A high diversity of non-target site resistance mechanisms to acetolactate-synthase (ALS) inhibiting herbicides has evolved within and among field populations of common ragweed (Ambrosia artemisiifolia L.)

BACKGROUND

Non-target site resistance (NTSR) to herbicides is a polygenic trait that threatens the chemical control of agricultural weeds. NTSR involves differential regulation of plant secondary metabolism pathways, but its precise genetic determinisms remain fairly unclear. Full-transcriptome sequencing had previously been implemented to identify NTSR genes. However, this approach had generally been applied to a single weed population, limiting our insight into the diversity of NTSR mechanisms. Here, we sought to explore the diversity of NTSR mechanisms in common ragweed (Ambrosia artemisiifolia L.) by investigating six field populations from different French regions where NTSR to acetolactate-synthase-inhibiting herbicides had evolved.

RESULTS

A de novo transcriptome assembly (51,242 contigs, 80.2% completeness) was generated as a reference to seek genes differentially expressed between sensitive and resistant plants from the six populations. Overall, 4,609 constitutively differentially expressed genes were identified, of which none were common to all populations, and only 197 were shared by several populations. Similarly, population-specific transcriptomic response was observed when investigating early herbicide response. Gene ontology enrichment analysis highlighted the involvement of stress response and regulatory pathways, before and after treatment. The expression of 121 candidate constitutive NTSR genes including CYP71, CYP72, CYP94, oxidoreductase, ABC transporters, gluco and glycosyltransferases was measured in 220 phenotyped plants. Differential expression was validated in at least one ragweed population for 28 candidate genes. We investigated whether expression patterns at some combinations of candidate genes could predict phenotype. Within populations, prediction accuracy decreased when applied to an additional, independent plant sampling. Overall, a wide variety of genes linked to NTSR was identified within and among ragweed populations, of which only a subset was captured in our experiments.

CONCLUSION

Our results highlight the complexity and the diversity of NTSR mechanisms that can evolve in a weed species in response to herbicide selective pressure. They strongly point to a non-redundant, population-specific evolution of NTSR to ALS inhibitors in ragweed. It also alerts on the potential of common ragweed for rapid adaptation to drastic environmental or human-driven selective pressures.

Stable isotope labeling as a promising tool for rapid drug susceptibility testing in Neisseria gonorrhoeae

The world is heading towards an era of intractable and impending untreatable N. gonorrhoeae, thereby underlining the significance of rapid and accurate prediction of drug resistance as an indispensable need of the hour. In the present study, we optimized and evaluated a stable isotope labeling-based approach using the MALDI-TOF MS (Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry) for rapid and reliable detection of ciprofloxacin and azithromycin resistance in N. gonorrhoeae. All the isolates were cultured under three varied condition setups viz. medium supplemented with normal lysine, heavy lysine (isotope), and heavy lysine along with the antibiotics (ciprofloxacin/azithromycin), respectively. After incubation, spectra were acquired using the MALDI-TOF MS which were further screened for unique patterns (media-specific spectra) to differentiate drug-susceptible and resistant isolates. The results of the stable isotope labeling assay were comparable to the results of phenotypic methods used for susceptibility testing.

Development of a LAMP method for detecting F129L mutant in azoxystrobin-resistant Pyricularia oryzae

Azoxystrobin has been widely used since 1996 to control rice blast caused by Pyricularia oryzae. Azoxystrobin resistance related to mutations at the P. oryzae target protein (F129L of Cytb) has been reported worldwide. To quickly identify and detect resistant strains in the field, this research established a rapid loop-mediated isothermal amplification (LAMP) detection system for the F129L mutation. The system could detect the P. oryzae F129L (TTC-TTA) mutation at 62 °C within 60 min, with a detection limit of 100 fg/μL, which is 10 times higher than for conventional PCR. The method had high specificity and repeatability and could detect the F129L (TTC-TTA) mutation in plant tissues within 3 h. The LAMP method established in this study will be useful to detect azoxystrobin-resistant P. oryzae F129L mutant strains and generate significant data for the management of resistant P. oryzae isolates.

