Phylogenetic Structure and fitness of extended spectrum beta-lactamase-producing Escherichia coli from bloodstream infections in intensive care during implementation of a national 4C antimicrobial stewardship policy. Escherichia coli

Background: Extended spectrum beta-lactamase (ESBL)-producing Escherichia coli (E. coli) is a major cause of hospital-acquired bloodstream infections (BSI) worldwide, including countries with high antimicrobial stewardship compliance.Methods: We carried out a longitudinal study over 10 years of clonal structure, antimicrobial resistance, virulence gene profile, and fitness of ESBL-producing E. coli isolates from bloodstream infections in a major Intensive Care Unit (ICU) in Scotland soon after introduction of the "4C" antimicrobial stewardship policy. The genomes of 178 isolates from cases that occurred between 2010 and 2020 were sequenced for analysis of SNP-core genome phylogenetic structure, antimicrobial resistance and virulence genes, serotype, and fimH alleles. Fitness of the isolates was determined in growth kinetic assays. Non-metric multidimensional scaling was used to evaluate the clonal structure, antimicrobial resistance, and virulence profiles in early and later years after the 4C policy introduction. temporal analysis using a generalized additive model was employed to determine the clonal and fitness trends over the study period. The relationship between clonal structure, antimicrobial resistance, and fitness was evaluated in regression analyses.Results:We identified three phylogenetic clusters, the most dominant of which (Cluster III) included all ST131 isolates and other minor clonal types. All Cluster III isolates belonged to serotype O25:H4 and carried fimH30 alleles suggesting high phylogenetic relatedness to a single previously defined ST131 sub-lineage. All Cluster II and III isolates belonged to Group B2 (defined by arpA, chuA and yjaA and TSPE4.C2 carriage). ST38 isolates belonged to Cluster I. The prevalence of endemic and multidrug resistant clonal type ST131 was largely stable throughout the 10-year study period. The prevalence of resistance to aminoglycosides and aztreonam in ST131 isolates was lower (X^2 = 9.61, p = 0.019; X^2 = 12.36, p = 0.004, respectively) during later years (2016-2020) by 28% on average compared to early years soon after 4C policy implementation (2010-2014). Genome-wide carriage of virulence factors involved in colonization, iron uptake, adherence, host invasion and immune evasion was higher in ST131 compared to non-ST131 but mostly stable in early vs later years. Temporal analysis of fitness of ST131 over the study period disclosed a significant increase in earlier years followed by a decline in later years. In regression analyses clonal status (ST131 vs non-ST131) was a significant predictor of fitness (beta = -0.242, p = 0.004), whilst there was no definitive linear relationship between antimicrobial resistance (aminoglycosides beta = 0.053, p = 0.527; aztreonam beta = 0.137, p = 0.068) and fitness.Conclusion: On a backdrop of stable genomic carriage of virulence factors, we show a reassuring decline of ST131 resistance to aminoglycosides and aztreonam and concurrent fitness decline years after the introduction of the 4C stewardship policy, but not a linear relationship between antimicrobial resistance and fitness in ST131.

背景：产超广谱β-内酰胺酶（Extended Spectrum Beta-Lactamase, ESBL）的大肠埃希菌（Escherichia coli, E. coli）是全球医院获得性血流感染（Bloodstream Infection, BSI）的主要致病菌，即便在抗菌药物管理依从性较高的国家也不例外。
方法：本研究在苏格兰某大型重症监护病房（Intensive Care Unit, ICU）推行“4C”抗菌药物管理政策后不久，开展了一项为期10年的纵向研究，旨在分析血流感染分离的产ESBL大肠埃希菌的克隆结构、抗菌药物耐药性、毒力基因谱及适合度。研究对2010至2020年间的178株分离株进行全基因组测序，用于分析核心基因组单核苷酸多态性（Single Nucleotide Polymorphism, SNP）系统发育结构、抗菌药物耐药与毒力基因、血清型以及fimH等位基因。通过生长动力学实验测定分离株的适合度。采用非度量多维标度法（Non-metric Multidimensional Scaling）评估“4C”政策推行后早期与后期的克隆结构、抗菌药物耐药及毒力特征。使用广义加性模型（Generalized Additive Model）进行时间序列分析，以明确研究周期内克隆特征与适合度的变化趋势。通过回归分析评估克隆结构、抗菌药物耐药性与适合度之间的关联。
结果：本研究共鉴定出3个系统发育簇，其中最优势的簇（簇III）包含所有ST131分离株及其他次要克隆型。所有簇III分离株均属于血清型O25:H4，且携带fimH30等位基因，提示与此前定义的单一ST131亚谱系具有高度系统发育相关性。簇II与簇III的所有分离株均属于B2群（通过arpA、chuA、yjaA及TSPE4.C2基因的携带情况定义）。ST38分离株属于簇I。在10年研究周期内，流行且多重耐药的克隆型ST131的检出率整体保持稳定。与“4C”政策实施初期（2010-2014年）相比，政策实施后期（2016-2020年）ST131分离株对氨基糖苷类与氨曲南的耐药率平均下降28%，差异具有统计学意义（χ²=9.61，P=0.019；χ²=12.36，P=0.004）。与非ST131分离株相比，ST131分离株携带的与定植、铁摄取、黏附、宿主入侵及免疫逃逸相关的毒力因子更为丰富，但该特征在早期与后期基本保持稳定。对ST131适合度的时间序列分析显示，其适合度在研究前期显著升高，随后在后期出现下降。回归分析结果显示，克隆状态（ST131 vs 非ST131）是适合度的显著预测因子（β=-0.242，P=0.004），而抗菌药物耐药性（氨基糖苷类β=0.053，P=0.527；氨曲南β=0.137，P=0.068）与适合度之间未发现明确的线性关联。
结论：在毒力因子基因组携带情况保持稳定的背景下，本研究发现“4C”抗菌药物管理政策推行数年后，ST131对氨基糖苷类与氨曲南的耐药性出现了令人欣慰的下降，同时其适合度也随之降低，但未发现ST131的抗菌药物耐药性与适合度之间存在线性关联。