Data_Sheet_1_Acinetobacter pittii: the emergence of a hospital-acquired pathogen analyzed from the genomic perspective.PDF

Acinetobacter pittii has increasingly been associated with several types of hospital-acquired severe infections. Genes implicated in carbapenem resistance, tigecycline resistance, or genes encoding extended spectrum cephalosporinases, such as blaADC, are commonly found in isolates implicated in these infections. A. pittii strains that are pandrug resistant have occasionally been identified. Food for human consumption, animals and plants are environmental sources of this pathogen. An alarming situation is that A. pitti has been identified as responsible for outbreaks in different regions worldwide. In this study, 384 genomes of A. pittii were analyzed, comprising sequences from clinical and non-clinical origins from 32 countries. The objective was to investigate if clinical strains possess genetic traits facilitating hospital adaptation. Results indicate significant genomic variability in terms of size and gene content among A. pittii isolates. The core genome represents a small portion (25–36%) of each isolate’s genome, while genes associated with antibiotic resistance and virulence predominantly belong to the accessory genome. Notably, antibiotic resistance genes are encoded by a diverse array of plasmids. As the core genome between environmental and hospital isolates is the same, we can assume that hospital isolates acquired ARGs due to a high selective pressure in these settings. The strain’s phylogeographic distribution indicates that there is no geographical bias in the isolate distribution; isolates from different geographic regions are dispersed throughout a core genome phylogenetic tree. A single clade may include isolates from extremely distant geographical areas. Furthermore, strains isolated from the environment or animal, or plant sources frequently share the same clade as hospital isolates. Our analysis showed that the clinical isolates do not already possess specific genes, other than antibiotic-resistant genes, to thrive in the hospital setting.

皮氏不动杆菌（Acinetobacter pittii）与多种医院获得性重症感染的关联日益紧密。从此类感染的分离株中，常可检出与碳青霉烯类耐药、替加环素耐药相关的基因，或编码超广谱头孢菌素酶的基因（如blaADC）。泛耐药的皮氏不动杆菌菌株偶有被报道。人类食用食品、动植物均为该病原菌的环境储存宿主。令人警惕的是，皮氏不动杆菌已被证实可在全球多个地区引发暴发疫情。
本研究共分析了384株皮氏不动杆菌的全基因组，涵盖来自32个国家的临床与非临床来源的序列，旨在探究临床菌株是否携带有助于医院环境适应的遗传特征。研究结果显示，皮氏不动杆菌分离株在基因组大小与基因组成上存在显著的基因组变异。核心基因组（core genome）仅占单株分离株基因组的25%~36%，而与抗生素耐药、毒力相关的基因主要属于附属基因组（accessory genome）。值得注意的是，抗生素耐药基因（antibiotic resistance genes, ARGs）由多种不同的质粒编码。由于环境分离株与医院分离株的核心基因组一致，我们可推测医院分离株是在该环境下的高选择压力下获得了抗生素耐药基因。
菌株的系统地理分布分析表明，分离株的分布不存在地理偏好性：来自不同地理区域的分离株在核心基因组系统发育树中呈散在分布，单个进化枝（clade）可能包含来自极远距离地理区域的分离株。此外，从环境、动物或植物来源分离的菌株，常可与医院分离株处于同一进化枝中。本分析显示，临床分离株除携带抗生素耐药基因外，并未携带其他有助于在医院环境中存活的特异性基因。