var. sativum were the most frequent gap-colonizers. On average, biomass of non-experimental species contributed only 11% to the total aboveground biomass in treatment mixtures after four growing seasons. The initial proportions of species (annuals vs perennials) had no significant effect on the community's resistance to colonisation by non-experimental species. Biomass of non-experimental species was negatively correlated to transplant survival. Thus, high plant density increases resistance to invasion, but long-term persistence of forb vegetation is species-specific. In practice some disturbance is necessary to facilitate regeneration of desirable forbs.

Apart from effective hygiene regimes in poultry houses, measures to increase the resistance of birds against intestinal colonisation with EEC (= extended-spectrum β-lactamases [ESBL] and AmpC-type [AmpC] beta-lactamses producing Escherichia coli) might be one tool to reduce the risk of transferring these organisms from broilers via poultry meat to humans. The study aimed to gain detailed information on the efficacy of a competitive exclusion culture (CE culture) against EEC exposure in very young chicks. Administration of only 104 cfu/bird on day 2 of life with seven EEC strains (different ESBL and AmpC genes) induced a high and rapid intestinal colonisation in untreated chicks which lasted until an age of 5 weeks. Pretreatment of the birds with a CE culture resulted in a relevant reduction (about 4.0 log10 units) of the different EEC strains. A considerable protective effect (reduction of 2.0 log10 units) by the CE culture could be detected after exposure of the chicks with very high doses of 106 to 108 cfu/bird. Invasion of the liver by EEC organisms was completely prevented by the CE culture even in case of very high challenge doses. The CE culture of undefined composition used here resulted in a substantial decrease of caecal colonisation of EEC strains in young chickens over a lifetime of broilers. Because of the different protective effects against the single EEC strains, modifications in the composition of undefined CE cultures or the development of defined cultures effective against EEC might improve the efficacy of gut flora preparations.

Penicillium digitatum was recently identified as a postharvest pathogen of plum. Little is known of this host-pathogen association. Disease occurrence and severity was higher on older fruit. This study aimed to determine the effect of ripening on the infection and colonisation of P. digitatum and P. expansum on plum at a physical (disease incidence/severity, pH and firmness) and molecular (gene expression) level. Storage conditions and inoculum loads were also considered. Disease incidence and severity of P. digitatum was significantly affected by ripeness, cold storage and inoculum load. Both species acidified tissue and advanced host ripening. Host ripening had a small effect on gene expression (P. digitatum: ACCD decreased; P. expansum: pacC and creA increased). A dual mechanism of pH modulation was discussed; higher pH at and beyond lesion borders will facilitate invasion, maceration and colonisation (nutrient uptake and growth) by/during acidification. The pH of lesions was comparable to that of controls. Alkalinisation via accumulation of ammonium/ammonia can be linked to the pathogen’s nitrogen metabolism. Host ripening directly (elicited) or indirectly (ethylene stress) caused by pathogen attack can increase the pH of uncolonised tissue. P. digitatum can be considered an important pathogen of riper fruit often found in long or ill-managed distribution chains. It is still unclear what stimulates (molecular) the opportunistic lifestyle expressed by P. digitatum on plum. There was little to no correlation between gene expression and the increase in disease incidence and severity on riper fruit. Future work should consider the decline of host resistance during ripening.

By analogy with Pavlov's dogs, certain pathogens have evolved anticipatory behaviours that exploit specific signals in the human host to prepare themselves against imminent host challenges. This adaptive prediction, a type of history-dependent microbial behaviour, represents a primitive form of microbial memory. For fungal pathogens, adaptive prediction helps them circumvent nutritional immunity, protects them against phagocytic killing, and activates immune evasion strategies. We describe how these anticipatory responses, and the contrasting lifestyles and evolutionary trajectories of fungal pathogens, have influenced the evolution of such adaptive behaviours, and how these behaviours affect host colonisation and infection.

