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 Ampliseq^TM 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 MLS_B (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 Ampliseq^TM Antimicrobial Resistance Research panel, which is sensitive and user-friendly, or combining several methods to increase the detected diversity.

肠道微生物群是一个巨大的抗菌素耐药基因 (ARG) 库，即所谓的“抵抗基因”。在澳大利亚，抗生素的使用率很高，一些常见病原体的耐药率也在增加，但人们对人类的耐药组知之甚少。为了评估来自维多利亚州东南部的澳大利亚人肠道中 ARG 的存在和多样性，我们使用非靶向（鸟枪宏基因组学测序或 SMS）和靶向测序（两个 Ion Ampliseq ^TM面板）。所有方法都检测到所有样品中的 ARG，总共检测到 64 个独特基因，这些基因赋予对 12 类抗生素的抗性。主要的 ARGs 属于澳大利亚最常用的三类抗生素：四环素、β-内酰胺类和 MLS _B（大环内酯、林可酰胺、链球菌素 B）。通常被确定为携带 ARG 的三个细菌目是梭菌目、拟杆菌目和肠杆菌目。我们的初步结果表明，在澳大利亚维多利亚州东南部的临床健康人群的肠道微生物群中，ARG 无处不在且多种多样。观察到的耐药模式与澳大利亚人类医学中的抗菌药物使用部分重叠，但对四环素的 ARGs 比预期的更为常见。我们目前的样本很小，仅限于维多利亚州东南部，需要更多关于健康个体的数据来更好地描述人群水平的耐药性模式，这可以指导人群和/或环境监测以及各种空间的抗生素耐药性监测。澳大利亚的时间尺度。^TM抗微生物药物耐药性研究面板，灵敏且用户友好，或结合多种方法来增加检测到的多样性。