Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing

Escherichia coli strains are classified based on O-antigens that are components of the lipopolysaccharide (LPS) in the cell envelope. O-antigens are important virulence factors, targets of both the innate and adaptive immune system, and play a role in host-pathogen interactions. Because they are highly immunogenic and display antigenic specificity unique for each strain, O-antigens are the biomarkers for designating O-types. Immunologically, 185 O-serogroups and 11 OX-groups exist for classification. Conventional serotyping for O-typing entails agglutination reactions between the O-antigen and antisera generated against each O-group. The procedure is labor intensive, not always accurate, and exhibits equivocal results. In this report, we present the sequences of 71 O-antigen gene clusters (O-AGC) and a comparison of all 196 O- and OX-groups. Many of the designated O-types, applied for classification over several decades, exhibited similar nucleotide sequences of the O-AGCs and cross-reacted serologically. Some O-AGCs carried insertion sequences and others had only a few nucleotide differences between them. Thus, based on these findings, it is proposed that several of the E. coli O-groups may be merged. Knowledge of the O-AGC sequences facilitates the development of molecular diagnostic platforms that are rapid, accurate, and reliable that can replace conventional serotyping. Additionally, with the scientific knowledge presented, new frontiers in the discovery of biomarkers, understanding the roles of O-antigens in the innate and adaptive immune system and pathogenesis, the development of glycoconjugate vaccines, and other investigations, can be explored.     

Towards more equal footing in north–south biodiversity research: European and sub-Saharan viewpoints

Research collaboration between developed countries from the northern hemisphere and developing countries in the southern hemisphere is essential for the understanding and protection of the major proportion of biodiversity located in the tropics. Focusing on the case of sub-Saharan Africa, we here assess the real involvement of northern versus southern contributors, and caution against unequal academic benefit sharing arising from non-commercial biodiversity research that may ultimately hamper sustainable knowledge transfer and long-term biodiversity conservation. We discuss possible drivers that may have led to a business of raw biodiversity data. While we fully support the current efforts to stamp out biopiracy through international biodiversity policies and agreements, we illustrate that such legislative frameworks may further constrain biodiversity research, especially in countries where regulations are poorly streamlined and bureaucracy remains rather inert. We therefore ask for workable solutions towards more equal footing in north–south biodiversity research, and propose a number of steps to transgress the current barriers towards a more fair and equitable sharing of benefits arising from biodiversity research.     

PCR analysis of the presence and location of Mycobacterium avium in a constructed reed bed, with implications for avian tuberculosis control

The potential of reed beds to act as biofilters of pathogenic and environmental mycobacteria was investigated through examination of the fate of mycobacteria in a constructed reed bed filtering effluent from a large captive wildfowl collection. Particular emphasis was placed on the presence and location of Mycobacterium avium – the causal agent of avian tuberculosis (ATB) – in an effort to clarify the potential role of reed beds in the control of this disease. Water, sediment, and stems and roots of common reed ( Phragmites australis ) and greater reedmace ( Typha latifolia ) were taken from 15 locations within the reed bed plus sites upstream and downstream. Samples were analysed for mycobacteria using PCR and specifically for M. avium using nested PCR. Environmental mycobacteria were found throughout the entire reed bed but M. avium was not found downstream of the first vegetation growth. The reed bed was found to effectively remove M. avium from the water through a combination of sedimentation and adsorption onto vegetation stems. The results of this study show that constructed reed beds composed of a settlement lagoon and one or more vegetation beds can act as valuable and ecologically friendly tools in the environmental control of ATB.     

Physiological and ecological warnings that dodders pose an exigent threat to farmlands in Eastern Africa

Invasive holoparasitic plants of the genus Cuscuta (dodder) threaten African ecosystems due to their rapid spread and attack on various host plant species. Most Cuscuta species cannot photosynthesize and hence rely on host plants for nourishment. After attachment through a peg-like organ called a haustorium, the parasites deprive hosts of water and nutrients, which negatively affects host growth and development. Despite their rapid spread in Africa, dodders have attracted limited research attention, although data on their taxonomy, host range, and epidemiology are critical for their management. Here, we combine taxonomy and phylogenetics to reveal the presence of field dodder (Cuscuta campestris) and C. kilimanjari (both either naturalized or endemic to East Africa), in addition to the introduction of the giant dodder (C. reflexa), a south Asian species, in continental Africa. These parasites have a wide host range, parasitizing species across 13 angiosperm orders. We evaluated the possibility of C. reflexa to expand this host range to tea (Camelia sinensis), coffee (Coffea arabica), and mango (Mangifera indica), crops of economic importance to Africa, for which haustorial formation and vascular-bundle connections in all three crops revealed successful parasitism. However, only mango mounted a successful postattachment resistance response. Furthermore, species distribution models predicted high habitat suitability for Cuscuta spp. across major tea- and coffee-growing regions of Eastern Africa, suggesting an imminent risk to these crops. Our findings provide relevant insights into a poorly understood threat to biodiversity and economic wellbeing in Eastern Africa, and provide critical information to guide development of management strategies to avert Cuscuta spp. spread.

