PDF(Pubmed)
Abstract：
BACKGROUND: Plague, a zoonotic disease caused by Yersinia pestis, was responsible for 3 historical human pandemics that killed millions of people. It remains endemic in rodent populations in Africa, Asia, North America, and South America but human plague is rare in most of these locations. However, human plague is still highly prevalent in Madagascar, which typically records a significant part of all annual global cases. This has afforded an opportunity to study contemporary human plague in detail using various typing methods for Y. pestis.
OBJECTIVE: This review aims to summarize the methods that have been used to type Y. pestis in Madagascar along with the major discoveries that have been made using these approaches.
METHODS: Pubmed and Google Scholar were used to search for the keywords: \"typing Yersinia pestis Madagascar,\" \"evolution Yersinia pestis Madagascar,\" and \"diversity Yersinia pestis Madagascar.\" Eleven publications were relevant to our topic and further information was retrieved from references cited in those publications.
RESULTS: The history of Y. pestis typing in Madagascar can be divided in 2 periods: the pre-genomics and genomics eras. During the pre-genomics era, ribotyping, direct observation of plasmid content and plasmid restriction fragment length polymorphisms (RFLP) were employed but only revealed a limited amount of diversity among Malagasy Y. pestis strains. Extensive diversity only started to be revealed in the genomics era with the use of clustered regularly interspaced palindromic repeats (CRISPR), multiple-locus variable number tandem repeats (VNTR) analysis (MLVA), and single-nucleotide polymorphisms (SNPs) discovered from whole genome sequences. These higher-resolution genotyping methods have made it possible to highlight the distribution and persistence of genotypes in the different plague foci of Madagascar (Mahajanga and the Central and Northern Highlands) by genotyping strains from the same locations across years, to detect transfers between foci, to date the emergence of genotypes, and even to document the transmission of antimicrobial resistant (AMR) strains during a pneumonic plague outbreak. Despite these discoveries, there still remain topics that deserve to be explored, such as the contribution of horizontal gene transfer to the evolution of Malagasy Y. pestis strains and the evolutionary history of Y. pestis in Madagascar.
CONCLUSIONS: Genotyping of Y. pestis has yielded important insights on plague in Madagascar, particularly since the advent of whole-genome sequencing (WGS). These include a better understanding of plague persistence in the environment, antimicrobial AMR and multi-drug resistance in Y. pestis, and the person-to-person spread of pneumonic plague. Considering that human plague is still a significant public health threat in Madagascar, these insights can be useful for controlling and preventing human plague in Madagascar and elsewhere, and also are relevant for understanding the historical pandemics and the possible use of Y. pestis as a biological weapon.
OBJECTIVE: This review aims to summarize the methods that have been used to type Y. pestis in Madagascar along with the major discoveries that have been made using these approaches.
METHODS: Pubmed and Google Scholar were used to search for the keywords: \"typing Yersinia pestis Madagascar,\" \"evolution Yersinia pestis Madagascar,\" and \"diversity Yersinia pestis Madagascar.\" Eleven publications were relevant to our topic and further information was retrieved from references cited in those publications.
RESULTS: The history of Y. pestis typing in Madagascar can be divided in 2 periods: the pre-genomics and genomics eras. During the pre-genomics era, ribotyping, direct observation of plasmid content and plasmid restriction fragment length polymorphisms (RFLP) were employed but only revealed a limited amount of diversity among Malagasy Y. pestis strains. Extensive diversity only started to be revealed in the genomics era with the use of clustered regularly interspaced palindromic repeats (CRISPR), multiple-locus variable number tandem repeats (VNTR) analysis (MLVA), and single-nucleotide polymorphisms (SNPs) discovered from whole genome sequences. These higher-resolution genotyping methods have made it possible to highlight the distribution and persistence of genotypes in the different plague foci of Madagascar (Mahajanga and the Central and Northern Highlands) by genotyping strains from the same locations across years, to detect transfers between foci, to date the emergence of genotypes, and even to document the transmission of antimicrobial resistant (AMR) strains during a pneumonic plague outbreak. Despite these discoveries, there still remain topics that deserve to be explored, such as the contribution of horizontal gene transfer to the evolution of Malagasy Y. pestis strains and the evolutionary history of Y. pestis in Madagascar.
CONCLUSIONS: Genotyping of Y. pestis has yielded important insights on plague in Madagascar, particularly since the advent of whole-genome sequencing (WGS). These include a better understanding of plague persistence in the environment, antimicrobial AMR and multi-drug resistance in Y. pestis, and the person-to-person spread of pneumonic plague. Considering that human plague is still a significant public health threat in Madagascar, these insights can be useful for controlling and preventing human plague in Madagascar and elsewhere, and also are relevant for understanding the historical pandemics and the possible use of Y. pestis as a biological weapon.
