Central European Institute of Technology, University of Veterinary Sciences Brno, Brno, Czech Republic.
Department of Biology and Wildlife Diseases, University of Veterinary Sciences VETUNI Brno, Brno, Czech Republic.
Antimicrob Resist Infect Control. 2024 Nov 26;13(1):141. doi: 10.1186/s13756-024-01496-0.
Multidrug-resistant (MDR) bacteria pose a significant challenge to the treatment of infectious diseases. Of particular concern are members of the Klebsiella pneumoniae species complex (KpSC), which are frequently associated with hospital-acquired infections and have the potential to spread outside hospitals via wastewaters. In this study, we aimed to investigate the occurrence and phylogenetic relatedness of MDR KpSC from patients with urinary tract infections (UTIs), hospital sewage, municipal wastewater treatment plants (mWWTPs) and surface waters and to evaluate the clinical relevance of the KpSC subspecies.
A total of 372 KpSC isolates resistant to third-generation cephalosporins and/or meropenem were collected from patients (n = 130), hospital sewage (n = 95), inflow (n = 54) and outflow from the mWWTPs (n = 63), river upstream (n = 13) and downstream mWWTPs (n = 17) from three cities in the Czech Republic. The isolates were characterized by antimicrobial susceptibility testing and whole-genome sequencing (Illumina). The presence of antibiotic resistance genes, plasmid replicons and virulence-associated factors was determined. A phylogenetic tree and single nucleotide polymorphism matrix were created to reveal the relatedness between isolates.
The presence of MDR KpSC isolates (95%) was identified in all water sources and locations. Most isolates (99.7%) produced extended-spectrum beta-lactamases encoded by bla. Resistance to carbapenems (5%) was observed mostly in wastewaters, but carbapenemase genes, such as bla (n = 10), bla (n = 4), bla (n = 4) and bla (n = 1), were found in isolates from all tested locations and different sources except rivers. Among the 73 different sequence types (STs), phylogenetically related isolates were observed only among the ST307 lineage. Phylogenetic analysis revealed the transmission of this lineage from patients to the mWWTP and from the mWWTP to the adjacent river and the presence of the ST307 clone in the mWWTP over eight months. We confirmed the frequent abundance of K. pneumoniae (K. pneumoniae sensu stricto and K. pneumoniae subsp. ozaenae) in patients suffering from UTIs. K. variicola isolates formed only a minor proportion of UTIs, and K. quasipneumoniae was not found among UTIs isolates; however, these subspecies were frequently observed in hospital sewage communities during the first sampling period.
This study provides evidence of the transmission and persistence of the ST307 lineage from UTIs isolates via mWWTPs to surface waters. Isolates from UTIs consisted mostly of K. pneumoniae. Other isolates of KpSC were observed in hospital wastewaters, which implies the impact of sources other than UTIs. This study highlights the influence of urban wastewaters on the spread of MDR KpSC to receiving environments.
多药耐药（MDR）细菌对传染病的治疗构成重大挑战。特别值得关注的是肺炎克雷伯菌种复合体（KpSC）的成员，它们经常与医院获得性感染有关，并有可能通过废水在医院外传播。在这项研究中，我们旨在调查尿路感染（UTI）患者、医院污水、城市污水处理厂（mWWTP）和地表水分离的 MDR KpSC 的发生和系统发育相关性，并评估 KpSC亚种的临床相关性。
从捷克共和国三个城市的患者（n=130）、医院污水（n=95）、进水（n=54）和 mWWTP 流出物（n=63）、河流上游（n=13）和下游 mWWTP（n=17）中收集了总共 372 株对第三代头孢菌素和/或美罗培南耐药的 KpSC 分离株。通过抗生素敏感性试验和全基因组测序（Illumina）对分离株进行了表征。确定了抗生素耐药基因、质粒复制子和毒力相关因子的存在。创建了系统发育树和单核苷酸多态性矩阵，以揭示分离株之间的相关性。
在所检测的所有水源和地点均发现了存在 MDR KpSC 分离株（95%）。大多数分离株（99.7%）产生了 bla 编码的扩展谱β-内酰胺酶。碳青霉烯类耐药（5%）主要见于废水，但 bla (n=10)、bla (n=4)、bla (n=4) 和 bla (n=1) 等碳青霉烯酶基因在所有检测地点和不同来源的分离株中均有发现，除了河流。在 73 个不同的序列型（ST）中，仅在 ST307 谱系中观察到具有系统发育关系的分离株。系统发育分析显示，该谱系从患者传播到 mWWTP，再从 mWWTP 传播到相邻的河流，并且在 mWWTP 中存在 ST307 克隆超过八个月。我们证实了 K. pneumoniae（K. pneumoniae 严格意义上和 K. pneumoniae 亚种 ozaenae）在患有 UTI 的患者中频繁存在。K. variicola 分离株仅构成 UTI 的一小部分，而 K. quasipneumoniae 未在 UTI 分离株中发现；然而，这些亚种在第一次采样期间经常在医院污水群落中观察到。
本研究提供了证据表明，ST307 谱系从 UTI 分离株通过 mWWTP 传播到地表水，并在其中持续存在。UTI 分离株主要由 K. pneumoniae 组成。其他 KpSC 分离株在医院废水中被发现，这意味着存在除 UTI 以外的来源。本研究强调了城市废水对 MDR KpSC 传播到受纳环境的影响。
