Pseudomonas aeruginosa transcriptome adaptations from colonization to chronic infection of skin wounds

In burn patients Pseudomonas aeruginosa infection is a major cause of morbidity. Analysis of the pathogen's gene expression as it transitions from colonization to acute and then chronic wound infection may provide strategies for infection-control. Toward this goal, we seeded log-phase P. aeruginosa (PAO1) into three-day-old full-thickness excision wounds (rabbit ear) and harvested the bacteria at colonization (Hrs 2 and 6), acute infection (Hr 24), and chronic infection (Days 5 and 9) for transcriptome analysis (RNA-Seq). At Hrs 2-6, the COGs of log-phase-culture PAO1 related to metabolism and cell replication down-regulated while wound-adaptation COGs up-regulated. From acute to chronic infection, more genes up-regulated than down-regulated, but more down-regulated genes enriched in pathways, possibly because pathways bacteria already colonizing wounds up-regulate to establish chronic infection are less well annotated. Pathways involved in carbon utilization shifted across stages of infection. During acute infection, myeloid-cell-produced itaconate appears to have been a carbon source, suggested by the coincidence of peak myeloid cell wound infiltration, ACOD1 expression (for itaconate production), and PAO1 expression of itaconate-catabolism genes. Additionally, branched chain amino acids are a suggested carbon source in acute infection and in chronic infection when fatty acid degradation was additionally up-regulated. These carbon sources produce the end-product acetate that feeds into the up-regulated glyoxylate shunt to provide precursors P. aeruginosa needs to synthesize macromolecules in establishing wound infection.

烧伤患者中，铜绿假单胞菌（Pseudomonas aeruginosa）感染是导致其发病的主要诱因。解析该病原菌从创面定植进展为急性、慢性感染过程中的基因表达特征，可为感染防控策略的开发提供理论依据。为此，我们将对数生长期（log-phase）的铜绿假单胞菌PAO1接种至3日龄兔耳全层切除创面上，分别于定植阶段（接种后2、6小时）、急性感染阶段（接种后24小时）以及慢性感染阶段（接种后5、9日）收集细菌样本，开展转录组测序（RNA-Seq）分析。在接种后2-6小时，与代谢及细胞增殖相关的同源基因簇（Clusters of Orthologous Groups, COGs）表达下调，而创面适应相关的COGs表达上调。从急性感染进展至慢性感染阶段，上调基因的数量多于下调基因，但下调基因富集的通路更多，这可能是因为已定植于创面的细菌为建立慢性感染而上调的通路注释度相对较低。碳利用通路随感染进程呈现动态变化。在急性感染阶段，创面髓系细胞浸润峰值、衣康酸生成相关基因ACOD1的表达，以及铜绿假单胞菌衣康酸分解代谢基因的表达三者出现重合，提示髓系细胞产生的衣康酸可能作为细菌的碳源被利用。此外，支链氨基酸被提示为急性感染阶段及慢性感染阶段的碳源，此时脂肪酸降解通路同时出现上调。上述碳源最终生成终产物乙酸，该产物可进入上调的乙醛酸分流通路，为铜绿假单胞菌合成创面感染建立所需的生物大分子提供前体物质。