Microbiology and Immunology Department, Faculty of Pharmacy, Alexandria University, El-Khartoom Square, Azarita, Alexandria, Egypt.
Quadram Institute Bioscience, Norwich, UK.
Ann Clin Microbiol Antimicrob. 2023 Sep 9;22(1):82. doi: 10.1186/s12941-023-00632-9.
Egypt has witnessed elevated incidence rates of multidrug-resistant Klebsiella pneumoniae infections in intensive care units (ICUs). The treatment of these infections is becoming more challenging whilst colistin-carbapenem-resistant K. pneumoniae is upsurging. Due to the insufficiently available data on the genomic features of colistin-resistant K. pneumoniae in Egypt, it was important to fill in the gap and explore the genomic characteristics, as well as the antimicrobial resistance, the virulence determinants, and the molecular mechanisms of colistin resistance in such a lethal pathogen.
Seventeen colistin-resistant clinical K. pneumoniae isolates were collected from ICUs in Alexandria, Egypt in a 6-month period in 2020. Colistin resistance was phenotypically detected by modified rapid polymyxin Nordmann/Poirel and broth microdilution techniques. The isolates susceptibility to 20 antimicrobials was determined using Kirby-Bauer disk diffusion method. Whole genome sequencing and bioinformatic analysis were employed for exploring the virulome, resistome, and the genetic basis of colistin resistance mechanisms.
Out of the tested K. pneumoniae isolates, 82.35% were extensively drug-resistant and 17.65% were multidrug-resistant. Promising susceptibility levels towards tigecycline (88.24%) and doxycycline (52.94%) were detected. Population structure analysis revealed seven sequence types (ST) and K-types: ST383-K30, ST147-K64, ST17-K25, ST111-K63, ST11-K15, ST14-K2, and ST525-K45. Virulome analysis revealed yersiniabactin, aerobactin, and salmochelin siderophore systems in ˃ 50% of the population. Hypervirulence biomarkers, iucA (52.94%) and rmpA/A2 (5.88%) were detected. Extended-spectrum β-lactamase- and carbapenemase-producers accounted for 94.12% of the population, with bla, bla and bla reaching 64.71%, 82.35%, and 82.35%, respectively. Chromosomal alterations in mgrB (82.35%) were the most prevailing colistin resistance-associated genetic change followed by deleterious mutations in ArnT (23.53%, L54H and G164S), PmrA (11.76%, G53V and D86E), PmrB (11.76%, T89P and T134P), PmrC (11.76%, S257L), PhoQ (5.88%, L322Q and Q435H), and ArnB (5.88%, G47D) along with the acquisition of mcr-1.1 by a single isolate of ST525.
In this study, we present the genotypic colistin resistance mechanisms in K. pneumoniae isolated in Egypt. More effective antibiotic stewardship protocols must be implemented by Egyptian health authorities to restrain this hazard and safeguard the future utility of colistin. This is the first characterization of a complete sequence of mcr-1.1-bearing IncHI2/IncHI2A plasmid recovered from K. pneumoniae clinical isolate belonging to the emerging high-risk clone ST525.
埃及重症监护病房（ICU）中出现了耐多药肺炎克雷伯菌感染发病率升高的情况。随着黏菌素-碳青霉烯类耐药肺炎克雷伯菌的出现，这些感染的治疗变得更加具有挑战性。由于埃及缺乏关于耐黏菌素肺炎克雷伯菌基因组特征的充分数据，因此填补这一空白并探索这种致命病原体的基因组特征、抗菌药物耐药性、毒力决定因素以及黏菌素耐药的分子机制非常重要。
在 2020 年的 6 个月期间，从埃及亚历山大的 ICU 中收集了 17 株耐黏菌素的临床肺炎克雷伯菌分离株。采用改良的快速多粘菌素 Nordmann/Poirel 和肉汤微量稀释技术对黏菌素耐药性进行表型检测。采用 Kirby-Bauer 纸片扩散法测定分离株对 20 种抗菌药物的敏感性。采用全基因组测序和生物信息学分析方法，探讨了毒力组、耐药组以及黏菌素耐药机制的遗传基础。
在所测试的肺炎克雷伯菌分离株中，82.35%为广泛耐药，17.65%为多重耐药。对替加环素（88.24%）和强力霉素（52.94%）的敏感性水平较高。群体结构分析显示了 7 种序列类型（ST）和 K 型：ST383-K30、ST147-K64、ST17-K25、ST111-K63、ST11-K15、ST14-K2 和 ST525-K45。毒力组分析显示，超过 50%的分离株存在耶尔森菌素、aerobactin 和 salmochelin 铁载体系统。检测到高毒力生物标志物 iucA（52.94%）和 rmpA/A2（5.88%）。产超广谱β-内酰胺酶和碳青霉烯酶的分离株占 94.12%，bla、bla和 bla分别达到 64.71%、82.35%和 82.35%。mgrB（82.35%）的染色体改变是与黏菌素耐药相关的最普遍的遗传变化，其次是 ArnT（23.53%，L54H 和 G164S）、PmrA（11.76%，G53V 和 D86E）、PmrB（11.76%，T89P 和 T134P）、PmrC（11.76%，S257L）、PhoQ（5.88%，L322Q 和 Q435H）和 ArnB（5.88%，G47D）中的有害突变以及单个 ST525 分离株中 mcr-1.1 的获得。
在这项研究中，我们展示了埃及肺炎克雷伯菌的基因型黏菌素耐药机制。埃及卫生当局必须实施更有效的抗生素管理方案，以遏制这种危害并保护黏菌素的未来应用。这是首次从属于新兴高风险克隆 ST525 的肺炎克雷伯菌临床分离株中鉴定出完整的 mcr-1.1 携带 IncHI2/IncHI2A 质粒。