Rice planthoppers (RPH) are the most serious insect pests of rice production in East Asia, frequently out-breaking in China, Korea and Japan each summer. They are unable to overwinter in temperate East Asia, and summer populations arise anew each year via northward spring migration from south-east Asia. The annual migration cycle is generally believed to be a closed loop with mass returns to south-east Asia in the autumn, but this leg of the journey and the overwintering dynamics are much less studied than the spring immigrations. Previous studies have indicated that the north-central Vietnam (NCV) region is a key location for both the spring colonisation of China and for receiving return migrants from southern China each autumn. However, NCV experiences a three-month rice-free fallow period during mid-winter, and so it cannot be the principal over-wintering region for RPH populations. In this study, the continental-scale migration patterns of RPH in East Asia were explored using data from light trap catches, field surveys and atmospheric trajectory simulations. Our results confirmed that large numbers of return migrants arrive in NCV from southern China each autumn, but that they are unable to survive there over winter. The NCV region is recolonised in the early-spring (mid-February to mid-March) of each year by migrants from winter rice-growing regions in north-east Thailand, southern Laos and south-central coastal Vietnam, which are transported on favourable high-altitude synoptic winds. The following generation initiates the colonisation of East Asia from a large source population in NCV. Our results provide a new perspective on RPH migration patterns and over-wintering dynamics in East Asia, which is governed by crop production, environmental conditions and synoptic wind patterns at a continental scale.

International audience; Secondary dispersal of terrestrial plant species through watercourses increases the dispersal range of floating seeds but their exposure to water may also challenge their viability and colonisation potential. Many terrestrial invasive species benefit from watercourses to extend their invasive range because water exposure can favour seed germination and early survival of seedlings for species sensitive to dry conditions and water flow enhances their dispersal distance downstream. Floatability, germination rate and survival after water exposure are seed traits involved in water dispersal and their variability may lead to different dispersal strategies. To address the question of the variability of achene traits involved in dispersal, we experimentally measured these three traits for Fallopia × bohemica achenes collected from 10 different stands. The floatability of achenes varied between stands from 2.5 to 5 days and their germination in water extended this period to 20 days through the emergence of floating seedlings. Germination proportions also differed between stands from 0.3 to 0.95 and were negatively related to the median germination time. Seedling survival after planting in soil was affected by their exposure time. This effect differed between stands, but a short germination time did not explain a better survival of some stands. These results show that achenes may differ in their dispersal potential in terms of floatability, as well as tolerance of seedlings to water exposure during dispersal. This study also highlights the fact that achenes of some stands present a combination of traits particularly adapted to long distance dispersal through watercourses, which can contribute to the extension of the invaded area.

We aimed to detect species distribution patterns at landscape level that have arisen following the colonisation of a mine spoil heap (MSH) by macrolichens. All taxa occurring on various substrates and the degree of occupancy by different vegetation patch types were recorded at a resolution of 50 m × 50 m within a regular square grid of 25 ha, which extended over a 60-year-old abandoned MSH and its adjacent agro-pastoral area. The fraction of MSH was the most important predictor of the lichen composition and richness at grid cell level, followed by the terrain slope and the proportion of heathland. Almost all lichen taxa positively correlated with the MSH fraction were terricolous, fruticose, oligotrophilous, acidophilous species that occurred preferentially on the steep, barren slopes. The few corticolous, nitrophilous species were negatively correlated with the MSH fraction. Except for the corticolous and saprophytic species, the proportion of MSH and the elevation range had each a positive effect on both total and terricolous lichen richness. Conversely, taxonomic distinctness displayed an opposite pattern. Such a contrast was determined by the numerous conspecific (Cladonia) lichens occurring on the steeper MSH slopes, with scarce vegetation. A conspicuous nestedness, but no pattern of species turnover, was detected along the main ecological gradient. This was due to both the corticolous/saprophytic species shared with the adjacent, tailings-free habitats and the terricolous/saxicolous lichens dispersed from proximal source-habitats. The MSH studied can be considered a hotspot for lichen species richness but not for taxonomic diversity.

