Project description:Understanding constraints which shape antibiotic resistance is key for predicting and controlling drug resistance. Here, we performed high-throughput laboratory evolution of Escherichia coli. The transcriptome, resistance, and genomic profiles for the evolved strains in 48 environments were quantitatively analyzed. By analyzing the quantitative datasets through interpretable machine learning techniques, the emergence of low dimensional phenotypic states within the 192 strains was observed. Further analysis revealed the underlying biological processes responsible for the distinct states. We also report a novel constraint which leads to decelerated evolution. These findings bridge the genotypic, gene expression, and drug resistance space, and lead to a comprehensive understanding of constraints for antibiotic resistance.
Project description:Antimicrobial resistance (AMR) data from agroecosystems in low- and middle-income countries is limited. We surveyed chicken (n = 52) and pig (n = 47) farms in Kenya to understand AMR in animal-environment pathways. Using LC-MS/MS, we validated the methods for analyzing eight common antibiotics and quantified the associated risks. Chicken compost (25.8%, n = 97/376) had the highest antibiotics prevalence, followed by pig manure-fertilized soils (23.1%, n = 83/360). The average antibiotic concentration was 63.4 µg/kg, which is below the environmentally relevant threshold (100 µg/kg), except for trimethoprim (221.4 µg/kg) among antibiotics and pig manure-fertilized soils (129.3 µg/kg) across sample types. Similarly, the average AMR risk quotient (RQ) was low (RQ < 0.1), except for trimethoprim and sulfamethoxazole (RQ ≥ 1). Ecotoxicity and AMR risks increased with flock size and the number of antibiotics used by pigs. Continuous environmental monitoring and large-scale studies on antibiotic contamination are crucial for evidence-based pollution control and the effective mitigation of environmental AMR.
Project description:Conjugative plasmids, major vehicles for the spread of antibiotic resistance genes, often contain multiple toxin‒antitoxin (TA) systems. However, the physiological functions of TA systems remain obscure. By studying TA families commonly found on colistin-resistant IncI2 mcr-1-bearing plasmids, we discovered that the HicAB TA, acts as a crucial addiction module to increase horizontal plasmid‒plasmid competition.
Project description:Clostridioides difficile infection (CDI) represents a significant global public health concern. The Phosphatidylinositol Glycan Class L (pig-L) gene in C. difficile encodes an enzyme critical for the biosynthesis of phosphatidylinositol glycan anchors (PGAs), which play a vital role in bacterial surface protein localization and function
Project description:In this study, miRNA-seq technique was used to identify differentially expressed miRNAs (DE miRNAs) in cardiac muscle of the Tibetan pig (TP) and Yorkshire pig (YP), which were both raised in highland environments. We obtained 108 M clean reads and 372 unique miRNAs that included 210 known pre-miRNAs and 162 novel pre-miRNAs. In addition, 20 DE miRNAs, including 10 upregulated and 10 downregulated miRNAs, were identified by comparing TP and YP. Based on the expression abundance and differentiation between the two populations, we predicted their targets, and KEGG pathway analyses suggested that DE miRNAs between the Tibetan pigs and Yorkshire pigs are involved in hypoxia-related pathways, such as the MAPK, mTOR, and VEGF signaling pathways, cancer-related signaling pathways, etc. Five DE miRNAs were randomly selected to validate the veracity of miRNA-seq using real-time PCR. The results showed that the expression corresponds to the trend in miRNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related miRNAs in pig and indicated that the expression patterns of hypoxia-related miRNAs are significantly altered in the Tibetan pig. DE miRNAs may play important roles in hypoxic adaptation after migration to hypoxic environments. mRNA profiles of 6-month old Tibetan pig (TP) and Yorkshire pig (YP) were generated by deep sequencing, in duplicate, using Hiseq 2000.
Project description:We used a DNA microarray chip covering 369 resistance types to investigate the relation of antibiotic resistance gene diversity with humansM-bM-^@M-^Y age. Metagenomic DNA from fecal samples of 123 healthy volunteers of four different age groups, i.e. pre-school Children (CH), School Children (SC), High School Students (HSS) and Adults (AD) were used for hybridization. The results showed that 80 different gene types were recovered from the 123 individuals gut microbiota, among which 25 were present in CH, 37 in SC, 58 in HSS and 72 in AD. Further analysis indicated that antibiotic resistance genes in groups of CH, SC and AD can be independently clustered, and those ones in group HSS are more divergent. The detailed analysis of antibiotic resistance genes in human gut is further described in the paper DNA microarray analysis reveals the antibiotic resistance gene diversity in human gut microbiota is age-related submitted to Sentific Reports The antibiotic resistance gene microarray is custom-designed (Roche NimbleGen), based on a single chip containing 3 internal replicated probe sets of 12 probes per resistance gene, covering the whole 315K 12-plex platform spots.
Project description:We have generated a mini-pig model to study the transmission of naturally occuring mitochondrial DNA variants. To determine the chromosomal genotype of the model's founders, we have used the Illumina PorcineSNP60 v2 BeadChip.