Abstract
Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance ...(AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436
Escherichia coli
were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype–phenotype associations. No significant differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations. The study also revealed limitations of in-silico technology on detecting resistance to certain antimicrobials due to lack of specific fine-tuning options in bioinformatics tool or a lack of representation of resistance mechanisms in reference databases. Lastly, we noted user friendliness of tools was also an important consideration. Therefore, our recommendations are timely for widespread standardisation of bioinformatics for genomic diagnostics and surveillance globally.
Wheat quality, a complex term, depends upon intentional use for unambiguous products. The foremost determinants of wheat quality are endosperm texture (grain hardness), protein content and gluten ...strength. Endosperm texture in wheat is the single most important and defining quality characteristic, as it facilitates wheat classification and affects milling, baking and end-use quality. Various techniques used for grain hardness measurement are classified into diverse groups according to grinding, crushing and abrasion. The most extensively used methods for texture measurement are PSI, NIR hardness, SKCS, pearling index, SDS-PAGE and PCR markers. Friabilin is a 15 kDa endosperm specific protein associated with starch granules of wheat grain and is unswervingly related to grain softness. Chemically, it is a concoction of different polypeptides, primarily puroindolines; Pin a and Pin b. Hardness (Ha) locus of chromosome 5DS makes the distinction between soft and hard classes of wheat. Some additional modifying genes are also present which contribute to the disparity within wheat classes. Numerous allelic mutations in Pin have been reported and their relation to end product quality has been established. This treatise elaborates the consequence of grain hardness in wheat eminence.
Research in the field of aluminum batteries has focused heavily on electrodes made of carbonaceous materials. Still, the capacities reported for these multivalent systems remain stubbornly low. It is ...believed that a high structural quality of graphitic carbons and/or specific surface areas of >1000 m2 g‐1 are key factors to obtain optimal performance and cycling stability. Here an aluminum chloride battery is presented in which reduced graphene oxide (RGO) powder, dried under supercritical conditions, is used as the active cathode material and niobium foil as the current collector. With a specific surface area of just 364 m2 g‐1, the RGO enables a gravimetric capacity of 171 mAh g‐1 at 100 mA g‐1 and remarkable stability over a wide range of current densities (<15% decrease over 100 cycles in the interval 100–20000 mA g‐1). These properties, up to now achieved only with much larger surface area materials, result from the cathode's tailored mesoporosity. The 20 nm wide mesopores facilitate the movement of the chloroaluminate ions through the RGO, effectively minimizing the inactive mass content of the electrode. This more than compensates for the ordinary micropore volume of the graphene powder.
Tailoring the pore size distribution of carbon‐based cathodes is a decisive factor for the electrochemical performance of aluminum batteries. Here, the mesopores in a reduced graphene oxide powder facilitate the movement of large chloroaluminate ions, effectively minimizing the inactive mass content of the electrode and compensating for an ordinary micropore volume.
•Significant increase in fully susceptible E. coli after reduced antimicrobial use.•Multidrug resistant E. coli decline significantly after withdrawing group treatment.•However, resistant commensal ...E. coli remain after withdrawal of group treatment.•Resistant E. coli survived pen cleaning and could be detected on farm equipment.•Plasmids have an important role for the maintenance and dissemination of resistance.
An important element in the control of antimicrobial resistance (AMR) is reduction in antimicrobial usage. In the veterinary sector individual antimicrobial treatment of livestock, rather than the use of group treatment, can help achieve this goal. The aim of this study was to investigate how cessation of group antimicrobial treatment impacted the prevalence of AMR in commensal Escherichia coli in pigs at one farm over an 11-month period. Minimum inhibitory concentrations of eight antimicrobials were determined for 259 E. coli isolates collected during the study. A significant reduction in the prevalence of multidrug resistance and a significant increase in the proportion of full susceptibility to the panel of nine antimicrobials tested was seen after 11 months. Whole genome sequencing of 48 multidrug resistant isolates revealed E. coli clones that persisted across multiple visits and provided evidence for the presence of plasmids harbouring AMR genes shared across multiple E. coli lineages. E. coli were also isolated from on-farm environmental samples. Whole genome sequencing of one multidrug resistant isolate obtained from cleaning tools showed it was clonal to pig-derived E. coli that persisted on the farm for 11 months. In this study we provide evidence that withdrawal of group antimicrobial use leads to significant reductions in key indicators for AMR prevalence and the importance of the farm environment as a reservoir of resistant bacteria. These findings support policy makers and producers in the implementation of measures to control AMR and reduce antimicrobial use.
