Whole-genome sequence of Porphyromonas pogonae PP01-1, a human strain harbouring blaOXA-347 and tet(Q)with chromosomal location

IF 3.7 3区 医学 Q2 INFECTIOUS DISEASES
Junwei Huang , Yijun Zhu , Daojun Gong , Shanshan Ma , Yongjun Ma , Cong Wu
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Abstract

Objectives

The aim of this study was to characterise the first complete genome of Porphyromonas pogonae strain PP01-1 of human origin in China.

Methods

The Illumina NovaSeq 6000 (200X coverage) and Nanopore MinION platforms (100× coverage) were used for genome sequencing. A de novo hybrid assembly of short Illumina reads and long MinION reads was performed using Unicycler (v.0.5.0). Genome annotation of PP01-1 was performed using the prokaryotic gene-prediction tool Prokka1.14.6. The genome was further analysed using several bioinformatics tools, including ResFinder, VFDB, VirulenceFinder, Type Strain Genome Server, AntiSMASH, PathogenFinder, MobileElementfinder, CRISPRFinder, and IslandViewer.

Results

The assembled circular genome of P. pogonae strain PP01-1 was 2 916 423 bp in length, with a GC content of 41.0%, and no plasmid sequence was detected. A total of 2399 coding sequences were predicted by Prokka. PP01-1 harbours antimicrobial resistance genes blaOXA-347 (β-lactamase resistance), tet(Q) (tetracycline resistance), and floR (chloramphenicol and florfenicol resistance).

Conclusions

Here, we are the first to report the complete genome of P. pogonae strain PP01-1 of human origin. In this strain, we first identified blaOXA-347 and tet(Q) in P. pogonae, which will pave the way for further analysis that could identify the potential mechanism of antibiotic resistance and virulence factors in P. pogonae.

Porphyromonas pogonae PP01-1 的全基因组序列,这是一株携带 blaOXA-347 和 tet(Q)并具有染色体位置的人类菌株。
研究目的本研究旨在鉴定中国首个人源卟啉单胞菌 PP01-1 株的完整基因组:方法:采用Illumina NovaSeq 6000(200倍覆盖率)和Nanopore MinION平台(100倍覆盖率)进行基因组测序。使用 Unicycler(v.0.5.0)对短的 Illumina 读数和长的 MinION 读数进行从头混合组装。使用多个生物信息学工具对 PP01-1 进行了进一步分析,包括 ResFinder、VFDB、VirulenceFinder、TYGS、AntiSMASH、PathogenFinder、MobileElementfinder、CRISPRFinder 和 IslandViewer:Porphyromonas pogonae菌株PP01-1的环状基因组长度为2,916,423 bp,GC含量为41.0%,未检测到质粒序列。Prokka 共预测出 2399 个编码序列。PP01-1 含有抗菌药耐药性基因 blaOXA-347(β-内酰胺酶耐药性)、tet(Q)(四环素)和 floR(氯霉素和氟苯尼考):在此,我们首次报道了人源卟啉单胞菌 PP01-1 株的完整基因组。在该菌株中,我们首次发现了卟啉单胞菌中的 blaOXA-347 和 tet(Q),这将为进一步分析卟啉单胞菌中 ARGs 和毒力因子的潜在机制铺平道路。
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
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.
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