Even though the Eurasian lynx is a less controversial species than the wolf or brown bear, poaching remains a major cause of lynx mortality in Europe, potentially threatening population expansion in key areas. Our study was designed to explore the attitude of hunters and other stakeholders (students of secondary forestry schools and University forestry faculties) towards lynx and their experience with illegal killing of lynx in the Czech Republic. Self-administered questionnaires were addressed to local hunters and to students in 2001 and again in 2015. The survey in 2001 was conducted in two separate hunting regions of Bohemia, one where lynx have been artificially reintroduced and another in which lynx have become established through natural colonisation. In 2015 the survey was extended to two further areas where lynx have re-established themselves through natural colonisation, in the east of the Czech Republic. Altogether 415 and 922 questionnaires were completed in 2001 and 2015, respectively. The attitude of hunters towards lynx was not affected by hunting region, lynx population density or nature of the population (human re-introductions vs natural recolonisation), but attitudes became more negative in 2015 than they had been in 2001. The majority of hunters still believed that lynx had negative effects on other wildlife and 27% stated that they do not wish to co-exist with lynx. Half of secondary school students and a third of tertiary students still believe that lynx threaten roe deer stocks, even though roe and red deer are present at high density and cause extensive damage in commercial forestry. Hunters as well as forestry students had first-hand knowledge about illegal hunting of lynx. The proportion of hunters admitting to having poached lynx themselves was 10% with the proportion of repeated illegal kills made by the same person increasing between 2001 and 2015. Population modelling suggested that at least 25% of the population might be poached annually, sufficient to restrict population growth and further expansion of lynx distribution.

Background Nasopharyngeal colonisation (CNF) is considered a “major point” in the evaluation of pneumococal conjugate vaccines (PCVs). A year after the administration of PCVs in Cienfuegos, Cuba, we described the changes in CNF due to Streptococcus pneumoniae in children between 1 and 5 years included in a clinical trial of the new Cuban vaccine candidate PCV7-TT compared to PCV13. Method A pre–post vaccination evaluation study was conducted based on two cross-sectional surveys. The first pre vaccination survey (2014–2015) included 1135 children. A subsample (n2 = 555) of vaccinated children was selected through a simple random sample in 2016. The proportions and percentage differences of global CNF and serotypes and for each age group were estimated and compared before and after vaccination. Results The overall proportion of CNF in preschool children ranged from 34.0% to 26.7%, one year after vaccination (p = .00878). The greatest reduction was observed in the group between 2 and 5 years (from 45.8% to 17.6; [p Conclusions Despite the limitations of the study due to not having a concurrent control group of unvaccinated, the reduction in CNF by vaccine serotypes suggests that the introduction of the PCV7-TT could significantly impact the burden of CNF in children and consequently reduce the rates of disease associated with pneumococcal infection. Subsequent studies would be necessary to evaluate the phenomenon of serotype replacement and its influence on the reduction of effectiveness over pneumococcal disease.

International audience; Streptococcus agalactiae (group B Streptococcus, GBS) remains the leading cause of invasive diseases in neonates and an important cause of infections in the elderly. The aim of this study was to access the prevalence of GBS genito-rectal colonisation of pregnant women and to evaluate the genetic characteristics of invasive and non-invasive GBS isolates recovered throughout Serbia. A total of 432 GBS isolates were tested for antimicrobial susceptibility, capsular polysaccharide (CPS) types and the presence of the hvgA gene. One hundred one randomly selected isolates were further characterized by clustered regularly interspaced short palindromic repeats (CRISPRs) analysis and/or multilocus sequence typing (MLST). The prevalence of GBS colonization in pregnant women was 15%. Overall, six capsular types (Ia, Ib, II to V) were identified, the most common being III (32.2%) and V (25.2%). The hiper-virulent clone type III/ST17 was present in 43.1% and 6.3% (p

Peatlands in the Western Balkans are becoming rapidly reduced due to vegetation succession, further enhanced by climate change and abandonment of traditional land management practices. Currently, the peatlands of this region act as habitat islands embedded mainly in a forest landscape matrix. This allows them to host more forest and generalist species of animals and plants than would be expected from such ecosystem. We were interested in testing if a taxon, unspecialized for such extreme habitats, can maintain stable populations in a peatland, and how environmental fluctuations affect its spatio-temporal distributions along a successional gradient. Terrestrial isopods were sampled in four habitat types: a fen, two successional habitats and a beech forest, with pitfall traps during two consecutive years. In total, 1069 individuals belonging to five species were recorded. Activity density increased more than four-fold along the successional gradient, from the fen to an older and more complex successional habitat. This pattern was governed by an increase in the structural complexity of the habitat, where succession habitats supported more favourable shelter sites for terrestrial isopods. Soil moisture decreased over 30% along the successional gradient. Additionally, the older successional habitat was more nutrient rich than the fen, providing higher substrate quality for decomposers and enabling the survival of forest species. The fen was inhabited by a single species, Ligidium germanicum, while other species were extremely rare. Its seasonal activity started in the spring, reaching the maximum in June and decreasing at the end of summer. Spatial changes in isopod assemblages along the successional gradient imply that the groundwater level in the fen was sufficiently high to supress the invasion of forest species into the fen. Colonisation of the fen by terrestrial isopods will likely progress as environmental conditions become more suitable by progressive vegetation succession and climate change.