Development of a LAMP method for detecting the N75S mutant in SDHI-resistant Corynespora cassiicola

The replacement of asparagine with serine at codon 75 of the sdhC gene (N75S) confers succinate dehydrogenase inhibitor resistance in Corynespora cassiicola, which caused by consecutive fungicide application. To rapidly detect the mutation of N75S, a method based on loop-mediated isothermal amplification (LAMP) was developed in this study. The optimal primer set among the six primer sets designed could clearly identify N75S from the wild-type genotype. The detection threshold of the optimized LAMP mixture (10 μL) was 8.8 fg of target DNA at 63 °C within 60 min. This method specifically showed a color change and ladder-like band only when DNA extracted from isolates containing the N75S mutation was added. The results of stability tests suggested a satisfactory repeatability of this method. Additionally, the assay could positively distinguish N75S mutants from crude DNA isolated from conidia and mycelia of C. cassiicola. Given the high efficiency, sensitivity, specificity, repeatability and simplicity of operation, the LAMP method established here could be useful to evaluate the shift in the sensitivity of C. cassiicola to SDHIs and will provide significant data for the management of Corynespora leaf spot.

Hidden Selection of Bacterial Resistance to Fluoroquinolones In Vivo: The Case of Legionella pneumophila and Humans

Background

Infectious diseases are the leading cause of human morbidity and mortality worldwide. One dramatic issue is the emergence of microbial resistance to antibiotics which is a major public health concern. Surprisingly however, such in vivo adaptive ability has not been reported yet for many intracellular human bacterial pathogens such as Legionella pneumophila.

Methods

We examined 82 unrelated patients with Legionnaire's disease from which 139 respiratory specimens were sampled during hospitalization and antibiotic therapy. We both developed a real time PCR assay and used deep-sequencing approaches to detect antibiotic resistance mutations in L. pneumophila and follow their selection and fate in these samples.

Findings

We identified the in vivo selection of fluoroquinolone resistance mutations in L. pneumophila in two infected patients treated with these antibiotics. By investigating the mutational dynamics in patients, we showed that antibiotic resistance occurred during hospitalization most likely after fluoroquinolone treatment.

Interpretation

In vivo selection of antibiotic resistances in L. pneumophila may be associated with treatment failures and poor prognosis. This hidden resistance must be carefully considered in the therapeutic management of legionellosis patients and in the control of the gradual loss of effectiveness of antibiotics.

•

Legionellosis is a pneumonia caused by the inhalation of aerosols containing Legionella, mainly L. pneumophila.

•

Its average mortality rate is 10%, despite availability of effective antibiotics such as the macrolides and the fluoroquinolones.

•

Using modern molecular approaches, we identified the selection of fluoroquinolone resistance in L. pneumophila in patients under fluoroquinolone therapy.

•

This may lead to reduction of treatment efficacy and prognosis worsening.

•

Our findings should lead to revised guidelines for therapeutic management and prognosis evaluation of legionellosis.

Toxicodynamic mechanisms and monitoring of acaricide resistance in the two-spotted spider mite

The two-spotted spider (Tetranychus urticae) is one of the most serious pests world-wide and has developed resistance to many types of acaricides. Various mutations on acaricide target site genes have been determined to be responsible for toxicodynamic resistance, and the genotyping and frequency prediction of these mutations can be employed as an alternative resistance monitoring strategy. A quantitative sequencing (QS) protocol was reported as a population-based genotyping technique, and applied for the determination of resistance allele frequencies in T. urticae field populations. In addition, a modified glass vial bioassay method (residual contact vial bioassay, RCV) was implemented as a rapid on-site resistance monitoring tool. The QS protocol, together with the RCV, would greatly facilitate monitoring of T. urticae resistance. Recent completion of T. urticae genome analysis should facilitate the identification of additional resistance genetic markers that can be employed for molecular resistance monitoring.