Genome changes are central to the adaptation of bacteria, especially under antibiotic pressure. The aim of this study was to report phenotypic and genomic adaptations undergone by an Enterobacter hormaechei clinical strain that became highly resistant to key antimicrobials during a 4-month period in a patient hospitalized in an intensive care unit (ICU). All six clinical E. hormaechei strains isolated in one ICU-hospitalized patient have been studied. MICs regarding 17 antimicrobial molecules have been measured. Single nucleotide polymorphisms (SNPs) were determined on the sequenced genomes. The expression of genes involved in antibiotic resistance among Enterobacter cloacae complex strains were determined by reverse transcription-quantitative PCR (qRT-PCR). All the strains belonged to sequence type 66 and were distant by a maximum of nine SNPs. After 3 months of hospitalization, three strains presented a significant increase in MICs for ceftazidime, cefepime, temocillin, ertapenem, tigecycline, ciprofloxacin, and chloramphenicol. Those resistant strains did not acquire additional antibiotic resistance genes but harbored a 16-bp deletion in the ramR gene. This deletion led to upregulated expression of RamA, AcrA, AcrB, and TolC and downregulated expression of OmpF. The ΔramR mutant harbored the same phenotype as the resistant clinical strains regarding tigecycline, chloramphenicol, and ciprofloxacin. The increased expression of RamA due to partial deletion in the ramR gene led to a cross-resistance phenotype by an increase of antibiotic efflux through the AcrAB-TolC pump and a decrease of antibiotic permeability by porin OmpF. ramR appears to be an important adaptative trait for E. hormaechei strains.

中文翻译：

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hormechei肠杆菌分离物中的ramR缺失是长期住院患者中关键抗生素治疗失败的后果。

基因组的变化对于细菌的适应至关重要，特别是在抗生素压力下。这项研究的目的是报告在重症监护病房（ICU）住院的患者中，霍曼肠杆菌临床菌株经历的表型和基因组适应性变化，该菌株在4个月内对关键的抗菌药物高度耐药。已经研究了在一名重症监护病房住院患者中分离出的全部六种临床霍马大肠杆菌菌株。已经测量了有关17种抗菌分子的MIC。在测序的基因组上确定单核苷酸多态性（SNP）。阴沟肠杆菌中抗生素抗性相关基因的表达通过逆转录定量PCR（qRT-PCR）确定复杂菌株。所有菌株都属于序列类型66，并且最多相隔9个SNP。住院三个月后，三种菌株的头孢他啶，头孢吡肟，替莫西林，厄他培南，替加环素，环丙沙星和氯霉素的MIC显着增加。这些抗性菌株没有获得额外的抗生素抗性基因，但在ramR基因中保留了16 bp的缺失。这种删除导致RamA，AcrA，AcrB和TolC的表达上调，而OmpF的表达下调。该Δ RAMR该突变体具有与关于替加环素，氯霉素和环丙沙星的耐药性临床菌株相同的表型。由于ramR基因中部分缺失而引起的RamA表达增加，通过AcrAB-TolC泵引起的抗生素流出增加和孔蛋白OmpF引起的抗生素渗透性下降，导致了交叉耐药表型。ramR似乎是霍马埃希氏菌菌株的重要适应性状。