Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa.
Department of Pathology and Laboratory Medicine, Cummings School of Medicine, University of Calgary, Calgary, Canada.
Sci Rep. 2024 Nov 9;14(1):27337. doi: 10.1038/s41598-024-70910-9.
Klebsiella pneumoniae multidrug-resistant (MDR) high-risk clones drive the spread of antimicrobial resistance (AMR) associated infections, resulting in limited therapeutic options. This study described the genomic characteristics of K. pneumoniae MDR high-risk clones in Gauteng, South Africa. Representative carbapenem-resistant [K. pneumoniae carbapenemase (KPC)-2, New-Delhi metallo-beta (β)-lactamase (NDM)-1, oxacillinase (OXA)-181, OXA-232, OXA-48, Verona integron-encoded metallo-β-lactamase (VIM)-1] K. pneumoniae isolates (n = 22) obtained from inpatient and outpatient's urine (n = 9) and inpatients rectal carriage (n = 13) were selected for short-read whole genome sequencing. Klebsiella pneumoniae population include sequence type (ST)-307 (n = 3), ST2497 (n = 5) and ST17 (n = 4). The ST17 strains were exclusively obtained from rectal screening. Ten isolates co-harboured carbapenemase genes including β-lactamase gene encoding KPC-2 + OXA-181, NDM-1 + OXA-48 and NDM-1 + OXA-181. One ST307 isolate (UP-KT-73CKP) co-harboured three carbapenemase genes (bla + bla + bla), while all the ST2497 strains co-harboured (bla + bla). Phenotypically, hypermucoviscosity was observed in a single ST307 isolate. The ST307 isolate UP-KT-151UKP harboured colibactin genotoxins. The following mobile genetic elements were detected: plasmids [incompatibility group (Inc)-FIB(K), IncX3], and bacteriophages [e.g. Klebsi_ST16_OXA48phi5.4_NC_049450, Klebsi_3LV2017_NC_047817(36)]. The study highlights the importance of local genomic surveillance systems to characterise K. pneumoniae MDR high-risk clones. This data will aid in designing infection and prevention measures for limiting the spread of carbapenemase-producing K. pneumoniae in Gauteng, South Africa.
肺炎克雷伯菌多药耐药（MDR）高危克隆驱动与抗生素耐药性（AMR）相关感染的传播，导致治疗选择有限。本研究描述了南非豪登省肺炎克雷伯菌 MDR 高危克隆的基因组特征。从住院和门诊患者尿液（n=9）和住院患者直肠携带（n=13）中获得了代表耐碳青霉烯类[肺炎克雷伯菌碳青霉烯酶（KPC）-2、新德里金属β（β）-内酰胺酶（NDM）-1、氧西林酶（OXA）-181、OXA-232、OXA-48、维罗纳整合子编码金属β-内酰胺酶（VIM）-1]的肺炎克雷伯菌耐碳青霉烯类分离株（n=22），用于短读全基因组测序。肺炎克雷伯菌种群包括序列型（ST）-307（n=3）、ST2497（n=5）和 ST17（n=4）。ST17 株仅从直肠筛查中获得。10 株分离株共同携带碳青霉烯酶基因，包括β-内酰胺酶基因编码 KPC-2+OXA-181、NDM-1+OXA-48 和 NDM-1+OXA-181。一株 ST307 分离株（UP-KT-73CKP）共同携带三种碳青霉烯酶基因（bla+bla+bla），而所有 ST2497 株均共同携带（bla+bla）。表型上，单个 ST307 分离株表现出超粘液性。ST307 分离株 UP-KT-151UKP 携带 colibactin 基因毒素。检测到以下移动遗传元件：质粒[不相容群（Inc）-FIB（K）、IncX3]和噬菌体[例如 Klebsi_ST16_OXA48phi5.4_NC_049450、Klebsi_3LV2017_NC_047817（36）]。该研究强调了建立当地基因组监测系统以描述肺炎克雷伯菌 MDR 高危克隆的重要性。这些数据将有助于设计感染和预防措施，以限制南非豪登省产碳青霉烯酶肺炎克雷伯菌的传播。