The gastrointestinal tract microbiota is involved in the development and function of many body processes. Studies demonstrate that early-life microbial colonisation is the most important time for shaping intestinal and immune development, with perturbations to the microbiota during this time having long-lasting negative implications for the host. Piglets face many early-life events that shape the acquisition and development of their intestinal microbiota. The pork industry has a unique advantage in that the producer has a degree of control over what piglets are exposed to, providing conditions that allow for optimum piglet growth and development. An influx of publications within this area has occurred in recent times and with this, interest surrounding its application in pork production has increased. However, it can be difficult to distinguish which research is of most relevance to industry in terms of delivering repeatable and reliable production outcomes. In this review, we describe the literature surrounding research within pigs, predominantly during the preweaning period that has either provided solutions to industry problems or is generating information targeted at addressing relevant industry issues, with the focus being on studies demonstrating causation where possible. This review will provide a basis for the development of new studies targeted at understanding how to better support initial intestinal microbiota colonisation in order to improve piglet health and survival.

Streptococcus agalactiae (Strep. agalactiae) and Staphylococcus aureus (Staph. aureus) are originally regarded as contagious mastitis pathogens, however, both pathogens have recently been isolated from extramammary and environmental sites, indicating that other sites than the udder might contribute to the spread of these pathogens potentially causing intramammary infections. Diagnostic tools to identify pathogens at extramammary sites are available but still needs to be validated. The objective of this cross-sectional field study was to estimate the diagnostic sensitivity (Se) and specificity (Sp) of the commercially available Mastit4 qPCR assay and bacterial culture (BC) in identifying Strep. agalactiae and Staph. aureus from milk and teat skin samples. We randomly selected 30-40 cows with high somatic cell counts from eight Danish Strep. agalactiae-positive dairy herds with automatic milking systems. Teat skin samples and aseptic milk samples were collected from right rear quarters (n = 287) for BC and PCR analysis. Se and Sp were estimated in a Bayesian latent class analysis. For milk samples, the Se and Sp of qPCR for Strep. agalactiae were estimated to 0.97 and 0.99, respectively, whereas the Se and Sp of BC were 0.41 and 1.00, respectively. The Se and Sp of qPCR for Staph. aureus were estimated to 0.95 and 0.99, respectively, whereas the Se and Sp of BC were 0.54 and 0.77, respectively. For teat skin samples, the Se and Sp of qPCR for Strep. agalactiae were estimated to be 0.97 and 0.96, respectively, whereas the Se and Sp of BC were 0.33 and 1.00, respectively. The Se and Sp of qPCR for Staph. aureus were estimated to 0.94 and 0.98, respectively, whereas the Se and Sp of BC were 0.44 and 0.74, respectively. In conclusion, the Se for diagnosing Strep. agalactiae and Staph. aureus IMI was higher for qPCR than BC, suggesting that qPCR is a valuable method for detecting both pathogens from quarter-level milk samples. The performance of BC in the detection of Strep. agalactiae and Staph. aureus on teat skin was poor compared to qPCR, indicating that differences in the target condition of the two methods should be considered when implementing them as routine diagnostic tests for detecting teat skin colonisers. The low Se of BC may preclude the use of BC for skin testing, and qPCR is better for this task. info:eu-repo/semantics/publishedVersion

