Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil.
Whole genome sequencing of the multidrug-resistant Chryseobacterium indologenes isolated from a patient in Brazil.
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DOI：
10.3389/fmed.2022.931379
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发表时间：
2022
影响因子：
3.9
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产吲哚金黄杆菌是一种非葡萄糖发酵革兰氏阴性杆菌。这种新出现的多药耐药机会性院内病原体可引起新生儿和免疫功能低下患者的严重感染。本研究的目的是提出第一个详细的基因组序列草案的多重耐药的C。从巴西三级医院新生儿重症监护室住院的婴儿的脑脊液中分离的吲哚原杆菌菌株。我们首先分析了C.使用VITEK 2系统测定吲哚原杆菌菌株对不同抗生素的敏感性。该菌株表现出对所有测试的抗生素类别的显著抗性，包括β-内酰胺类、氨基糖苷类、甘氨酰环素和多粘菌素。下一个，C.对吲哚基因进行全基因组测序，使用Prokka和使用子系统技术的快速注释（RAST）进行注释，并使用不同的软件工具筛选直链组（EggNOG）、基因本体（GO）、抗性基因、毒力基因和移动的遗传元件。基因组草图含有一条环状染色体，长度为4，836，765 bp，GC含量为37.32%。染色体的基因组特征呈现出许多与细菌所必需的细胞过程相关的基因。MDR C. indologenes显示存在与耐药表型相对应的基因，包括β-内酰胺酶（blaIND-13、blaCIA-3、blaTEM-116、blaOXA-209、blaVEB-15）、喹诺酮（mcbG）、替加环素（泰特（X6））的基因，以及编码外排泵的基因，该外排泵赋予氨基糖苷类（RanA/RanB）和粘菌素（HlyD/TolC）耐药。在GyrA（S83 Y）和GyrB（L425 I和K473 R）中观察到与喹诺酮类耐药相关的氨基酸替换。在lpxA（G68 D）中检测到可能在粘菌素耐药性发展中起作用的突变。产吲哚金杆菌分离株含有19种毒力因子，其中大部分参与了感染途径。我们鉴定了13个基因组岛（GI）和一些与一个整合和接合元件（ICE）相关的元件。与移动的遗传元件（MGEs）连锁的其他元件如插入序列（ISEIsp 1）、转座子（Tn 5393）和整合子（In 31）也存在于C.吲哚基因组。虽然未检测到质粒，但在未对齐的支架中鉴定了ColRNAi复制子类型和在单例中检测到的大多数抗性基因。本研究为深入了解C. indologenes，这可以有助于控制这种病原体在医疗保健环境中的进化和传播。
Chryseobacterium indologenes is a non-glucose-fermenting Gram-negative bacillus. This emerging multidrug resistant opportunistic nosocomial pathogen can cause severe infections in neonates and immunocompromised patients. This study aimed to present the first detailed draft genome sequence of a multidrug-resistant C. indologenes strain isolated from the cerebrospinal fluid of an infant hospitalized at the Neonatal Intensive Care Unit of Brazilian Tertiary Hospital. We first analyzed the susceptibility of C. indologenes strain to different antibiotics using the VITEK 2 system. The strain demonstrated an outstanding resistance to all the antibiotic classes tested, including β-lactams, aminoglycosides, glycylcycline, and polymyxin. Next, C. indologenes was whole-genome-sequenced, annotated using Prokka and Rapid Annotation using Subsystems Technology (RAST), and screened for orthologous groups (EggNOG), gene ontology (GO), resistance genes, virulence genes, and mobile genetic elements using different software tools. The draft genome contained one circular chromosome of 4,836,765 bp with 37.32% GC content. The genomic features of the chromosome present numerous genes related to cellular processes that are essential to bacteria. The MDR C. indologenes revealed the presence of genes that corresponded to the resistance phenotypes, including genes to β-lactamases (blaIND–13, blaCIA–3, blaTEM–116, blaOXA–209, blaVEB–15), quinolone (mcbG), tigecycline (tet(X6)), and genes encoding efflux pumps which confer resistance to aminoglycosides (RanA/RanB), and colistin (HlyD/TolC). Amino acid substitutions related to quinolone resistance were observed in GyrA (S83Y) and GyrB (L425I and K473R). A mutation that may play a role in the development of colistin resistance was detected in lpxA (G68D). Chryseobacterium indologenes isolate harbored 19 virulence factors, most of which were involved in infection pathways. We identified 13 Genomic Islands (GIs) and some elements associated with one integrative and conjugative element (ICEs). Other elements linked to mobile genetic elements (MGEs), such as insertion sequence (ISEIsp1), transposon (Tn5393), and integron (In31), were also present in the C. indologenes genome. Although plasmids were not detected, a ColRNAI replicon type and the most resistance genes detected in singletons were identified in unaligned scaffolds. We provided a wide range of information toward the understanding of the genomic diversity of C. indologenes, which can contribute to controlling the evolution and dissemination of this pathogen in healthcare settings.