Aims
This study investigated the occurrence and genetic diversity of Enterobacteriaceae with extended‐spectrum β‐lactamase (ESBL)‐, AmpC‐ and carbapenemase‐mediated resistance in British beef cattle, ...and related risk factors.
Methods and Results
Faecal samples (n = 776) were obtained from farms in England and Wales (n = 20) and Scotland (n = 20) in 2015. Isolates from selective agars were identified by MALDI ToF mass spectrometry. Selected isolates were characterized by multiplex PCR (blaCTX‐M, blaOXA, blaSHV and blaTEM genes), whole‐genome sequencing (WGS), minimum inhibitory concentrations and pulsed‐field gel electrophoresis. None of the faecal samples yielded carbapenem‐resistant Escherichia coli. Ten (25%) of the farms tested positive for ESBL‐producing CTX‐M Enterobacteriaceae, 15 (37·5%) of the farms were positive for AmpC phenotype E. coli and none were positive for carbapenem‐resistant E. coli. WGS showed a total of 30 different resistance genes associated with E. coli, Citrobacter and Serratia from ESBL agars, and colocation of resistance genes with blaCTX‐M1. Buying bulls and bringing in fattening cattle from another farm were identified as significant risk factors for positive samples harbouring CTX‐M Enterobacteriaceae or AmpC phenotype E. coli respectively.
Conclusions
Beef cattle on a proportion of farms in GB carry ESBL‐producing Enterobacteriaceae. Factors, such as operating as a closed herd, may have an important role in reducing introduction and transmission of resistant Enterobacteriaceae. The results indicate management factors may play an important role in impacting ESBL prevalence. In particular, further study would be valuable to understand the impact of maintaining a closed herd on reducing the introduction of resistant Enterobacteriaceae.
Significance and Impact of the Study
This is the first study showing the presence of ESBL‐producing Enterobacteriaceae in British beef cattle.
Stability of fortified whole wheat flour (WWF) was evaluated using NaFeEDTA, elemental iron, ZnSO4 and ZnO as fortificants. Fortified WWF was stored in tin boxes and polypropylene bags for 60 days ...under ambient storage condition (ASC) and controlled storage condition (CSC). Fortification significantly (p⩽0.05) decreased moisture and protein content and increased ash content to 5.44%, 6% and 23%, as compared to control. Fortified WWF, assayed periodically for mould contamination manifested a significant inhibition (∼1 log reduction) in flours containing elemental iron. Low storage temperature and relative humidity (RH) indicated lower level of mould count during extended storage time. Tin boxes, as storage material, exhibited a better protection against mould attack, acting as an effective barrier for moisture. Fortificants exerted a slight deteriorative effect on texture characteristics of the chapattis made of these flours but chapattis were still accepted by the judges. Zinc fortificants seemed like having little or no effect on the quality of the flours and chapattis, made of such flours. Shelf life of fortified flour may be extended by using elemental iron as fortificant and storing the product in tin boxes under relatively low temperature and RH.
Aims
In 2015, colistin‐resistant Escherichia coli and Salmonella with the mcr‐1 gene were isolated from a pig farm in Great Britain. Pigs were subsequently monitored over a ~20‐month period for the ...occurrence of mcr‐1‐mediated colistin resistance and the risk of mcr‐1 E. coli entering the food chain was assessed.
Methods and Results
Pig faeces and slurry were cultured for colistin‐resistant E. coli and Salmonella, tested for the mcr‐1 gene by PCR and selected isolates were further analysed. Seventy‐eight per cent of faecal samples (n = 275) from pigs yielded mcr‐1 E. coli after selective culture, but in positive samples only 0·2–1·3% of the total E. coli carried mcr‐1. Twenty months after the initial sampling, faecal samples (n = 59) were negative for E. coli carrying mcr‐1.
Conclusions
The risk to public health from porcine E. coli carrying mcr‐1 was assessed as very low. Twenty months after cessation of colistin use, E. coli carrying mcr‐1 was not detected in pig faeces on a farm where it was previously present.