Objective To evaluate the colonisation rate of Staphylococcus aureus in the oropharynx and the insertion site of central venous catheters in intensive care unit patients. Design Cross-sectional study. Setting Brazilian intensive care unit. Measurements Samples were collected from October to December 2015 from the oropharyngeal cavity and central venous catheter insertion site of 110 patients. Samples that presented growth of Staphylococcus aureus were isolated and their sensitivity profiles were tested for several antimicrobials. Findings The study participants (110) were mostly females older than 60 years (53.6%). The mean length of hospitalisation was 15.5 days (±31.3). A total of 188 biological samples were collected: 110 collected from the oropharynx and 78 from the central venous catheter insertion site. A 35% (n = 38/110) S. aureus colonisation rate of the patients was observed in at least one collection site. In the oropharynx alone, a 31% rate (n = 34/110) was found, and a 12.8% rate (n = 10/78) at central venous catheter insertion sites only. MRSA colonisation in the oropharynx or at the central venous catheter occurred in 29 (26.4%) patients and vancomycin resistant Staphylococcus aureus was present in 24 (22.4%) of the patients studied. Patients hospitalised for seven days or more were 4.8 times more likely to be colonised compared to patients hospitalised less than seven days (95% CI = 1.2–28.5). Conclusion The oropharynx and the central venous catheter are important reservoirs of this bacterium that in critical conditions may become pathogenic. The data showed a high degree of resistance of the bacterial populations isolated to different drugs, which may hinder the control of these organisms.

Objectives The aim of this study was to investigate the carriage rates of Staphylococcus aureus and methicillin-resistant S. aureus (MRSA) among healthcare workers (HCWs) at a tertiary-care hospital in southeastern China and to analyse the epidemiological relatedness of the S. aureus isolates. Methods A total of 242 pharynx swabs were collected in March–April 2016 from 242 HCWs working in seven different wards and departments. Isolates were identified as S. aureus based on morphology, coagulase test and Vitek test. Antimicrobial susceptibility testing was performed by using the Kirby–Bauer disk diffusion method. The epidemiological relatedness of the S. aureus isolates was determined by pulsed-field gel electrophoresis (PFGE). Results From the 242 HCWs, 70 (28.9%) S. aureus strains, including 10 (4.1%) MRSA strains, were identified during screening, with the highest MRSA rate detected in nurses (8/107; 7.5%). Carriage rates of S. aureus and MRSA among surgical HCWs were 30.0% (63/210) and 4.3% (9/210), respectively. Methicillin-susceptible S. aureus (MSSA) isolates were grouped by PFGE analysis into five similar groups (A–E), with most isolates belonging to groups D and E, accounting for 63.0% of isolates. Furthermore, two MRSA isolates from gastrointestinal surgery had identical PFGE patterns. Conclusions The prevalence of S. aureus colonisation among HCWs was high in this hospital, although the MRSA carriage rate in surgical wards was low. The identical PFGE pattern detected in two MRSA isolates from the same surgical department supports that effective control for possible cross-infection should be implemented.

Anthropogenic contaminants, including nutrient enrichment, frequently alter environmental conditions in marine systems and affect the development of communities on hard-substrata. Biofilms can influence the settlement of marine invertebrates and hence impact on the structure of fouling communities. Few studies have examined bacteria, invertebrates and nutrient-rich contaminants in concert, with none yet to examine the effects of nutrient-rich contaminants on both biofilms and the recruitment of sessile invertebrate communities in-situ to ascertain the mechanistic basis behind observed impacts. Biofilm treatments were allowed to develop under manipulated environmental conditions of either ambient or enriched nutrient levels. Enrichment conditions were elevated via slow-release fertiliser and invertebrate recruitment was prevented during initial biofilm development. Biofilm treatments (including a no film control) were then subject to either ambient or enriched water-borne nutrients (in a fully-factorial design) during a period of invertebrate colonisation in the field. Effects of nutrient-rich contaminants on invertebrate recruitment were observed as changes to community composition and the abundances of taxonomic groups. Communities on no biofilm control treatments differed from those with pre-developed biofilms. Naturally developed biofilms promoted recruitment by all organisms, except barnacles, which preferred nutrient-enriched biofilms. Water-borne nutrients increased the recruitment of ascidians and barnacles, but suppressed bryozoan, serpulid polychaete and sponge recruitment. The direct and indirect impacts observed on biofilm and invertebrate communities suggest that increasing nutrient levels via nutrient-rich contaminants will result in structural community shifts that may ultimately impact ecosystem functioning within estuaries.

