人畜共患病病原体艰难梭菌的比较基因组学,以了解其多样性。

IF 2.6 4区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY 3 Biotech Pub Date : 2024-11-01 Epub Date: 2024-10-04 DOI:10.1007/s13205-024-04102-7
Kumaragurubaran Karthik, Subbaiyan Anbazhagan, Murugaiyan Latha Mala Priyadharshini, Rajeev Kumar Sharma, Seeralan Manoharan
{"title":"人畜共患病病原体艰难梭菌的比较基因组学,以了解其多样性。","authors":"Kumaragurubaran Karthik, Subbaiyan Anbazhagan, Murugaiyan Latha Mala Priyadharshini, Rajeev Kumar Sharma, Seeralan Manoharan","doi":"10.1007/s13205-024-04102-7","DOIUrl":null,"url":null,"abstract":"<p><p><i>Clostridioides difficile</i>, a zoonotic pathogen causing enteric diseases in different animals and humans. A comprehensive study on the presence of toxin genes and antimicrobial resistance genes based on genome data of <i>C. difficile</i> in animals is scanty. In the present study, a total of 15 <i>C. difficile</i> isolates were recovered from dogs and isolates with toxin genes (D1, CD15 and CD26) along with two other non-toxigenic strains (CD28, CD32) were used for whole genome sequencing and comparative genomics. Sequence type-based clustering was noted in the whole genome phylogeny with 4 known multi-locus sequence typing (MLST) clades namely I, II, IV, and V and a cryptic clade. ST11 and ST54 were reported for the 2<sup>nd</sup> time worldwide in dogs. Out of 109 genomes used in the study, 29 genomes were predicted with all four toxin genes (<i>toxA</i>, <i>toxB</i>, <i>cdtA</i>, <i>cdtB</i>) while 22 did not have any of the toxin genes. ST11 of MLST clade V had the maximum number of 46 genomes predicted with at least one toxin gene. Among the genomes sequenced in this study, CD26 had a maximum of 5 AMR genes (<i>aac(6')-aph(2″)</i>, <i>ant(6)-Ia</i>, <i>catP</i>, <i>erm(B)_18</i>, and <i>tet(M)_11</i>) and CD15 was predicted with 2 AMR genes (<i>aac(6')-aph(2″)</i>, <i>erm(B)_18</i>). Tetracycline resistance genes were predicted most in the ST11 genome. Of the 22 non-toxigenic strains, 9 genomes (ST48 = 5, ST3 = 2, ST109 = 1, ST15 = 1) were predicted with a minimum of one AMR gene. Pangenome analysis indicated that the <i>Bpan</i> value is 0.12 showing that <i>C. difficile</i> has an open pangenome structure. This indicates that the organism can evolve by the addition of new genes. This study reports the circulation of clinically important ST11 and multidrug-resistant non-toxigenic strains among animals.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04102-7.</p>","PeriodicalId":7067,"journal":{"name":"3 Biotech","volume":null,"pages":null},"PeriodicalIF":2.6000,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452369/pdf/","citationCount":"0","resultStr":"{\"title\":\"Comparative genomics of zoonotic pathogen <i>Clostridioides difficile</i> of animal origin to understand its diversity.\",\"authors\":\"Kumaragurubaran Karthik, Subbaiyan Anbazhagan, Murugaiyan Latha Mala Priyadharshini, Rajeev Kumar Sharma, Seeralan Manoharan\",\"doi\":\"10.1007/s13205-024-04102-7\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p><i>Clostridioides difficile</i>, a zoonotic pathogen causing enteric diseases in different animals and humans. A comprehensive study on the presence of toxin genes and antimicrobial resistance genes based on genome data of <i>C. difficile</i> in animals is scanty. In the present study, a total of 15 <i>C. difficile</i> isolates were recovered from dogs and isolates with toxin genes (D1, CD15 and CD26) along with two other non-toxigenic strains (CD28, CD32) were used for whole genome sequencing and comparative genomics. Sequence type-based clustering was noted in the whole genome phylogeny with 4 known multi-locus sequence typing (MLST) clades namely I, II, IV, and V and a cryptic clade. ST11 and ST54 were reported for the 2<sup>nd</sup> time worldwide in dogs. Out of 109 genomes used in the study, 29 genomes were predicted with all four toxin genes (<i>toxA</i>, <i>toxB</i>, <i>cdtA</i>, <i>cdtB</i>) while 22 did not have any of the toxin genes. ST11 of MLST clade V had the maximum number of 46 genomes predicted with at least one toxin gene. Among the genomes sequenced in this study, CD26 had a maximum of 5 AMR genes (<i>aac(6')-aph(2″)</i>, <i>ant(6)-Ia</i>, <i>catP</i>, <i>erm(B)_18</i>, and <i>tet(M)_11</i>) and CD15 was predicted with 2 AMR genes (<i>aac(6')-aph(2″)</i>, <i>erm(B)_18</i>). Tetracycline resistance genes were predicted most in the ST11 genome. Of the 22 non-toxigenic strains, 9 genomes (ST48 = 5, ST3 = 2, ST109 = 1, ST15 = 1) were predicted with a minimum of one AMR gene. Pangenome analysis indicated that the <i>Bpan</i> value is 0.12 showing that <i>C. difficile</i> has an open pangenome structure. This indicates that the organism can evolve by the addition of new genes. This study reports the circulation of clinically important ST11 and multidrug-resistant non-toxigenic strains among animals.</p><p><strong>Supplementary information: </strong>The online version contains supplementary material available at 10.1007/s13205-024-04102-7.</p>\",\"PeriodicalId\":7067,\"journal\":{\"name\":\"3 Biotech\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":2.6000,\"publicationDate\":\"2024-11-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11452369/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"3 Biotech\",\"FirstCategoryId\":\"5\",\"ListUrlMain\":\"https://doi.org/10.1007/s13205-024-04102-7\",\"RegionNum\":4,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/10/4 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q3\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"3 Biotech","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1007/s13205-024-04102-7","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/10/4 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0

