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Abstract：
Antibiotic-resistant Klebsiella pneumoniae has emerged as a critical public health threat worldwide. Understanding the antimicrobial resistance mechanisms of multidrug-resistant K. pneumoniae (MDR-Kp) and its prevalence in time and space would provide clinical significance for managing pathogen infection.
Eighteen clinical MDR-Kp strains were analyzed by whole genome sequencing (WGS), and the antimicrobial resistance genes and associated resistance mechanisms were compared with results obtained from the conventional microbiological test (CMT). The sequence homology across strains in our study and those previously collected over time from a wide geographical region was assessed by phylogenetic analysis.
MDR-Kp strains were collected from eighteen patients who had received empirical treatment before strain collection, with sputum (83.3%, 15/18) being the primary source of clinical samples. The commonly received treatments include β-lactamase inhibitors (55.6%, 10/18) and carbapenems (50%, 9/18). Using CMT, we found that all 18 strains were resistant to aztreonam and ciprofloxacin, while 14 (77.8%) showed resistance to carbapenem. Polymyxin B and tigecycline were the only antibiotics to which MDR-Kp strains were sensitive. A total of 42 antimicrobial resistance mechanisms were identified by WGS, surpassing the 40 detected by the conventional method, with 25 mechanisms shared between the two techniques. Despite a 100% accuracy rate of WGS in detecting penicillin-resistant strains, the accuracy in detecting cephalosporin-resistant strains was only at 60%. Among all resistance genes identified by WGS, Klebsiella pneumoniae carbapenemase-2 (KPC-2) was present in all 14 carbapenem-resistant strains. Phenotypic analysis indicated that sequence type (ST) 11 isolates were the primary cause of these MDR-Kp infections. Additionally, phylogenic clustering analysis, encompassing both the clinical and MDR-Kp strains previously reported in China, revealed four distinct subgroups. No significant difference was observed in the sequence homology between K. pneumoniae strains in our study and those previously collected in East China over time.
The application of WGS in identifying potential antimicrobial-resistant genes of MDR-Kp has demonstrated promising clinical significance. Comprehensive genomic information revealed by WGS holds the promise of guiding treatment decisions, enabling surveillance, and serving as a crucial asset in understanding antibiotic resistance.
Eighteen clinical MDR-Kp strains were analyzed by whole genome sequencing (WGS), and the antimicrobial resistance genes and associated resistance mechanisms were compared with results obtained from the conventional microbiological test (CMT). The sequence homology across strains in our study and those previously collected over time from a wide geographical region was assessed by phylogenetic analysis.
MDR-Kp strains were collected from eighteen patients who had received empirical treatment before strain collection, with sputum (83.3%, 15/18) being the primary source of clinical samples. The commonly received treatments include β-lactamase inhibitors (55.6%, 10/18) and carbapenems (50%, 9/18). Using CMT, we found that all 18 strains were resistant to aztreonam and ciprofloxacin, while 14 (77.8%) showed resistance to carbapenem. Polymyxin B and tigecycline were the only antibiotics to which MDR-Kp strains were sensitive. A total of 42 antimicrobial resistance mechanisms were identified by WGS, surpassing the 40 detected by the conventional method, with 25 mechanisms shared between the two techniques. Despite a 100% accuracy rate of WGS in detecting penicillin-resistant strains, the accuracy in detecting cephalosporin-resistant strains was only at 60%. Among all resistance genes identified by WGS, Klebsiella pneumoniae carbapenemase-2 (KPC-2) was present in all 14 carbapenem-resistant strains. Phenotypic analysis indicated that sequence type (ST) 11 isolates were the primary cause of these MDR-Kp infections. Additionally, phylogenic clustering analysis, encompassing both the clinical and MDR-Kp strains previously reported in China, revealed four distinct subgroups. No significant difference was observed in the sequence homology between K. pneumoniae strains in our study and those previously collected in East China over time.
The application of WGS in identifying potential antimicrobial-resistant genes of MDR-Kp has demonstrated promising clinical significance. Comprehensive genomic information revealed by WGS holds the promise of guiding treatment decisions, enabling surveillance, and serving as a crucial asset in understanding antibiotic resistance.