Background ESBL-producing Enterobacteriaceae (ESBL-E) are an emerging cause of infections in children. Data are scarce on incidence rates and risk factors for acquisition of colonisation with ESBL-E. Methods A total of 46 and 50 newborns from colonised and non-colonised mothers, respectively, were followed during one year after birth. Rectal swabs were performed every 3 months to detect ESBL-E; blaESBL were characterised and isolates were typed for comparison. Multivariate analysis for risk factors was performed using Cox regression. Results Incidence density of any new acquisition and of first acquisition of ESBL-E was 2.7 and 1.9 episodes per 100 children-month, respectively, among children whose mothers were colonised, and 1.2 and 1.3, respectively, among children whose mothers were not. The weighted average prevalence of colonisation rates during the first year were 15.9% and 8%, respectively. No infections due to ESBL-E were detected. Living with pets at home, breastfeeding, sterilisation of feeding bottles and out-of-home childcare were protective for ESBL-E acquisition; having a colonised mother increased the risk. The most frequent ESBL types were CTX-M-14 and CTX-M-1. In 5/19 (26.3%) children with acquisition of new clones, the acquired ESBL-E was shared with their mothers. Conclusions Acquisition of ESBL-E colonisation is not rare during the first year of life. Breastfeeding and out-of-home childcare were protective for acquisition, and colonised mothers were associated with increased risk. However, the same clone was shared by mother and child in only a subset of acquisition episodes.

Farmed fish are commonly exposed to stress in intensive aquaculture systems, often leading to immune impairment and increased susceptibility to disease. As microbial communities associated with the gut and skin are vital to host health and disease resilience, disruption of microbiome integrity could contribute to the adverse consequences of stress exposure. Little is known about how stress affects the fish microbiome, especially during sensitive early life stages when initial colonisation and proliferation of host-associated microbial communities take place. Therefore, we compared the effects of two aquaculture-relevant early-life stressors on the gut and skin microbiome of Atlantic salmon fry (four months post hatching) using 16S rRNA amplicon sequencing. Acute cold stress applied during late embryogenesis had a pronounced, lasting effect on the structure of the skin microbiome, as well as a less consistent effect on the gut microbiome. Follow-up targeted qPCR assays suggested that this is likely due to disruption of the egg shell microbial communities at the initial stages of microbiome colonisation, with persistent effects on community structure. In contrast, chronic post hatching stress altered the structure of the gut microbiome, but not that of the skin. Both types of stress promoted similar Gammaproteobacteria ASVs, particularly within the genera Acinetobacter and Aeromonas, which include several important opportunistic fish pathogens. Our results demonstrate the sensitivity of the salmon microbiome to environmental stressors during early life, with potential associated health impacts on the host. We also identified common signatures of stress in the salmon microbiome, which may represent useful microbial stress biomarkers., Graphical abstract Unlabelled Image, Highlights • The salmon microbiome is sensitive to early life environmental stressors. • Cold shock just before hatching induced lasting effects on the skin microbiome. • Pre- and post-hatch stressors also altered the gut microbiome. • Common stress signatory bacteria including opportunistic fish pathogens

Imperialism is one of the most significant phenomena in human history. It resulted in magnificent empires that lasted for centuries as territories were annexed and became colonies. On one hand, this practice created the conditions for a few nations to emerge as economic powerhouses by capitalising on the trade and investment opportunities made possible by the process of colonisation. On the other hand, a number of nations were relative victims of colonial policies that prioritised the commercial goals of entrepreneurs who were prominent throughout the colonial encounter. Amongst the latter, Sri Lanka, formerly known as Ceylon, is one of the Asian nations whose history has been shaped by the significance of commerce in the context of establishing and ruling of a particular colony. Whilst exploring her history, this paper details the importance of trade in general, and trade in cinnamon in particular, as the most significant feature of the process by which Ceylon was exposed to colonisation. It further identifies investment in the plantation sector as the subsequent method by which the colonial grip over the island was tightened.

Using a cross-section of 124 colonised countries, we evaluate the effect of the European share of the colonial population on human development as measured by life expectancy, fertility rate, and infant mortality rate. We find that European colonial settlement is positively related to life expectancy and negatively associated with both fertility and infant mortality rates. We show that 17.4% of life expectancy, 1.5% of the fertility rate, and 3% of the decline in infant mortality rate currently being enjoyed by non-Europe countries can be linked to their contacts with European settlers during colonisation.

