Peterson S W, Demczuk W, Martin I, Adam H, Bharat A, Mulvey M R
National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada.
Diagnostic Services, Shared Health Manitoba, Health Sciences Centre, Winnipeg, Manitoba, Canada.
Genomics. 2023 Mar;115(2):110580. doi: 10.1016/j.ygeno.2023.110580. Epub 2023 Feb 14.
Bloodstream infections are a major cause of morbidity and mortality worldwide. Early administration of appropriate antimicrobial therapy can improve patient survival and prevent antimicrobial resistance (AMR). Whole genome sequencing (WGS) can provide information for pathogen identification, AMR prediction and sequence typing earlier than current phenotypic diagnostic methods. WGS was performed on 97 clinical blood specimens and matched culture isolate pairs. Specimen/isolate pairs were MLST sequence-typed and further characterization was performed on Streptococcus species. WGS correctly identified 91.7% of clinical specimens and 93.2% of matched isolates representing 35 different microbial species. MLST types were assigned for 89.9% of matched cultures and 21.7% of blood specimens, with higher success for blood culture specimens extracted within 3 days (52% characterized) than 7 days (9.3%). This study demonstrates the potential use of WGS for identification and characterization of pathogens directly from blood culture specimens to facilitate timely initiation of appropriate antimicrobial therapies.
血流感染是全球发病和死亡的主要原因。早期给予适当的抗菌治疗可提高患者生存率并预防抗菌药物耐药性（AMR）。全基因组测序（WGS）能够比当前的表型诊断方法更早地提供病原体鉴定、AMR预测和序列分型信息。对97份临床血液标本及匹配的培养分离株进行了WGS。对标本/分离株进行多位点序列分型（MLST），并对链球菌属进行进一步鉴定。WGS正确鉴定出91.7%的临床标本和93.2%的匹配分离株，代表35种不同的微生物物种。89.9%的匹配培养物和21.7%的血液标本成功进行了MLST分型，3天内提取的血培养标本分型成功率（52%）高于7天内提取的标本（9.3%）。本研究证明了WGS直接从血培养标本中鉴定和鉴定病原体以促进及时开始适当抗菌治疗的潜在用途。
