Microbiology, Ramón y Cajal University Hospital and Ramón y Cajal Health Research Institute (IRYCIS), Madrid, Spain.
Member of the ESCMID Study Group for Epidemiological Markers (ESGEM), Basel, Switzerland.
mBio. 2024 May 8;15(5):e0305423. doi: 10.1128/mbio.03054-23. Epub 2024 Apr 2.
is an opportunistic pathogen historically associated with sudden outbreaks in intensive care units (ICUs) and the spread of carbapenem-resistant genes. However, the ecology of populations in the hospital ecosystem remains largely unknown. We combined epidemiological information of 1,432 spp. isolates collected from sinks of a large ICU that underwent demographic and operational changes (2019-2021) and 99 non-redundant outbreak/non-outbreak isolates from the same hospital (2003-2019) with 165 genomic data. These genomes were grouped into clades (1-4) and subclades (A and B) associated with distinct species: (1A), (1B), (2A), (2B), / (3), and (4A and 4B). They may be classified into an complex (SMC) due to the similarity between/within subclades (average nucleotide identity >95%-98%), with clades 3 and 4 predominating in our study and publicly available databases. Chromosomal AmpC β-lactamase with unusual basal-like expression and prodigiosin-lacking species contrasted classical features of . We found persistent and coexisting clones in sinks of subclades 4A (ST92 and ST490) and 4B (ST424), clonally related to outbreak isolates carrying or on prevalent IncL/pB77-CPsm plasmids from our hospital since 2017. The distribution of SMC populations in ICU sinks and patients reflects how species acquire, maintain, and enable plasmid evolution in both "source" (permanent, sinks) and "sink" (transient, patients) hospital patches. The results contribute to understanding how water sinks serve as reservoirs of clones and plasmids that enable the persistence of carbapenemase genes in healthcare settings, potentially leading to outbreaks and/or hospital-acquired infections.IMPORTANCEThe "hospital environment," including sinks and surfaces, is increasingly recognized as a reservoir for bacterial species, clones, and plasmids of high epidemiological concern. Available studies on epidemiology have focused mainly on outbreaks of multidrug-resistant species, overlooking local longitudinal analyses necessary for understanding the dynamics of opportunistic pathogens and antibiotic-resistant genes within the hospital setting. This long-term genomic comparative analysis of isolated from the ICU environment with isolates causing nosocomial infections and/or outbreaks within the same hospital revealed the coexistence and persistence of populations in water reservoirs. Moreover, predominant sink strains may acquire highly conserved and widely distributed plasmids carrying carbapenemase genes, such as the prevalent IncL-pB77-CPsm (pOXA48), persisting in ICU sinks for years. The work highlights the relevance of ICU environmental reservoirs in the endemicity of certain opportunistic pathogens and resistance mechanisms mainly confined to hospitals.
是一种机会性病原体,历史上与重症监护病房 (ICU) 的突然爆发和碳青霉烯类耐药基因的传播有关。然而,医院生态系统中 的种群生态仍知之甚少。我们将从经历人口统计学和运营变化的大型 ICU 水槽中收集的 1432 株 spp. 分离株的流行病学信息与来自同一医院的 99 个非冗余暴发/非暴发分离株(2003-2019 年)与 165 个基因组数据相结合。这些基因组被分为与不同物种相关的进化枝(1-4)和亚进化枝(A 和 B): (1A), (1B), (2A), (2B), / (3),和 (4A 和 4B)。由于亚进化枝内/之间的相似性(平均核苷酸同一性>95%-98%),它们可能被归类为一个 复杂(SMC),其中进化枝 3 和 4 在我们的研究和公开可用的数据库中占主导地位。具有不寻常的基础样表达的染色体 AmpC β-内酰胺酶和缺乏普罗迪辛的物种与 的经典特征形成对比。我们发现亚进化枝 4A(ST92 和 ST490)和 4B(ST424)水槽中持续存在和共存的克隆,这些克隆与携带 或 的暴发分离株密切相关,这些分离株携带的 或 是我们医院自 2017 年以来流行的 IncL/pB77-CPsm 质粒。在 ICU 水槽和患者中 SMC 种群的分布反映了 物种如何在“源”(永久、水槽)和“汇”(瞬态、患者)医院斑块中获得、维持和促进质粒进化。结果有助于了解水水槽如何作为能够在医疗保健环境中持续存在碳青霉烯酶基因的克隆和质粒的储库,从而导致暴发和/或医院获得性感染。
重要性
“医院环境”,包括水槽和表面,越来越被认为是具有高流行病学意义的细菌物种、克隆和质粒的储库。关于 流行病学的现有研究主要集中在多药耐药物种的暴发上,而忽略了在医院环境中了解机会性病原体和抗生素耐药基因动态所需的本地纵向分析。对从 ICU 环境中分离的 与在同一医院引起医院感染和/或暴发的分离株进行的长期基因组比较分析显示,水储库中存在 和 种群的共存和持续存在。此外,主要水槽菌株可能获得高度保守且广泛分布的携带碳青霉烯酶基因的质粒,例如流行的 IncL-pB77-CPsm(pOXA48),在 ICU 水槽中持续存在多年。该工作强调了 ICU 环境储库在某些机会性病原体和主要限于医院的耐药机制的地方性中的相关性。