Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology
Antibiotic resistance is a dire clinical problem with important ecological dimensions. While antibiotic resistance in human pathogens continues to rise at alarming rates, the impact of environmental resistance on human health is still unclear. To investigate the relationship between human-associated and environmental resistomes, we analyzed functional metagenomic selections for resistance against 18 clinically relevant antibiotics from soil and human gut microbiota as well as a set of multidrug-resistant cultured soil isolates. These analyses were enabled by Resfams, a new curated database of protein families and associated highly precise and accurate profile hidden Markov models, confirmed for antibiotic resistance function and organized by ontology. We demonstrate that the antibiotic resistance functions that give rise to the resistance profiles observed in environmental and human-associated microbial communities significantly differ between ecologies. Antibiotic resistance functions that most discriminate between ecologies provide resistance to β-lactams and tetracyclines, two of the most widely used classes of antibiotics in the clinic and agriculture. We also analyzed the antibiotic resistance gene composition of over 6000 sequenced microbial genomes, revealing significant enrichment of resistance functions by both ecology and phylogeny. Together, our results indicate that environmental and human-associated microbial communities harbor distinct resistance genes, suggesting that antibiotic resistance functions are largely constrained by ecology.
wget http://dantaslab.wustl.edu/resfams/Resfams-proteins.tar.gz tar xzvf Resfams-proteins.tar.gz cat proteins/* >resfams.faa diamond makedb --in Resfams.fa -d Resfams wget http://dantaslab.wustl.edu/resfams/Resfams.hmm.gz ./ gunzip Resfams.hmm.gz hmmpress Resfams.hmm
抗生素抗性基因注释在病原微生物基因组测序、metagenome测序等项目中的关注度很高，先前有 Antibiotic Resistance Database (ARDB)、Resistance Database (CARD)等序列库用于抗性基因注释，Resfams 提供了基于谱序列相似性搜索的策略，用于基因序列注释（功能谱注释），对于拼装的序列来说，HMMER还是可以提供比较快的执行速度，但是对于 Metagenome项目来说， 如果不拼装，直接使用reads翻译的ORF注释的话，计算序列还是很大，基于序列相似性搜索的工具Diamond/Usearch等可以快速鉴定可能的抗性基因（使用阈值足够大确保不遗漏），然后在使用HMM谱过滤掉一些假阳性序列可以达到加速目的。