Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review

Background

Antimicrobial resistance (AMR) is a rising health threat with 10 million annual casualties estimated by 2050. Appropriate treatment of infectious diseases with the right antibiotics reduces the spread of antibiotic resistance. Today, clinical practice relies on molecular and PCR techniques for pathogen identification and culture-based antibiotic susceptibility testing (AST). Recently, WGS has started to transform clinical microbiology, enabling prediction of resistance phenotypes from genotypes and allowing for more informed treatment decisions. WGS-based AST (WGS-AST) depends on the detection of AMR markers in sequenced isolates and therefore requires AMR reference databases. The completeness and quality of these databases are material to increase WGS-AST performance.

Methods

We present a systematic evaluation of the performance of publicly available AMR marker databases for resistance prediction on clinical isolates. We used the public databases CARD and ResFinder with a final dataset of 2587 isolates across five clinically relevant pathogens from PATRIC and NDARO, public repositories of antibiotic-resistant bacterial isolates.

Results

CARD and ResFinder WGS-AST performance had an overall balanced accuracy of 0.52 (±0.12) and 0.66 (±0.18), respectively. Major error rates were higher in CARD (42.68%) than ResFinder (25.06%). However, CARD showed almost no very major errors (1.17%) compared with ResFinder (4.42%).

Conclusions

We show that AMR databases need further expansion, improved marker annotations per antibiotic rather than per antibiotic class and validated multivariate marker panels to achieve clinical utility, e.g. in order to meet performance requirements such as provided by the FDA for clinical microbiology diagnostic testing.

High genomic diversity of multi-drug resistant wastewater Escherichia coli

Wastewater treatment plants play an important role in the emergence of antibiotic resistance. They provide a hot spot for exchange of resistance within and between species. Here, we analyse and quantify the genomic diversity of the indicator Escherichia coli in a German wastewater treatment plant and we relate it to isolates’ antibiotic resistance. Our results show a surprisingly large pan-genome, which mirrors how rich an environment a treatment plant is. We link the genomic analysis to a phenotypic resistance screen and pinpoint genomic hot spots, which correlate with a resistance phenotype. Besides well-known resistance genes, this forward genomics approach generates many novel genes, which correlated with resistance and which are partly completely unknown. A surprising overall finding of our analyses is that we do not see any difference in resistance and pan genome size between isolates taken from the inflow of the treatment plant and from the outflow. This means that while treatment plants reduce the amount of bacteria released into the environment, they do not reduce the potential for antibiotic resistance of these bacteria.

Design, synthesis and antiinflammatory activity of some 1,3,4-oxadiazole derivatives

A series of substituted 1,3,4-oxadiazole derivatives 19-34 were synthesized as antiinflammatory agents. The target compounds were obtained by cyclodesulfurization of the corresponding thiosemicarbazides 3-18 using either dicyclohexylcarbodiimide DCC, or I(2)/NaOH. Intermediates 3-18 are readily accessible through conversion of the carboxylic acids 1a-d to the respective hydrazides 2a-d followed by treatment with appropriate isothiocyanate derivatives. The structures of the synthesized compounds were confirmed by elemental as well as spectroscopic analyses. The antiinflammatory activity was investigated by determination of the inhibitory effects of the oxadiazole derivatives 19-34 on histamine-induced edema in rat abdomen. Compounds 19a, 21a, 23b, 28c and 32d proved to be more potent antiinflammatory agents at 200 mg/kg po than ibuprofen, the standard reference drug. Other compounds such as 20a, 25b, 27c, 29c, and 33d showed significant antiinflammatory activity but less than ibuprofen at the same dose level. The low toxicity of the most potent compounds was reflected by their higher LD(50) value, ranging from ~1000 to 1500 mg/kg, as well as the lower ulcerogenic liability at 200 mg/kg po. Furthermore, some of the newly synthesized derivatives were better analgesics than the reference drug as observed from the percentage writhing inhibition in the p-benzoquinone (PBQ)-induced writhing test in mice.

[Allergic granulomatous angiitis in the Churg-Strauss syndrome. Two case reports]

The Churg-Strauss Syndrome (CSS) or allergic granulomatosis and angiitis is a relatively unusual disease. It is a subset of the group of systemic necrotizing vasculitis and the clinical manifestations involve multiple organ system. The CSS is characterized typically by three phases, asthma or atopic disease, peripheral eosinophilia and ultimately, vasculitis. The authors report two cases of CSS. The first patient presented allergic rhinitis and asthma for 19 years when she developed acute abdominal pain, mononeuritis of her right leg, pulmonary infiltrates and hypereosinophilia. The lung biopsy showed extravascular granulomas and eosinophilic infiltration. The second patient presented asthma for two years when she developed a mononeuritis of the left leg and then a hypereosinophilia with cutaneous eruption of hands and feet, and a myo-pericarditis. In both cases, treatment with prednisolone produced a dramatic improvement in symptoms and eosinophilia.