Metadata of study samples.

Antimicrobial resistance (AMR) is a rising global health threat and estimated to cause 700,000 deaths annually. Although blood cultures (BCs) are the reference standard to diagnose bloodstream infections and inference of antimicrobial susceptibility testing (AST), the method could fail to differentiate bacteria with similar biochemical characteristics. This study compared phenotypic method (AST) and whole genome sequencing (WGS) in bacterial species identification and assessment of AMR. Blood samples came from children who had been prescribed antibiotics at admission at the county referral hospitals in western Kenya and around the Lake Victoria region. BCs and AST were performed on BD Bactec 9050 and Phoenix 100 respectively. Out of the 960 BCs, 17 isolates were useable and were evaluated by WGS on the Oxford Nanopore PromethION platform. BD Phoenix system identified the 17 bacteria isolates as: 4 Escherichia coli, 8 Salmonella enterica serovar Typhi, 1 unspeciated Salmonella, 3 Staphylococcus aureus and 1 Streptococcus pneumoniae. WGS results differed from BCs in identifying the 9 Salmonella species, with WGS identifying the species as Salmonella enterica serovar Typhimurium. Conversely, WGS detected AMR determinants in bacteria that AST had classified as susceptible. In conclusion, we caution that BCs may not be providing correct identity of Salmonella species. The observed discrepancies between phenotypic and genotypic markers of drug resistance highlight the challenges in interpreting and predicting the functional utility of AMR determinants.

抗菌药物耐药性（Antimicrobial Resistance，AMR）是日益严峻的全球公共卫生威胁，据估算每年可导致70万例死亡。尽管血培养（Blood Cultures，BCs）是诊断血流感染并用于抗菌药物敏感性试验（Antimicrobial Susceptibility Testing，AST）结果推断的金标准，但该方法难以区分生化特征相似的细菌。本研究对比了表型检测法（即AST）与全基因组测序（Whole Genome Sequencing，WGS）在细菌菌种鉴定及AMR评估中的应用效果。研究样本取自肯尼亚西部及维多利亚湖周边地区县级转诊医院的入院患儿，这些患儿入院时已开具抗生素处方。血培养与抗菌药物敏感性试验分别采用BD Bactec 9050与Phoenix 100系统完成。在960份血培养样本中，共获得17株可用分离菌株，并通过牛津纳米孔PromethION平台开展全基因组测序分析。BD Phoenix系统鉴定出的17株细菌分离株分别为：大肠埃希菌（Escherichia coli）4株、伤寒沙门菌（Salmonella enterica serovar Typhi）8株、未分型沙门菌1株、金黄色葡萄球菌（Staphylococcus aureus）3株及肺炎链球菌（Streptococcus pneumoniae）1株。全基因组测序结果与血培养鉴定结果在9株沙门菌的菌种鉴定上存在差异：全基因组测序将其鉴定为鼠伤寒沙门菌（Salmonella enterica serovar Typhimurium）。反之，全基因组测序在AST判定为敏感的细菌中，检测到了AMR耐药决定因子。综上，本研究提示血培养可能无法准确鉴定沙门菌的菌种类型。本研究观察到的表型与基因型耐药标志物之间的差异，凸显了解读及预测AMR耐药决定因子功能效用所面临的挑战。