Data_Sheet_1_Diverse Bacterial Resistance Genes Detected in Fecal Samples From Clinically Healthy Women and Infants in Australia—A Descriptive Pilot Study.doc

The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs), the so-called “resistome.” In Australia, where antibiotic use is high and resistance rates in some common pathogens are increasing, very little is known about the human resistome. To assess the presence and diversity of ARGs in the gut of Australians from south-eastern Victoria, we investigated fecal samples from clinically healthy infants and pregnant women using non-targeted (shotgun metagenomics sequencing or SMS) and targeted sequencing (two Ion AmpliseqTM panels). All methods detected ARGs in all samples, with the detection overall of 64 unique genes conferring resistance to 12 classes of antibiotics. Predominant ARGs belonged to three classes of antibiotics that are the most frequently prescribed in Australia: tetracycline, β-lactams and MLSB (macrolide, lincosamide, streptogramin B). The three bacterial Orders commonly identified as carrying ARGs were Clostridiales, Bacteroidales, and Enterobacteriales. Our preliminary results indicate that ARGs are ubiquitously present and diverse among the gut microbiota of clinically healthy humans from south-eastern Victoria, Australia. The observed resistance pattern partly overlaps with antimicrobial usage in human medicine in Australia, but ARGs to tetracycline are more common than could be expected. Our current sample is small and limited to south-eastern Victoria, and more data on healthy individuals will be needed to better depict resistance patterns at the population level, which could guide population and/or environmental monitoring and surveillance of antibiotic resistance on various spatio-temporal scales in Australia. For future studies, we recommend using the Ion AmpliseqTM Antimicrobial Resistance Research panel, which is sensitive and user-friendly, or combining several methods to increase the detected diversity.

肠道菌群是抗菌耐药基因（antimicrobial resistance genes, ARGs）的巨大储存库，即所谓的“耐药组（resistome）”。在抗菌药物使用量较高、部分常见病原菌耐药率持续上升的澳大利亚，目前对人类耐药组的了解仍十分有限。为评估澳大利亚维多利亚州东南部人群肠道内抗菌耐药基因的存在情况与多样性，本研究针对临床健康婴儿与孕妇的粪便样本展开分析，分别采用非靶向测序（鸟枪法宏基因组测序，简称SMS）与靶向测序（两款Ion Ampliseq™ 测序面板）两种方法。所有检测方法均在所有样本中检出了抗菌耐药基因，总计检出64种可赋予12类抗生素耐药性的独特基因。优势抗菌耐药基因分属澳大利亚临床最常用的三类抗生素：四环素类、β-内酰胺类以及大环内酯-林可酰胺-链阳菌素B类（macrolide, lincosamide, streptogramin B，简称MLSB）。通常被检出携带抗菌耐药基因的三大细菌目分别为梭菌目（Clostridiales）、拟杆菌目（Bacteroidales）与肠杆菌目（Enterobacteriales）。本研究的初步结果显示，澳大利亚维多利亚州东南部临床健康人群的肠道菌群中，抗菌耐药基因广泛存在且具有丰富多样性。本次观测到的耐药模式与澳大利亚人类临床医学中的抗菌药物使用情况存在部分重合，但针对四环素类的抗菌耐药基因的检出频率远超预期。本研究当前的样本量较小且仅局限于维多利亚州东南部，若要更精准地描绘人群层面的耐药模式，还需要获取更多健康个体的相关数据。此类研究结果可为澳大利亚在不同时空尺度下开展的人群及/或环境抗菌耐药性监测工作提供指导。对于后续研究，我们建议采用灵敏度高、操作简便的Ion Ampliseq™ 抗菌耐药研究测序面板，或联合多种检测方法以提升可检出的基因多样性。