摘要：
背景：抗生素耐药性肺炎克雷伯菌已成为全球范围内严重的公共卫生威胁。了解多重耐药肺炎克雷伯菌（MDR-Kp）的耐药机制及其在时间和空间上的流行情况，将为控制病原体感染提供临床意义。
方法：通过全基因组测序（WGS）分析了18株临床MDR-Kp菌株，并将抗菌素耐药基因和相关耐药机制与常规微生物试验（CMT）的结果进行了比较。通过系统发育分析评估了我们研究中的菌株之间的序列同源性以及先前随时间从广泛的地理区域收集的序列同源性。
结果：MDR-Kp菌株从18名在菌株收集前接受经验性治疗的患者中收集，痰（83.3%，15/18）是临床样本的主要来源。普遍接受的治疗包括β-内酰胺酶抑制剂(55.6%，10/18）和碳青霉烯类（50%，9/18).使用CMT，我们发现所有18个菌株都对氨曲南和环丙沙星耐药，14例(77.8%)对碳青霉烯耐药。多粘菌素B和替加环素是唯一对MDR-Kp敏感的抗生素。WGS共鉴定了42种抗菌药耐药机制，超过常规方法检测到的40，这两种技术共享25种机制。尽管WGS检测青霉素耐药菌株的准确率为100%，检测头孢菌素耐药菌株的准确率仅为60%.在WGS鉴定的所有抗性基因中，肺炎克雷伯菌碳青霉烯酶-2（KPC-2）存在于所有14株碳青霉烯类耐药菌株中。表型分析表明，序列型（ST）11分离株是这些MDR-Kp感染的主要原因。此外,系统发育聚类分析，包括先前在中国报道的临床和MDR-Kp菌株，揭示了四个不同的亚组。在我们的研究中，肺炎克雷伯菌菌株与先前在华东地区收集的菌株之间的序列同源性没有显着差异。
结论：应用WGS鉴定MDR-Kp潜在耐药基因具有良好的临床意义。WGS揭示的全面基因组信息有望指导治疗决策，启用监视，并作为了解抗生素耐药性的重要资产。
方法：通过全基因组测序（WGS）分析了18株临床MDR-Kp菌株，并将抗菌素耐药基因和相关耐药机制与常规微生物试验（CMT）的结果进行了比较。通过系统发育分析评估了我们研究中的菌株之间的序列同源性以及先前随时间从广泛的地理区域收集的序列同源性。
结果：MDR-Kp菌株从18名在菌株收集前接受经验性治疗的患者中收集，痰（83.3%，15/18）是临床样本的主要来源。普遍接受的治疗包括β-内酰胺酶抑制剂(55.6%，10/18）和碳青霉烯类（50%，9/18).使用CMT，我们发现所有18个菌株都对氨曲南和环丙沙星耐药，14例(77.8%)对碳青霉烯耐药。多粘菌素B和替加环素是唯一对MDR-Kp敏感的抗生素。WGS共鉴定了42种抗菌药耐药机制，超过常规方法检测到的40，这两种技术共享25种机制。尽管WGS检测青霉素耐药菌株的准确率为100%，检测头孢菌素耐药菌株的准确率仅为60%.在WGS鉴定的所有抗性基因中，肺炎克雷伯菌碳青霉烯酶-2（KPC-2）存在于所有14株碳青霉烯类耐药菌株中。表型分析表明，序列型（ST）11分离株是这些MDR-Kp感染的主要原因。此外,系统发育聚类分析，包括先前在中国报道的临床和MDR-Kp菌株，揭示了四个不同的亚组。在我们的研究中，肺炎克雷伯菌菌株与先前在华东地区收集的菌株之间的序列同源性没有显着差异。
结论：应用WGS鉴定MDR-Kp潜在耐药基因具有良好的临床意义。WGS揭示的全面基因组信息有望指导治疗决策，启用监视，并作为了解抗生素耐药性的重要资产。