摘要：
背景：瘟疫，由鼠疫耶尔森氏菌引起的人畜共患疾病，造成3次历史人类大流行，导致数百万人死亡。它仍然是非洲啮齿动物种群的地方性疾病，亚洲,北美,和南美，但人类瘟疫在大多数这些地方很少见。然而,人类鼠疫在马达加斯加仍然非常普遍，通常记录所有年度全球病例的重要部分。这为使用鼠疫耶尔森氏菌的各种分型方法详细研究当代人类鼠疫提供了机会。
目的：这篇综述旨在总结马达加斯加鼠疫耶尔森氏菌的分型方法，以及使用这些方法取得的主要发现。
方法：使用Pubmed和GoogleScholar搜索关键字：\"键入鼠疫耶尔森氏菌马达加斯加，\“\”进化鼠疫耶尔森氏菌马达加斯加，“和”多样性鼠疫耶尔森氏菌马达加斯加。“有11份出版物与我们的主题有关，并从这些出版物中引用的参考文献中检索了更多信息。
结果：马达加斯加鼠疫耶尔森氏菌分型的历史可以分为两个时期：前基因组学和基因组学时代。在前基因组学时代，核糖分型,直接观察质粒含量和质粒限制性片段长度多态性（RFLP），但仅揭示了马达加斯加鼠疫耶尔森氏菌菌株之间的多样性有限。广泛的多样性在基因组学时代才开始被揭示，使用成簇的规则间隔回文重复（CRISPR），多位点可变数量串联重复序列（VNTR）分析（MLVA），和从全基因组序列中发现的单核苷酸多态性（SNP）。这些更高分辨率的基因分型方法通过对来自同一地点的菌株进行基因分型，可以突出马达加斯加不同鼠疫疫源地（Mahajanga和中部和北部高地）的基因型分布和持久性。为了检测焦点之间的转移，迄今为止，基因型的出现，甚至在肺鼠疫爆发期间记录抗菌素耐药性（AMR）菌株的传播。尽管有这些发现,还有一些值得探讨的话题，例如水平基因转移对马达加斯加鼠疫耶尔森氏菌菌株的进化和马达加斯加鼠疫耶尔森氏菌的进化史的贡献。
结论：鼠疫耶尔森氏菌的基因分型对马达加斯加的鼠疫产生了重要的见解，特别是自从全基因组测序（WGS）的出现。这些包括更好地了解鼠疫在环境中的持久性，鼠疫耶尔森氏菌的抗菌AMR和多药耐药性，以及肺鼠疫的人际传播。考虑到人类鼠疫仍然是马达加斯加的重大公共卫生威胁，这些见解可用于控制和预防马达加斯加和其他地方的人类鼠疫，也与了解历史大流行和可能使用鼠疫杆菌作为生物武器有关。
目的：这篇综述旨在总结马达加斯加鼠疫耶尔森氏菌的分型方法，以及使用这些方法取得的主要发现。
方法：使用Pubmed和GoogleScholar搜索关键字：\"键入鼠疫耶尔森氏菌马达加斯加，\“\”进化鼠疫耶尔森氏菌马达加斯加，“和”多样性鼠疫耶尔森氏菌马达加斯加。“有11份出版物与我们的主题有关，并从这些出版物中引用的参考文献中检索了更多信息。
结果：马达加斯加鼠疫耶尔森氏菌分型的历史可以分为两个时期：前基因组学和基因组学时代。在前基因组学时代，核糖分型,直接观察质粒含量和质粒限制性片段长度多态性（RFLP），但仅揭示了马达加斯加鼠疫耶尔森氏菌菌株之间的多样性有限。广泛的多样性在基因组学时代才开始被揭示，使用成簇的规则间隔回文重复（CRISPR），多位点可变数量串联重复序列（VNTR）分析（MLVA），和从全基因组序列中发现的单核苷酸多态性（SNP）。这些更高分辨率的基因分型方法通过对来自同一地点的菌株进行基因分型，可以突出马达加斯加不同鼠疫疫源地（Mahajanga和中部和北部高地）的基因型分布和持久性。为了检测焦点之间的转移，迄今为止，基因型的出现，甚至在肺鼠疫爆发期间记录抗菌素耐药性（AMR）菌株的传播。尽管有这些发现,还有一些值得探讨的话题，例如水平基因转移对马达加斯加鼠疫耶尔森氏菌菌株的进化和马达加斯加鼠疫耶尔森氏菌的进化史的贡献。
结论：鼠疫耶尔森氏菌的基因分型对马达加斯加的鼠疫产生了重要的见解，特别是自从全基因组测序（WGS）的出现。这些包括更好地了解鼠疫在环境中的持久性，鼠疫耶尔森氏菌的抗菌AMR和多药耐药性，以及肺鼠疫的人际传播。考虑到人类鼠疫仍然是马达加斯加的重大公共卫生威胁，这些见解可用于控制和预防马达加斯加和其他地方的人类鼠疫，也与了解历史大流行和可能使用鼠疫杆菌作为生物武器有关。
