Duplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria

Abstract Horizontal gene transfer (HGT) and gene duplication are often considered as separate mechanisms driving the evolution of new functions. However, the mobile genetic elements (MGEs) implicated in HGT can copy themselves, so positive selection on MGEs could drive gene duplications. Here, we use a combination of modeling and experimental evolution to examine this hypothesis and use long-read genome sequences of tens of thousands of bacterial isolates to examine its generality in nature. Modeling and experiments show that antibiotic selection can drive the evolution of duplicated antibiotic resistance genes (ARGs) through MGE transposition. A key implication is that duplicated ARGs should be enriched in environments associated with antibiotic use. To test this, we examined the distribution of duplicated ARGs in 18,938 complete bacterial genomes with ecological metadata. Duplicated ARGs are highly enriched in bacteria isolated from humans and livestock. Duplicated ARGs are further enriched in an independent set of 321 antibiotic-resistant clinical isolates. Our findings indicate that duplicated genes often encode functions undergoing positive selection and horizontal gene transfer in microbial communities

Determination and Difference Analysis of Phenolic Compounds in Smokers’ Saliva and Mainstream Smoke

To study the differences in phenolic compounds between tobacco smokers’ saliva and mainstream smoke, a method was developed for the analysis of 12 phenolic compounds in saliva and mainstream smoke based on ultrahigh-performance liquid chromatography with fluorescence detection (UPLC-FLD). The contents and distributions of phenolic compounds in tobacco smokers’ saliva and mainstream smoke were compared. The results were as follows: (1) Phenolic compounds were quantitatively analyzed by the internal standard method using 4-fluorophenol as an internal standard. For smokers’ saliva samples, the limits of quantification (LOQs) ranged from 2.2 to 19.1 μg/L, and the recoveries were from 80.2% to 119.2% at the three spiked levels. For mainstream smoke samples, the LOQs ranged from 0.03 to 0.26 μg/cig, and the recoveries ranged from 84.9% to 107.0% at the three spiked levels. (2) The contents of phenolic compounds from 14 cigarettes in mainstream smoke and smokers’ saliva were determined. In mainstream smoking, the main phenolic compounds were hydroquinone, catechol, phenol, meta- and para-Cresol, and o-methylhydroquinone. In smokers’ saliva, the main phenolic compounds were phenol and meta- and para-Cresol and the contents of phenolic compounds in smokers’ saliva from different cigarettes were significantly different. (3) The content distribution patterns of phenolic compounds in smokers’ saliva differed from those in mainstream smoke. The predominant phenolic compound in mainstream smoke was dihydroxybenzene, while monophenols predominated in smokers’ saliva. (4) The contents of phenolic compounds from five kinds of cigarettes were analyzed in the saliva of different smokers using principal component analysis, which indicated that cigarettes with different sensory effects were clearly distinguished by differences in the contents of phenolic compounds in saliva