Microscopy and habitat suitability modeling provide an early warning that dodder’s invasion in Eastern Africa poses a threat to important cash crops.     

Effects of plant diversity on invertebrate herbivory in experimental grassland

The rate at which a plant species is attacked by invertebrate herbivores has been hypothesized to depend on plant species richness, yet empirical evidence is scarce. Current theory predicts higher herbivore damage in monocultures than in species-rich mixtures. We quantified herbivore damage by insects and molluscs to plants in experimental plots established in 2002 from a species pool of 60 species of Central European Arrhenatherum grasslands. Plots differed in plant species richness (1, 2, 4, 8, 16, 60 species), number of functional groups (1, 2, 3, 4), functional group and species composition. We estimated herbivore damage by insects and molluscs at the level of transplanted plant individuals (“phytometer” species Plantago lanceolata, Trifolium pratense, Rumex acetosa) and of the entire plant community during 2003 and 2004. In contrast to previous studies, our design allows specific predictions about the relative contributions of functional diversity, plant functional identity, and species richness in relation to herbivory. Additionally, the phytometer approach is new to biodiversity-herbivory studies, allowing estimates of species-specific herbivory rates within the larger biodiversity-ecosystem functioning context. Herbivory in phytometers and experimental communities tended to increase with plant species richness and the number of plant functional groups, but the effects were rarely significant. Herbivory in phytometers was in some cases positively correlated with community biomass or leaf area index. The most important factor influencing invertebrate herbivory was the presence of particular plant functional groups. Legume (grass) presence strongly increased (decreased) herbivory at the community level. The opposite pattern was found for herbivory in T. pratense phytometers. We conclude that (1) plant species richness is much less important than previously thought and (2) plant functional identity is a much better predictor of invertebrate herbivory in temperate grassland ecosystems.     

The Mechanism of Heterogeneous Beta-Lactam Resistance in MRSA: Key Role of the Stringent Stress Response

All methicillin resistant S. aureus (MRSA) strains carry an acquired genetic determinant – mecA or mecC - which encode for a low affinity penicillin binding protein –PBP2A or PBP2A′ – that can continue the catalysis of peptidoglycan transpeptidation in the presence of high concentrations of beta-lactam antibiotics which would inhibit the native PBPs normally involved with the synthesis of staphylococcal cell wall peptidoglycan. In contrast to this common genetic and biochemical mechanism carried by all MRSA strains, the level of beta-lactam antibiotic resistance shows a very wide strain to strain variation, the mechanism of which has remained poorly understood. The overwhelming majority of MRSA strains produce a unique – heterogeneous – phenotype in which the great majority of the bacteria exhibit very poor resistance often close to the MIC value of susceptible S. aureus strains. However, cultures of such heterogeneously resistant MRSA strains also contain subpopulations of bacteria with extremely high beta-lactam MIC values and the resistance level and frequency of the highly resistant cells in such strain is a characteristic of the particular MRSA clone. In the study described in this communication, we used a variety of experimental models to understand the mechanism of heterogeneous beta-lactam resistance. Methicillin-susceptible S. aureus (MSSA) that received the mecA determinant in the laboratory either on a plasmid or in the form of a chromosomal SCCmec cassette, generated heterogeneously resistant cultures and the highly resistant subpopulations that emerged in these models had increased levels of PBP2A and were composed of bacteria in which the stringent stress response was induced. Each of the major heterogeneously resistant clones of MRSA clinical isolates could be converted to express high level and homogeneous resistance if the growth medium contained an inducer of the stringent stress response.     

NDVI‐based vegetation monitoring in Mau forest complex,Kenya

The normalized difference vegetation index (NDVI) measures vegetation health and density using plant reflectance characteristics recorded by satellite imagery. Dekadal NDVI data were obtained for January 1999–December 2009 from 1‐km resolution SPOT‐VEGETATION sensor for closed woody vegetation type in four blocks of the Mau forest complex. Vegetation response to yearly seasonal variations was plotted and used to compare deviations by specific years. Subnormal vegetation conditions were recorded by the standardized vegetation index (SVI) and persistently low SVI values indicated a drought season or degraded vegetation. The general linear trend of the vegetation was plotted for the study period to identify trends towards degradation or vegetation recovery. Analysis of variance was used to compare forest blocks and shows spatial vegetation variations and also among years to identify vegetation variations with time. Rainfall data recorded for 2002–2009 in east Mau were used to confirm rainfall‐related vegetation variations block. Results show that NDVI patterns within an year follow cyclic trends with a strong dependence on rainfall seasons. The forest vegetation indicated negligible changes over the study period but effects of extended dry periods in 2000 and 2009 were evident. There were significant differences (P < 0.05) in NDVI between forest blocks. East Mau had significantly inferior vegetation that can be attributed to forest type, level of human degradation prior to the study and the lower rainfall. There were significant variations (P < 0.05) of NDVI among years but the forests showed a natural resilience to disturbance and can retain original vegetation vigour once stress is removed. The study proposes further monitoring of the forests including other vegetation types that are more vulnerable to climatic variations and anthropogenic effects.