Antimicrobial Research Group, Centre for Immunology & Infectious Disease, Blizard Institute, Barts and The London, Queen Mary's School of Medicine and Dentistry, 4 Newark Street, London, E1 2AT, UK.
J Antimicrob Chemother. 2011 Jul;66(7):1499-503. doi: 10.1093/jac/dkr168. Epub 2011 May 12.
The whole genomes of two Acinetobacter baumannii isolates recovered from a single patient were sequenced to gain insight into the nature and extent of genomic plasticity in this important nosocomial pathogen over the course of a short infection. The first, AB210, was recovered before tigecycline therapy and was susceptible to this agent; the second, AB211, was recovered after therapy and was resistant.
DNA from AB210 was sequenced by 454 GS FLX pyrosequencing according to the standard protocol for whole-genome shotgun sequencing, producing ∼250 bp fragment reads. AB211 was shotgun sequenced using the Illumina Genetic Analyzer to produce fragment reads of exactly 36 bp. Single nucleotide polymorphisms (SNPs) and large deletions detected in AB211 in relation to AB210 were confirmed by PCR and DNA sequencing.
Automated gene prediction detected 3850 putative coding sequences (CDSs). Sequence analysis demonstrated the presence of plasmids pAB0057 and pACICU2 in both isolates. Eighteen putative SNPs were detected between the pre- and post-therapy isolates, AB210 and AB211. Three contigs in AB210 were not covered by reads in AB211, representing three deletions of ∼15, 44 and 17 kb.
This study demonstrates that significant differences were detectable between two bacterial isolates recovered 1 week apart from the same patient, and reveals the potential of whole-genome sequencing as a tool for elucidating the processes responsible for changes in antibiotic susceptibility profiles.
对从同一患者中分离得到的 2 株鲍曼不动杆菌的全基因组进行测序，以深入了解这种重要的医院获得性病原体在短时间感染过程中基因组可塑性的性质和程度。第一个菌株 AB210 在替加环素治疗前分离得到，对该药物敏感；第二个菌株 AB211 在治疗后分离得到，对该药物耐药。
AB210 的 DNA 采用 454 GS FLX 焦磷酸测序技术按全基因组鸟枪法测序的标准方案进行测序，产生约 250 bp 的片段读长。AB211 采用 Illumina Genetic Analyzer 进行鸟枪法测序，产生 36 bp 精确的片段读长。通过 PCR 和 DNA 测序证实了在 AB211 中相对于 AB210 检测到的单核苷酸多态性（SNP）和大片段缺失。
自动基因预测检测到 3850 个潜在的编码序列（CDS）。序列分析表明，两种分离株 AB210 和 AB211 均携带质粒 pAB0057 和 pACICU2。在治疗前和治疗后分离株 AB210 和 AB211 之间检测到 18 个潜在的 SNP。AB210 中有 3 个连续体在 AB211 中没有被读长覆盖，代表了约 15、44 和 17 kb 的 3 个缺失。
本研究表明，从同一患者中相隔 1 周分离得到的两个细菌分离株之间存在显著差异，并揭示了全基因组测序作为阐明导致抗生素敏感性谱变化的过程的工具的潜力。
