NRCS-A Staphylococcus capitis NICU sequencing

Background: S. capitis NRCS-A strain has emerged as a global cause of late onset sepsis in neonatal intensive care units (NICUs). Identifying outbreaks is critical for improving patient safety, antimicrobial stewardship and infection prevention. Methods: Demographic and clinical data for 45 neonates from Hospital 1 with S. capitis and 90 with other coagulase-negative staphylococci (CoNS) from sterile sites were reviewed and clinical significance determined by two clinicians. S. capitis isolated from sterile site samples in 27 neonates at two hospitals between 2017-2022 underwent sequencing of culture-derived bacterial DNA with long read (ONT) sequencing (n=27) and short read (Illumina) sequencing (n=18). These were compared with S. capitis sequenced from blood cultures isolates from other adult and paediatric patients in the same hospitals (n=6), S. capitis isolated from surface swabs (n=5), rectal swabs (n=2) in NICU patients, NICU environmental samples (n=5), and two well characterised reference strains. Reads from all samples were mapped to a hybrid assembly of a local sterile site strain, forming a newly created complete UK NRCS-A reference strain, for genomic analysis of the outbreak. Results: S. capitis bacteraemia was associated with lower gestational age (26 vs 27 weeks; p = 0.047) and increased age at sample (day 22 vs 12; p = 0.01). Phylogeny of sequenced S. capitis revealed that 25/27 sterile site isolates from neonates formed a cluster, which also included 3/5 superficial, 2/2 rectal and 1/5 environmental isolates. No isolates from other adult or paediatric wards belonged to this cluster. Comparison with published sequences confirmed the cluster were NRCS-A outbreak strain, but found relatively high genomic diversity indicative of multiple sub-lineages. S. capitis in superficial culture did not correlate with neonatal bacteraemia, but both neonates with rectal S. capitis carriage identified also experienced S. capitis bacteraemia. Conclusions: S. capitis bacteraemia occurred in patients with longer NICU admission than other CoNS. Genomic analysis confirms clinically significant infections with the NRCS-A S. capitis strain, distinct from S. capitis detected in non-NICU clinical samples, which demonstrated multiple introductions to the NICU setting. This has important implications for infection control measures and antimicrobial stewardship on the NICU.

背景：头状葡萄球菌（S. capitis）NRCS-A菌株已成为全球范围内新生儿重症监护病房（NICU）晚发性脓毒症的重要致病原。识别暴发疫情对于提升患者安全、推进抗菌药物管理及强化感染防控均具有关键意义。方法：回顾性分析来自1号医院的45名头状葡萄球菌感染新生儿以及90名从无菌部位分离到其他凝固酶阴性葡萄球菌（CoNS）新生儿的人口统计学与临床资料，并由两名临床医师判定其临床意义。2017年至2022年间，两家医院内27名新生儿无菌部位样本中分离得到的头状葡萄球菌，分别采用长读长（ONT，牛津纳米孔技术）测序（n=27）与短读长（Illumina，伊鲁米纳）测序（n=18）对培养来源的细菌DNA进行测序。将上述测序样本与以下来源的头状葡萄球菌测序结果进行比对：同医院内其他成人及儿科患者血培养分离株（n=6）、NICU患者的表面拭子（n=5）、直肠拭子（n=2）分离得到的头状葡萄球菌，NICU环境样本（n=5），以及两株经过充分鉴定的参考菌株。将所有样本的测序读段比对至本地无菌部位菌株的混合组装序列，进而构建得到一株新的完整英国NRCS-A参考菌株，用于暴发疫情的基因组分析。结果：头状葡萄球菌菌血症与更低的胎龄（26周 vs 27周；p=0.047）及样本采集时更高的日龄（第22天 vs 第12天；p=0.01）显著相关。对头状葡萄球菌的系统发育分析显示，27株新生儿无菌部位分离株中的25株形成了一个聚类簇，该簇同时包含5株表面拭子分离株中的3株、2株直肠拭子分离株全部2株以及5份环境样本分离株中的1株。其他成人及儿科病房的分离株均未归入该聚类簇。与已发表序列的比对结果证实，该聚类簇属于NRCS-A暴发菌株，但同时发现其基因组多样性相对较高，提示存在多个亚谱系。表面培养检出的头状葡萄球菌与新生儿菌血症无相关性，但2名经直肠拭子检出头状葡萄球菌定植的新生儿均发生了头状葡萄球菌菌血症。结论：相较于其他凝固酶阴性葡萄球菌感染患儿，头状葡萄球菌菌血症患者的NICU住院时长更长。基因组分析证实，NRCS-A头状葡萄球菌菌株引起的临床感染具有显著临床意义，且与非NICU临床样本中检出的头状葡萄球菌存在差异，后者提示该菌株已多次传入NICU环境。该结果对于NICU的感染防控措施及抗菌药物管理具有重要指导价值。