Versluis Dennis, Rodriguez de Evgrafov Mari, Sommer Morten O A, Sipkema Detmer, Smidt Hauke, van Passel Mark W J
Laboratory of Microbiology, Wageningen University Wageningen, Netherlands.
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark Hørsholm, Denmark.
Front Microbiol. 2016 Nov 17;7:1848. doi: 10.3389/fmicb.2016.01848. eCollection 2016.
Wide application of antibiotics has contributed to the evolution of multi-drug resistant human pathogens, resulting in poorer treatment outcomes for infections. In the marine environment, seawater samples have been investigated as a resistance reservoir; however, no studies have methodically examined sponges as a reservoir of antibiotic resistance. Sponges could be important in this respect because they often contain diverse microbial communities that have the capacity to produce bioactive metabolites. Here, we applied functional metagenomics to study the presence and diversity of functional resistance genes in the sponges , and . We obtained 37 insert sequences facilitating resistance to D-cycloserine ( = 6), gentamicin ( = 1), amikacin ( = 7), trimethoprim ( = 17), chloramphenicol ( = 1), rifampicin ( = 2) and ampicillin ( = 3). Fifteen of 37 inserts harbored resistance genes that shared <90% amino acid identity with known gene products, whereas on 13 inserts no resistance gene could be identified with high confidence, in which case we predicted resistance to be mainly mediated by antibiotic efflux. One marine-specific ampicillin-resistance-conferring β-lactamase was identified in the genus with 41% global amino acid identity to the closest β-lactamase with demonstrated functionality, and subsequently classified into a new family termed PSV. Taken together, our results show that sponge microbiota host diverse and novel resistance genes that may be harnessed by phylogenetically distinct bacteria.
抗生素的广泛应用促使了耐多药人类病原体的进化，导致感染的治疗效果更差。在海洋环境中，海水样本已被作为耐药性储存库进行研究；然而，尚无研究系统地考察海绵作为抗生素耐药性储存库的情况。海绵在这方面可能很重要，因为它们通常含有能够产生生物活性代谢物的多样微生物群落。在此，我们应用功能宏基因组学来研究海绵中功能抗性基因的存在和多样性。我们获得了37个插入序列，这些序列赋予了对D - 环丝氨酸（= 6）、庆大霉素（= 1）、阿米卡星（= 7）、甲氧苄啶（= 17）、氯霉素（= 1）、利福平（= 2）和氨苄青霉素（= 3）的抗性。37个插入序列中有15个含有与已知基因产物氨基酸同一性小于90%的抗性基因，而在13个插入序列中无法高置信度鉴定出抗性基因，在这种情况下，我们预测抗性主要由抗生素外排介导。在某属中鉴定出一种海洋特异性的赋予氨苄青霉素抗性的β - 内酰胺酶，与功能已证实的最接近β - 内酰胺酶的全球氨基酸同一性为41%，随后将其归类为一个新的家族，称为PSV。综上所述，我们的结果表明海绵微生物群含有多样且新颖的抗性基因，这些基因可能被系统发育上不同的细菌利用。
