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Abstract 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.

Summary: Background: Molecular diagnostics are considered the most promising route to achievement of rapid, universal drug susceptibility testing for Mycobacterium tuberculosis complex (MTBC). We aimed to generate a WHO-endorsed catalogue of mutations to serve as a global standard for interpreting molecular information for drug resistance prediction. Methods: In this systematic analysis, we used a candidate gene approach to identify mutations associated with resistance or consistent with susceptibility for 13 WHO-endorsed antituberculosis drugs. We collected existing worldwide MTBC whole-genome sequencing data and phenotypic data from academic groups and consortia, reference laboratories, public health organisations, and published literature. We categorised phenotypes as follows: methods and critical concentrations currently endorsed by WHO (category 1); critical concentrations previously endorsed by WHO for those methods (category 2); methods or critical concentrations not currently endorsed by WHO (category 3). For each mutation, we used a contingency table of binary phenotypes and presence or absence of the mutation to compute positive predictive value, and we used Fisher's exact tests to generate odds ratios and Benjamini-Hochberg corrected p values. Mutations were graded as associated with resistance if present in at least five isolates, if the odds ratio was more than 1 with a statistically significant corrected p value, and if the lower bound of the 95% CI on the positive predictive value for phenotypic resistance was greater than 25%. A series of expert rules were applied for final confidence grading of each mutation. Findings: We analysed 41 137 MTBC isolates with phenotypic and whole-genome sequencing data from 45 countries. 38 215 MTBC isolates passed quality control steps and were included in the final analysis. 15 667 associations were computed for 13 211 unique mutations linked to one or more drugs. 1149 (7·3%) of 15 667 mutations were classified as associated with phenotypic resistance and 107 (0·7%) were deemed consistent with susceptibility. For rifampicin, isoniazid, ethambutol, fluoroquinolones, and streptomycin, the mutations' pooled sensitivity was more than 80%. Specificity was over 95% for all drugs except ethionamide (91·4%), moxifloxacin (91·6%) and ethambutol (93·3%). Only two resistance mutations were identified for bedaquiline, delamanid, clofazimine, and linezolid as prevalence of phenotypic resistance was low for these drugs. Interpretation: We present the first WHO-endorsed catalogue of molecular targets for MTBC drug susceptibility testing, which is intended to provide a global standard for resistance interpretation. The existence of this catalogue should encourage the implementation of molecular diagnostics by national tuberculosis programmes. Funding: Unitaid, Wellcome Trust, UK Medical Research Council, and Bill and Melinda Gates Foundation.

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.