Despite modern antiseptic techniques, surgical site infection (SSI) remains a leading complication of surgery. However, the origins of SSI and the high rates of antimicrobial resistance observed in these infections are poorly understood. Using instrumented spine surgery as a model of clean (class I) skin incision, we prospectively sampled preoperative microbiomes and postoperative SSI isolates in a cohort of 204 patients. Combining multiple forms of genomic analysis, we correlated the identity, anatomic distribution, and antimicrobial resistance profiles of SSI pathogens with those of preoperative strains obtained from the patient skin microbiome. We found that 86% of SSIs, comprising a broad range of bacterial species, originated endogenously from preoperative strains, with no evidence of common source infection among a superset of 1610 patients. Most SSI isolates (59%) were resistant to the prophylactic antibiotic administered during surgery, and their resistance phenotypes correlated with the patient’s preoperative resistome ( P = 0.0002). These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients.

中文翻译：

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脊柱手术中患者微生物组对手术部位感染和抗生素预防失败的影响

尽管采用了现代消毒技术，手术部位感染（SSI）仍然是手术的主要并发症。然而，人们对 SSI 的起源以及在这些感染中观察到的高抗菌药物耐药率知之甚少。我们使用器械脊柱手术作为清洁（I 级）皮肤切口的模型，前瞻性地对 204 名患者的队列中的术前微生物组和术后 SSI 分离株进行了采样。结合多种形式的基因组分析，我们将 SSI 病原体的身份、解剖分布和抗菌谱与术前从患者皮肤微生物组中获得的菌株相关联。我们发现，86% 的 SSI（包含多种细菌种类）源自术前菌株的内源性，在 1610 名患者的超集中没有证据表明存在共同感染源。大多数 SSI 分离株 (59%) 对手术期间使用的预防性抗生素具有耐药性，其耐药表型与患者术前的耐药组相关。磷= 0.0002）。这些发现表明需要针对个体患者的术前微生物组和耐药组量身定制 SSI 预防策略。