Inclusion of minor alleles improves catalogue-based prediction of fluoroquinolone resistance in Mycobacterium tuberculosis.

Objectives: Fluoroquinolone resistance poses a threat to the successful treatment of tuberculosis. WGS, and the subsequent detection of catalogued resistance-associated mutations, offers an attractive solution to fluoroquinolone susceptibility testing but sensitivities are often less than 90%. We hypothesize that this is partly because the bioinformatic pipelines used usually mask the recognition of minor alleles that have been implicated in fluoroquinolone resistance. Methods: We analysed the Comprehensive Resistance Prediction for Tuberculosis: an International Consortium (CRyPTIC) dataset of globally diverse WGS Mycobacterium tuberculosis isolates, with matched MICs for two fluoroquinolone drugs and allowed putative minor alleles to contribute to resistance prediction. Results: Detecting minor alleles increased the sensitivity of WGS for moxifloxacin resistance prediction from 85.4% to 94.0%, without significantly reducing specificity. We also found no correlation between the proportion of an M. tuberculosis population containing a resistance-conferring allele and the magnitude of resistance. Conclusions: Together our results highlight the importance of detecting minor resistance-conferring alleles when using WGS, or indeed any sequencing-based approach, to diagnose fluoroquinolone resistance.

In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis.

Universal drug susceptibility testing (DST) for tuberculosis is a major goal of the END TB strategy. PCR-based molecular diagnostic tests have been instrumental in increasing DST globally and several assays have now been endorsed by the World Health Organization (WHO) for use in the diagnosis of drug resistance. These endorsed assays, however, each interrogate a limited number of mutations associated with resistance, potentially limiting their sensitivity compared to sequencing-based methods. We applied an in silico method to compare the sensitivity and specificity of WHO-endorsed molecular based diagnostics to the mutation set identified by the WHO mutations catalogue using phenotypic DST as the reference. We found that, in silico, the mutation sets used by probe-based molecular diagnostic tests to identify rifampicin, isoniazid, pyrazinamide, levofloxacin, moxifloxacin, amikacin, capreomycin and kanamycin resistance produced similar sensitivities and specificities to the WHO mutation catalogue. PCR-based diagnostic tests were most sensitive for drugs where mechanisms of resistance are well established and localised to small genetic regions or a few prevalent mutations. Approaches using sequencing technologies can provide advantages for drugs where our knowledge of resistance is limited, or where complex resistance signatures exist.

Predicting antibiotic resistance in complex protein targets using alchemical free energy methods.

Drug resistant Mycobacterium tuberculosis, which mostly results from single nucleotide polymorphisms in antibiotic target genes, poses a major threat to tuberculosis treatment outcomes. Relative binding free energy (RBFE) calculations can rapidly predict the effects of mutations, but this approach has not been tested on large, complex proteins. We use RBFE calculations to predict the effects of M. tuberculosis RNA polymerase and DNA gyrase mutations on rifampicin and moxifloxacin susceptibility respectively. These mutations encompass a range of amino acid substitutions with known effects and include large steric perturbations and charged moieties. We find that moderate numbers (n = 3-15) of short RBFE calculations can predict resistance in cases where the mutation results in a large change in the binding free energy. We show that the method lacks discrimination in cases with either a small change in energy or that involve charged amino acids, and we investigate how these calculation errors may be decreased.

Modern Solutions for Ancient Pathogens: Direct Pathogen Sequencing for Diagnosis of Lepromatous Leprosy and Cerebral Coenurosis.

Microbes unculturable in vitro remain diagnostically challenging, dependent historically on clinical findings, histology, or targeted molecular detection. We applied whole-genome sequencing directly from tissue to diagnose infections with mycobacteria (leprosy) and parasites (coenurosis). Direct pathogen DNA sequencing provides flexible solutions to diagnosis of difficult pathogens in diverse contexts.