摘要

艰难梭菌(Clostridioides difficile)是一种人畜共患病原,可导致不同动物和人类患上肠道疾病。根据艰难梭菌基因组数据对动物体内存在的毒素基因和抗菌药耐药性基因进行的全面研究还很少。在本研究中,从狗身上共分离出 15 株艰难梭菌,并将带有毒素基因(D1、CD15 和 CD26)的分离株与另外两株非致毒菌株(CD28 和 CD32)一起用于全基因组测序和比较基因组学研究。在全基因组系统发育中发现了基于序列类型的聚类,有 4 个已知的多焦点序列分型(MLST)支系,即 I、II、IV 和 V 支系以及一个隐性支系。ST11和ST54是全球范围内第二次在狗身上发现。在研究中使用的 109 个基因组中,29 个基因组被预测具有全部四个毒素基因(toxA、toxB、cttA、cttB),而 22 个基因组没有任何毒素基因。MLST 第 V 支系的 ST11 基因组最多,有 46 个基因组被预测含有至少一个毒素基因。在本研究测序的基因组中,CD26 最多有 5 个 AMR 基因(aac(6')-aph(2″)、ant(6)-Ia、catP、erm(B)_18 和 tet(M)_11),CD15 被预测有 2 个 AMR 基因(aac(6')-aph(2″)、erm(B)_18)。四环素抗性基因在 ST11 基因组中被预测得最多。在 22 个非致毒菌株中,有 9 个基因组(ST48 = 5、ST3 = 2、ST109 = 1、ST15 = 1)至少含有一个 AMR 基因。泛基因组分析表明,Bpan 值为 0.12,表明艰难梭菌具有开放的泛基因组结构。这表明该生物可通过增加新基因而进化。本研究报告了临床上重要的 ST11 菌株和耐多药的非致毒菌株在动物中的流通情况:在线版本包含补充材料,可查阅 10.1007/s13205-024-04102-7。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
Comparative genomics of zoonotic pathogen Clostridioides difficile of animal origin to understand its diversity.

Clostridioides difficile, a zoonotic pathogen causing enteric diseases in different animals and humans. A comprehensive study on the presence of toxin genes and antimicrobial resistance genes based on genome data of C. difficile in animals is scanty. In the present study, a total of 15 C. difficile isolates were recovered from dogs and isolates with toxin genes (D1, CD15 and CD26) along with two other non-toxigenic strains (CD28, CD32) were used for whole genome sequencing and comparative genomics. Sequence type-based clustering was noted in the whole genome phylogeny with 4 known multi-locus sequence typing (MLST) clades namely I, II, IV, and V and a cryptic clade. ST11 and ST54 were reported for the 2nd time worldwide in dogs. Out of 109 genomes used in the study, 29 genomes were predicted with all four toxin genes (toxA, toxB, cdtA, cdtB) while 22 did not have any of the toxin genes. ST11 of MLST clade V had the maximum number of 46 genomes predicted with at least one toxin gene. Among the genomes sequenced in this study, CD26 had a maximum of 5 AMR genes (aac(6')-aph(2″), ant(6)-Ia, catP, erm(B)_18, and tet(M)_11) and CD15 was predicted with 2 AMR genes (aac(6')-aph(2″), erm(B)_18). Tetracycline resistance genes were predicted most in the ST11 genome. Of the 22 non-toxigenic strains, 9 genomes (ST48 = 5, ST3 = 2, ST109 = 1, ST15 = 1) were predicted with a minimum of one AMR gene. Pangenome analysis indicated that the Bpan value is 0.12 showing that C. difficile has an open pangenome structure. This indicates that the organism can evolve by the addition of new genes. This study reports the circulation of clinically important ST11 and multidrug-resistant non-toxigenic strains among animals.

Supplementary information: The online version contains supplementary material available at 10.1007/s13205-024-04102-7.

求助全文
通过发布文献求助,成功后即可免费获取论文全文。 去求助
来源期刊
3 Biotech
3 Biotech Agricultural and Biological Sciences-Agricultural and Biological Sciences (miscellaneous)
CiteScore
6.00
自引率
0.00%
发文量
314
期刊介绍: 3 Biotech publishes the results of the latest research related to the study and application of biotechnology to: - Medicine and Biomedical Sciences - Agriculture - The Environment The focus on these three technology sectors recognizes that complete Biotechnology applications often require a combination of techniques. 3 Biotech not only presents the latest developments in biotechnology but also addresses the problems and benefits of integrating a variety of techniques for a particular application. 3 Biotech will appeal to scientists and engineers in both academia and industry focused on the safe and efficient application of Biotechnology to Medicine, Agriculture and the Environment.
期刊最新文献
Antidiabetic, anti-inflammatory, antioxidant, and cytotoxicity potentials of green-synthesized zinc oxide nanoparticles using the aqueous extract of Helichrysum cymosum. Bioinformatics analysis and experimental validation of the oncogenic role of COL11A1 in pan-cancer. Nanomaterial-enabled drug transport systems: a comprehensive exploration of current developments and future avenues in therapeutic delivery. Comparative genomics of zoonotic pathogen Clostridioides difficile of animal origin to understand its diversity. Discovery and characterization of novel lipopeptides produced by Virgibacillus massiliensis with biosurfactant and antimicrobial activities.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1