Junwei Huang , Yijun Zhu , Daojun Gong , Shanshan Ma , Yongjun Ma , Cong Wu
{"title":"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。","authors":"Junwei Huang , Yijun Zhu , Daojun Gong , Shanshan Ma , Yongjun Ma , Cong Wu","doi":"10.1016/j.jgar.2024.04.015","DOIUrl":null,"url":null,"abstract":"<div><h3>Objectives</h3><p>The aim of this study was to characterise the first complete genome of <em>Porphyromonas pogonae</em> strain PP01-1 of human origin in China.</p></div><div><h3>Methods</h3><p>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.</p></div><div><h3>Results</h3><p>The assembled circular genome of <em>P. pogonae</em> 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 <em>bla</em><sub>OXA-347</sub> (β-lactamase resistance), <em>tet(Q)</em> (tetracycline resistance), and <em>floR</em> (chloramphenicol and florfenicol resistance).</p></div><div><h3>Conclusions</h3><p>Here, we are the first to report the complete genome of <em>P. pogonae</em> strain PP01-1 of human origin. In this strain, we first identified <em>bla</em><sub>OXA-347</sub> and <em>tet(Q)</em> in <em>P. pogonae</em>, which will pave the way for further analysis that could identify the potential mechanism of antibiotic resistance and virulence factors in <em>P. pogonae</em>.</p></div>","PeriodicalId":15936,"journal":{"name":"Journal of global antimicrobial resistance","volume":null,"pages":null},"PeriodicalIF":3.7000,"publicationDate":"2024-05-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S2213716524000882/pdfft?md5=1956e05687e025681577cbb5229ab18b&pid=1-s2.0-S2213716524000882-main.pdf","citationCount":"0","resultStr":"{\"title\":\"Whole-genome sequence of Porphyromonas pogonae PP01-1, a human strain harbouring blaOXA-347 and tet(Q)with chromosomal location\",\"authors\":\"Junwei Huang , Yijun Zhu , Daojun Gong , Shanshan Ma , Yongjun Ma , Cong Wu\",\"doi\":\"10.1016/j.jgar.2024.04.015\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Objectives</h3><p>The aim of this study was to characterise the first complete genome of <em>Porphyromonas pogonae</em> strain PP01-1 of human origin in China.</p></div><div><h3>Methods</h3><p>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.</p></div><div><h3>Results</h3><p>The assembled circular genome of <em>P. pogonae</em> 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 <em>bla</em><sub>OXA-347</sub> (β-lactamase resistance), <em>tet(Q)</em> (tetracycline resistance), and <em>floR</em> (chloramphenicol and florfenicol resistance).</p></div><div><h3>Conclusions</h3><p>Here, we are the first to report the complete genome of <em>P. pogonae</em> strain PP01-1 of human origin. In this strain, we first identified <em>bla</em><sub>OXA-347</sub> and <em>tet(Q)</em> in <em>P. pogonae</em>, which will pave the way for further analysis that could identify the potential mechanism of antibiotic resistance and virulence factors in <em>P. pogonae</em>.</p></div>\",\"PeriodicalId\":15936,\"journal\":{\"name\":\"Journal of global antimicrobial resistance\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.7000,\"publicationDate\":\"2024-05-14\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.sciencedirect.com/science/article/pii/S2213716524000882/pdfft?md5=1956e05687e025681577cbb5229ab18b&pid=1-s2.0-S2213716524000882-main.pdf\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of global antimicrobial resistance\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2213716524000882\",\"RegionNum\":3,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"INFECTIOUS DISEASES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of global antimicrobial resistance","FirstCategoryId":"3","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2213716524000882","RegionNum":3,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"INFECTIOUS DISEASES","Score":null,"Total":0}
Whole-genome sequence of Porphyromonas pogonae PP01-1, a human strain harbouring blaOXA-347 and tet(Q)with chromosomal location
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.
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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