Novel Agmatine Derivatives in Maerua edulis With Bioactivity Against Callosobruchus maculatus, a Cosmopolitan Storage Insect Pest.

Food security in developing countries is threatened by crop pests and ectoparasites in livestock. Strategies for their management still rely on synthetic pesticides which are not always effective and the active ingredients persist in the environment with negative consequences for beneficial arthropods, farmers and consumers, hence necessitating research on sustainable alternatives. Botanical insecticides are increasingly relevant, typically having lower impacts on users, consumers and the environment. One example is the southern African shrub the Blue bush-berry, Maerua edulis. Recent work reported effective pest control using this plant species against cattle ticks, storage beetles and vegetable pests. However, little is known about the chemistry underlying activity and this is essential to optimize its use. Here, we identified two novel plant chemical structures, the E and Z isomers of cinnamoyl-4-aminobutylguanidine along with the E and Z isomers of 4-hydroxycinnamoyl-4-aminobutylguanidine in the leaves of M. edulis. We isolated these compounds from the leaves and elucidated their chemical structures using various spectroscopic techniques including High Resolution Mass Spectrometry and Nuclear Magnetic Resonance Spectroscopy. We also identified a further 11 closely related structures of which 6 are tentatively reported here for the first time. Stachydrine and 3-hydroxystachydrine were also identified in the leaf extract, and occurred at very high concentrations; up to 2% w/w of dry leaves. We tested these two compounds, along with the 4 main cinnamoylamides and the crude M. edulis leaf extract against the cowpea bruchid Callosobruchus maculatus at concentrations equivalent to those present in extracts used by smallholder farmers. Mortality of insects exposed to crude plant extracts after 72 h was significantly higher than the untreated control although still lower than for insects exposed to rotenone, the positive control. The two new compounds and stachydrine showed similar activity to the crude extracts suggesting that these compounds explained the activity of the extract. After 6 days, the mortality of insects exposed to crude extracts and isolated compounds was similar to that recorded with the positive control. The stachydrine fraction and the E and Z isomers of cinnamoyl-4-aminobutylguanidine also inhibited oviposition activity in fecund female beetles. Our data show that methanol extracts of M. edulis were toxic to C. maculatus and inhibited oviposition even at 0.1% w/v so these foliar chemicals may explain the activity of the plant material. We also synthesized the amides which facilitated structural elucidation, produced adequate quantities for testing and demonstrated the potential for commercial synthesis.

Distasteful Nectar Deters Floral Robbery.

Toxic nectar is an ecological paradox [1, 2]. Plants divert substantial resources to produce nectar that attracts pollinators [3], but toxins in this reward could disrupt the mutualism and reduce plant fitness [4]. Alternatively, such compounds could protect nectar from robbers [2], provided that they do not significantly alter pollinator visitation to the detriment of plant fitness [1, 5-8]. Indeed, very few studies have investigated the role of plant toxins in nectar for defense against nectar robbers [4, 9, 10]. Here, we compared two Aconitum species (A. napellus and A. lycoctonum) that have flowers specialized for long-tongued bumblebee pollinators (Bombus hortorum) but are occasionally robbed by short-tongued bumblebees (B. terrestris) [6, 11-13]. Pollinator visits to flowers were much more frequent than by robbers, but visits correlated negatively with nectar alkaloid concentration and declined sharply between 200 and 380 ppm. However, alkaloid concentrations of >20 ppm were deterrent to B. terrestris, suggesting that robbers were less tolerant of nectar alkaloids. Nectar of both plant species contained similar concentrations of carbohydrates and toxic alkaloids, but A. lycoctonum was more likely to secrete nectar in each flower and was also visited more frequently by pollinators and robbers. We conclude that alkaloids in Aconitum spp. nectar affect rates of both pollinator visitation and robbery but may have co-evolved with nectar availability to maintain the fitness benefits of specialized plant-pollinator relationships. Chemical defense of nectar is, however, ultimately constrained by pollinator gustatory sensitivity.