Genomic characterization of Achromobacter genogroup 20 and identification of a potential species-specific marker

IF 3.7 3区医学 Q2 INFECTIOUS DISEASES

Journal of global antimicrobial resistance Pub Date : 2025-01-01 DOI:10.1016/j.jgar.2024.11.012

Mariana Papalia , Rocio Stucchi , Valeria Alexander , Liliana Clara , Mariángeles Visus , Gabriel Gutkind , Marcela Radice

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引用次数: 0

Abstract

Objective

To describe the genome of Achromobacter genogroup 20 and explore the presence of resistance determinants.

Methods

Isolate 413638 was identified through nrdA and MLST analysis. Antimicrobial susceptibility testing was performed according CLSI 2024. NGS was conducted using Illumina MiSeq, on the NextSeq500 platform with 150 bp paired-end reads, and de novo assembly was assessed using Unicycler (Galaxy). Coding sequences were predicted and confirmed with RAST and BLAST, and resistance determinants were evaluated using Resfinder and manual curation. All Achromobacter spp. genomes were obtained from NCBI, and the presence of bla_OXA was investigated. Average nucleotide identity (ANI) and tetranucleotide analysis (TETRA) were calculated. Phylogenetic analysis of the new OXA variant was conducted against other species-specific markers in Achromobacter.

Results

Isolate 413638 was identified as Achromobacter genogroup 20 ST365, showing resistance to third- and fourth-generation cephalosporins, aminoglycosides, and fluoroquinolones. The genome included coding sequences for three putative β-lactamases (one new OXA type-class D β -lactamase and two new class C), 32 efflux pump proteins, two aminoglycoside-modifying enzymes and a dihydropteroate synthase; also, substitutions in parC and parE were detected. The OXA enzyme, designated OXA-1238 (PP446293), differs from OXA-114a by 85 amino acids, with 69% identity. In silico analysis found OXA-1238 variants in three additional Achromobacter spp. genomes, with 97% identity. Based on ANI and tetra analysis, the three genomes corresponded to Achromobacter genogroup 20.

Conclusion

Several resistance markers were found, probably contributing to the resistance profile observed in Achromobacter genogroup 20 ST365. The new OXA variant identified, OXA-1238, could constitute a useful molecular marker for species identification.

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无色杆菌基因组20的基因组特征及潜在物种特异性标记的鉴定。

目的：描述无色杆菌20基因组基因组，探讨耐药决定因素的存在。方法：分离物413638经nrdA和MLST鉴定。按照CLSI 2024进行药敏试验。NGS使用Illumina MiSeq，在NextSeq500平台上进行，配对端reads为150 bp，使用Unicycler （Galaxy）评估从头组装。使用RAST和BLAST预测和确认编码序列，使用Resfinder和人工筛选评估抗性决定因素。从NCBI中获得了所有无色杆菌的基因组，并对blaOXA的存在进行了研究。计算平均核苷酸同一性（ANI）和四核苷酸分析（TETRA）。新的OXA变异体与无色杆菌中其他种特异性标记进行了系统发育分析。结果：分离物413638鉴定为无色杆菌基因组20 ST365，对第三代和第四代头孢菌素、氨基糖苷类药物和氟喹诺酮类药物耐药。基因组包含3个推测的β-内酰胺酶（1个新的OXA型- D类β-内酰胺酶和2个新的C类β-内酰胺酶）、32个外排泵蛋白、2个氨基糖苷修饰酶和1个二氢蝶呤合成酶的编码序列；此外，还检测到parC和parE的替换。OXA酶被命名为OXA-1238 (PP446293)，与OXA-114a有85个氨基酸的差异，同源性为69%。在计算机分析中发现OXA-1238变体在另外三个无色杆菌的基因组中，具有97%的一致性。基于ANI和四环素分析，这三个基因组对应于无色杆菌基因组20。结论：在20 ST365无色杆菌基因群中发现了多个耐药标记，可能与耐药谱有关。新发现的OXA变异OXA-1238可作为一种有用的物种鉴定分子标记。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Journal of global antimicrobial resistance INFECTIOUS DISEASES-PHARMACOLOGY & PHARMACY

CiteScore

8.70

自引率

2.20%

发文量

285

审稿时长

34 weeks

期刊介绍： The Journal of Global Antimicrobial Resistance (JGAR) is a quarterly online journal run by an international Editorial Board that focuses on the global spread of antibiotic-resistant microbes. JGAR is a dedicated journal for all professionals working in research, health care, the environment and animal infection control, aiming to track the resistance threat worldwide and provides a single voice devoted to antimicrobial resistance (AMR). Featuring peer-reviewed and up to date research articles, reviews, short notes and hot topics JGAR covers the key topics related to antibacterial, antiviral, antifungal and antiparasitic resistance.