Significance and Impact of the Study
The results suggest that cessation of colistin use may help over time to reduce or possibly eliminate mcr‐1 E. coli on pig farms where it occurs.
The objective of the study was to compare the sensory profile of Cheddar cheese prepared from cow and buffalo milk using indigenous and commercial cultures. Commercially available and locally ...isolated, indigenous starter cultures were used to prepare cow and buffalo milk Cheddar cheese. The cheese was ripened at 4 and 12°C and analyzed for descriptive sensory profile by a panel of 10 assessors after 60 and 120d of ripening. On evaluation, the mean scores for odor, flavor, and texture attributes obtained for buffalo milk cheese were significantly higher than those obtained for cow milk cheese. For most of the traits, cheese samples prepared from indigenous cultures and ripened at higher temperature received higher descriptive scores compared with those of commercial cultures and ripened at lower degrees. Milk sources highly significantly affected the “creamy” and “sour” traits of odor; the “creamy,” “smoky,” and “soapy” flavors; and all the texture attributes except “maturity.” Starter cultures considerably influenced the production of “acidic,” “bitter,” “sweet,” and “sour” characteristics. The use of elevated ripening temperature showed noticeable effect on all the characteristics except the “creamy” odor and flavor. Principal component analysis and hierarchical cluster analysis also showed that milk sources, starter cultures, and ripening temperatures significantly influenced the sensory characteristics.
Premature senescence, unopened and rotted bolls are the primary constrictions hampering the accomplishment of yield potential in Bt cotton. An experiment was conducted with the objectives to delay ...senescence, enhance boll opening and reduce the boll rotting. The experiment was conducted at two randomly selected sites of University of Agriculture Faisalabad, Pakistan, during 2015 and repeated in 2016. Each experiment was laid out in randomised complete block design with two by two factorial arrangement structure and replicated five times. Treatments were comprised of R0 = no fruit removal; R1 = removal of early fruit branches (REFB) and two genotypes, viz. V1 = FH‐142 and V2 = MNH‐886. Genotypes were selected on the basis of abiotic stress tolerance (FH‐142) and susceptibility (MNH‐886). Nodes above cracked bolls, monopodial branches, opened bolls per plant and seed cotton yield were enhanced by 23, 12, 13 and 17%, respectively, under the influence of REFB over no fruit branch removal, while the REFB‐mediated decrease in boll rotting was 27%. Moreover, the response of MNH‐886 was more remarkable than FH‐142 for all studied variables. Conclusively, REFB increased the number of nodes above a cracked boll, monopodial branches, opened bolls per plant and seed cotton yield while decreased rotted bolls per plant in both genotypes.
Bad boll opening owing to early senescence and rotted bolls are chief hindrances to accomplish yield potential in cotton. The present study was aimed to delay the senescence and thus enhance the number of opened bolls and decrease the number of rotted bolls in cotton genotypes using removal of early fruit branches (REFB) as potential regulator of boll opening. Removal of two early fruit branches enhanced number of opened bolls, decreased rotted bolls, delayed the senescence and ultimately improved seed cotton yield in varying cotton genotypes compared to control.
Summary
Alpha‐lipoic acid (ALA) is a multifunction antioxidant that is produced in small amount by cells as well as its dietary provision facilitates fatty acid mobilization, energy expenditure as ...well as can scavenge free radicals in poultry birds. It exists in oxidized as well as reduced form, characterized by growth promoting, anti‐inflammatory, antioxidative, immunostimulatory, and hypocholesterolemic properties when fed as dietary supplement to farm animals particularly chicken birds. Recently, several studies reported that dietary supplementation of ALA can influence growth performance indicators, immunological, biochemical characteristics, lipid metabolism, and oxidative stress as well as increase antioxidant potential and storability of poultry meat and meat products. Accordingly, this paper adds the reviews and discusses the outcomes of studies documenting the effect of lipoic acid dietary fortification on growth performance, biochemical, and immunological characteristics as well as the effects on lipid peroxidation of fresh meat and meat‐based products. Furthermore, this paper also describes the possibilities of utilization of ALA as a feed additive in poultry nutrition to improve the growth performance of poultry as well as meat quality of resultant chicken birds.
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