The Opportunistic Pathogen Propionibacterium acnes: Insights into Typing, Human Disease, Clonal Diversification and CAMP Factor Evolution

We previously described a Multilocus Sequence Typing (MLST) scheme based on eight genes that facilitates population genetic and evolutionary analysis of P. acnes. While MLST is a portable method for unambiguous typing of bacteria, it is expensive and labour intensive. Against this background, we now describe a refined version of this scheme based on two housekeeping (aroE; guaA) and two putative virulence (tly; camp2) genes (MLST4) that correctly predicted the phylogroup (IA1, IA2, IB, IC, II, III), clonal complex (CC) and sequence type (ST) (novel or described) status for 91% isolates (n = 372) via cross-referencing of the four gene allelic profiles to the full eight gene versions available in the MLST database (http://pubmlst.org/pacnes/). Even in the small number of cases where specific STs were not completely resolved, the MLST4 method still correctly determined phylogroup and CC membership. Examination of nucleotide changes within all the MLST loci provides evidence that point mutations generate new alleles approximately 1.5 times as frequently as recombination; although the latter still plays an important role in the bacterium's evolution. The secreted/cell-associated ‘virulence’ factors tly and camp2 show no clear evidence of episodic or pervasive positive selection and have diversified at a rate similar to housekeeping loci. The co-evolution of these genes with the core genome might also indicate a role in commensal/normal existence constraining their diversity and preventing their loss from the P. acnes population. The possibility that members of the expanded CAMP factor protein family, including camp2, may have been lost from other propionibacteria, but not P. acnes, would further argue for a possible role in niche/host adaption leading to their retention within the genome. These evolutionary insights may prove important for discussions surrounding camp2 as an immunotherapy target for acne, and the effect such treatments may have on commensal lineages.

我们此前报道了一套基于8个基因的多位点序列分型（Multilocus Sequence Typing, MLST）方案，可用于痤疮丙酸杆菌（P. acnes）的群体遗传学与进化分析。尽管MLST是一种可跨平台应用、能实现细菌精准分型的方法，但其成本高昂且耗时费力。针对这一不足，本研究报道了一套优化后的该分型方案，基于2个持家基因（aroE、guaA）与2个推定毒力基因（tly、camp2），命名为MLST4。通过将4个基因的等位基因谱与MLST数据库（http://pubmlst.org/pacnes/）中收录的完整8基因分型数据交叉比对，该方案可准确判定91%的分离株（n=372）的系统群（IA1、IA2、IB、IC、II、III）、克隆复合体（Clonal Complex, CC）与序列型（Sequence Type, ST，包括新发现型与已报道型）状态。即便在少数无法完全确定具体ST的案例中，MLST4方案仍可正确判定分离株的系统群与CC归属。对所有MLST位点的核苷酸变异进行分析后发现，点突变产生新等位基因的频率约为重组的1.5倍；尽管重组在该细菌的进化过程中仍发挥着重要作用。分泌型/细胞关联的“毒力”因子tly与camp2未显示出明确的阶段性或普遍性正向选择迹象，其进化速率与持家基因位点相近。这些基因与核心基因组的共进化现象，或许提示它们在痤疮丙酸杆菌的共生/正常定植过程中发挥功能，这一功能约束了它们的多样性并防止其从痤疮丙酸杆菌种群中丢失。包括camp2在内的扩增CAMP因子蛋白家族成员，可能已从其他丙酸杆菌中丢失，但未在痤疮丙酸杆菌中出现该情况，这进一步支持了这类基因在生态位/宿主适应中发挥作用的假说，使其得以保留在痤疮丙酸杆菌的基因组中。这些进化层面的研究发现，对于以camp2为靶点的痤疮免疫治疗相关讨论，以及此类治疗可能对共生菌群谱系产生的影响，均具有重要参考价值。