Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France.
Collège doctoral, Sorbonne Université, F-75005, Paris, France.
Genome Med. 2020 Nov 27;12(1):107. doi: 10.1186/s13073-020-00805-7.
Corynebacterium diphtheriae, the agent of diphtheria, is a genetically diverse bacterial species. Although antimicrobial resistance has emerged against several drugs including first-line penicillin, the genomic determinants and population dynamics of resistance are largely unknown for this neglected human pathogen.
Here, we analyzed the associations of antimicrobial susceptibility phenotypes, diphtheria toxin production, and genomic features in C. diphtheriae. We used 247 strains collected over several decades in multiple world regions, including the 163 clinical isolates collected prospectively from 2008 to 2017 in France mainland and overseas territories.
Phylogenetic analysis revealed multiple deep-branching sublineages, grouped into a Mitis lineage strongly associated with diphtheria toxin production and a largely toxin gene-negative Gravis lineage with few toxin-producing isolates including the 1990s ex-Soviet Union outbreak strain. The distribution of susceptibility phenotypes allowed proposing ecological cutoffs for most of the 19 agents tested, thereby defining acquired antimicrobial resistance. Penicillin resistance was found in 17.2% of prospective isolates. Seventeen (10.4%) prospective isolates were multidrug-resistant (≥ 3 antimicrobial categories), including four isolates resistant to penicillin and macrolides. Homologous recombination was frequent (r/m = 5), and horizontal gene transfer contributed to the emergence of antimicrobial resistance in multiple sublineages. Genome-wide association mapping uncovered genetic factors of resistance, including an accessory penicillin-binding protein (PBP2m) located in diverse genomic contexts. Gene pbp2m is widespread in other Corynebacterium species, and its expression in C. glutamicum demonstrated its effect against several beta-lactams. A novel 73-kb C. diphtheriae multiresistance plasmid was discovered.
This work uncovers the dynamics of antimicrobial resistance in C. diphtheriae in the context of phylogenetic structure, biovar, and diphtheria toxin production and provides a blueprint to analyze re-emerging diphtheria.
白喉棒状杆菌是白喉的病原体，是一种遗传多样性的细菌。尽管包括一线青霉素在内的几种药物出现了抗药性，但对于这种被忽视的人类病原体，其耐药性的基因组决定因素和种群动态在很大程度上仍是未知的。
在这里，我们分析了抗菌药物敏感性表型、白喉毒素产生和白喉棒状杆菌基因组特征之间的相关性。我们使用了 247 株在多个世界区域收集的菌株，包括从 2008 年到 2017 年在法国本土和海外领土前瞻性收集的 163 株临床分离株。
系统发育分析显示存在多个深分支亚系，分为一个与白喉毒素产生密切相关的米蒂斯（Mitis）谱系和一个主要毒素基因阴性的格雷夫斯（Gravis）谱系，后者仅有少数产毒分离株，包括 20 世纪 90 年代前苏联爆发株。药敏表型的分布允许为大多数测试的 19 种药物提出生态截止值，从而定义获得性抗菌药物耐药性。前瞻性分离株中发现青霉素耐药率为 17.2%。17 株（10.4%）前瞻性分离株为多药耐药（≥3 种抗菌药物类别），包括 4 株对青霉素和大环内酯类耐药的分离株。同源重组频繁（r/m=5），水平基因转移导致多个亚系出现抗菌药物耐药性。全基因组关联图谱揭示了耐药的遗传因素，包括位于多种基因组背景下的一种辅助性青霉素结合蛋白（PBP2m）。基因 pbp2m 在其他棒状杆菌属物种中广泛存在，其在谷氨酸棒状杆菌中的表达证明了其对几种β-内酰胺类药物的作用。发现了一种新型 73kb 白喉棒状杆菌多耐药质粒。
这项工作揭示了白喉棒状杆菌在进化结构、生物型和白喉毒素产生背景下的抗菌药物耐药性动态，并为分析重新出现的白喉提供了蓝图。