Himalayan balsam (Impatiens glandulifera) is one of the most prolific non-native species in Europe. Since 2014, the highly-specific rust fungus, Puccinia komarovii var. glanduliferae, has been released into Great Britain as a classical biological control agent for this invasive weed. Prior to its release, research focused on ensuring the safety of the pathogen; elucidating its life cycle and verifying its host-specificity. However, limited studies were conducted to determine the likely impact of the rust on its host. Due to difficulties in assessing field populations, unforeseen complexities in the plant-pathogen relationship and the requirement for long-term monitoring, inoculation experiments were conducted to evaluate the effect of the rust on both seedlings and mature plants of Himalayan balsam under semi-natural conditions. The impact of the rust was determined through measuring plant-growth parameters in addition to assessing reproductive output. The rust significantly increased seedling mortality, with up to 80% of seedlings dying as a result of rust infection, or indirectly through the colonisation of secondary pathogens. Mature plants infected with the rust produced fewer leaves with a decrease in total plant biomass. Reproductive output was negatively affected through a reduction in both flower and seed production, but with no observed effects on seed viability. This study demonstrates the high potential of the rust for controlling fully susceptible field populations of Himalayan balsam.

The European oak bark beetle (Scolytus intricatus) has the potential to impact forest structures through its selection of certain trees. We investigated potential S. intricatus colonisation densities by setting up 150 trap trees and analysing them in 5-metre sections during a three-year period from 2014 to 2016 in a temperate forest in Slovakia, Central Europe. Understanding the population dynamics of S. intricatus and the drivers of its colonization density on trees is necessary if attempts to control or manage populations of S. intricatus in managed forests are to succeed. To explain the population dynamics of S. intricatus, ANOVA was used to assess the colonisation densities in the stem , and generalized linear mixed effect models (GLMMs) were used to analyse the main characteristics of the host trees and the meteorological variables. Structural equation modelling (SEM) was then used to explain the multitude of relationships among the predictor variables and bark beetle populations. Scolytus intricatus reached higher population levels under dry and warm conditions, when trees were prone to drought stress. The highest colonization densities at the trap trees occurred in May and June of 2014 and 2016; in 2015, the highest densities were reported in August and a second generation of S. intricatus was observed. This is unusual, as this species is usually univoltine, i.e. has one generation per year under Central European conditions. Population levels differed in different months during the 3-year study period, i.e. patterns of population dynamics and phenology are not repeating. The mixed-effects models demonstrated that the seasonal temperature influenced the occupation of trap trees by S. intricatus and that the lengths of the galleries were affected by the section surfaces. We conclude that environmental stress hastens the rate of drought stress in oak trees, resulting in faster population growth and higher survival of S. intricatus.

Arbuscular mycorrhizal (AM) fungi are ubiquitous components of the soil biota which live symbiotically with terrestrial plants. Plant-parasitic nematodes are an important group of soil-dwelling invertebrates that inflict considerable damage to crops, representing a serious threat to food security. The effects of the AM symbiosis on plant-parasitic nematodes can be variable, and the mechanisms driving such variability remain ambiguous. We tested the impacts of inoculation with AM fungi on the root metabolic profile and nutritional chemistry of two varieties of wheat (Triticum aestivum), and how this affected populations of the plant-parasitic nematode Pratylenchus neglectus. AM fungi reduced plant biomass by almost 24%, yet increased root concentrations of phosphorus, potassium and zinc by 50%, 15% and 16%, respectively. Contrary to our predictions, nematode populations were 47–117% higher on AM inoculated plants, depending on variety. Untargeted metabolomic profiling revealed significant effects of mycorrhizal colonisation on certain markers of biological interest, these compounds were the benzoxazinoid glucoside defence compounds DIBOA-Glc, HMBOA-Glc and HDMBOA-Glc. Overall, mycorrhizae reduced abundances of these defence metabolites, which were potentially driving AM fungi – nematode interactions; although for DIBOA-Glc this was dependent on wheat variety. Moreover, there was a negative correlation between total AM colonisation and DIBOA-Glc concentrations. Our results demonstrate AM fungi can reduce plant biomass and supress root defence compounds associated with plant resistance to invertebrate pests, while still providing nutritional benefit to the host plant. This highlights that mycorrhizal colonisation of wheat varieties can have simultaneous positive and negative effects on different plant traits which drive plant-herbivore interactions. In working towards effective exploitation of the AM symbiosis in sustainable plant production, the context dependent outcomes of mycorrhizal-plant-nematode interactions is a key challenge. Untargeted metabolomic profiling offers the ability to reveal some of the driving mechanisms underpinning such complex tripartite interactions in the soil.