摘要

      难辨梭状芽孢杆菌B1/NAP1/RT027/ST01是全球临床环境中抗生素相关性腹泻暴发的罪魁祸首，与严重的疾病表现和死亡率增加有关。20世纪90年代初，美国出现了两个流行株B1/NAP1/RT027/ST01的抗氟喹诺酮（FQR）谱系，并在大陆上传播（FQR1和FQR2）。然而，目前尚不清楚它们何时何地进入拉丁美洲，以及与来自世界其他地区的B1/NAP1/RT027/ST01菌株相比，来自拉丁美洲的菌株是否具有独特的基因组特征。为了回答第一个问题，我们将哥斯达黎加（n=16）、智利（n=5）、洪都拉斯（n=3）和墨西哥（n=1）的25个NAP1、RT027或ST01临床分离株的全基因组序列（WGS）与来自同一基因型的129个全球分离株的WGS进行了贝叶斯系统基因组学比较。第二个问题是通过对LA分离株的突变数量和类型以及它们的移动抗性的详细分析来解决的。除2株B1/NAP1/RT027/ST01菌株外，其余菌株均属于FQR2家系（n=2392%），证实其广泛分布。通过对154个WGS组成的数据集的分析表明，B1/NAP1/RT027/ST01菌株在1998年至2005年间从北美（两次）和欧洲（至少四次）被引入了四个洛杉矶国家。这些事件发生在FQR谱系出现后不久，在洛杉矶发现B1/NAP1/RT027/ST01的第一次报告之前的十多年。在所有被检测的基因组（3.8-4.3mb）中，共鉴定出552个snp，与R20291参考基因组成对比较。此外，配对单核苷酸多态性距离是迄今为止在该物种中确定的最小距离（0至55）。尽管如此高水平的基因组保守性，39个独特的单核苷酸多态性（7%）在基因中发挥作用的感染过程（即slpA）或抗生素抗性（即rpoB，fusA）区分了LA分离株。此外，来自智利、洪都拉斯和墨西哥的分离株的抗生素耐药基因（ARGs，n=4）是其他地区相关分离株的两倍。他们独特的ARGs包括一个cfr样基因和tetM，这两个基因被发现是假定的可移动遗传元素的一部分，其序列类似于未描述的整合和结合元素。这些结果表明，来自不同地理来源的FQR1和FQR2谱系的B1/NAP1/RT027/ST01菌株在LA中有多个独立的导入，并且LA菌株很快积累了明显的突变和获得的ARG。

       Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s and disseminated trans continentally (FQR1 and FQR2). However, it is unclear when and from where they entered Latin America (LA) and whether isolates from LA exhibit unique genomic features when compared to B1/NAP1/RT027/ST01 isolates from other regions of the world. To answer the first issue we compared whole-genome sequences (WGS) of 25 clinical isolates typed as NAP1, RT027 or ST01 in Costa Rica (n=16), Chile (n=5), Honduras (n=3) and Mexico (n=1) to WGS of 129 global isolates from the same genotype using Bayesian phylogenomics. The second question was addressed through a detailed analysis of the number and type of mutations of the LA isolates and their mobile resistome. All but two B1/NAP1/RT027/ST01 isolates from LA belong to the FQR2 lineage (n=23, 92 %), confirming its widespread distribution. As indicated by analysis of a dataset composed of 154 WGS, the B1/NAP1/RT027/ST01 strain was introduced into the four LA countries analysed between 1998 and 2005 from North America (twice) and Europe (at least four times). These events occurred soon after the emergence of the FQR lineages and more than one decade before the first report of the detection of the B1/NAP1/RT027/ST01 in LA. A total of 552 SNPs were identified across all genomes examined (3.8-4.3 Mb) in pairwise comparisons to the R20291 reference genome. Moreover, pairwise SNP distances were among the smallest distances determined in this species so far (0 to 55). Despite this high level of genomic conservation, 39 unique SNPs (7 %) in genes that play roles in the infection process (i.e. slpA) or antibiotic resistance (i.e. rpoB, fusA) distinguished the LA isolates. In addition, isolates from Chile, Honduras and Mexico had twice as many antibiotic resistance genes (ARGs, n=4) than related isolates from other regions. Their unique set of ARGs includes a cfr-like gene and tetM, which were found as part of putative mobile genetic elements whose sequences resemble undescribed integrative and conjugative elements. These results show multiple, independent introductions of B1/NAP1/RT027/ST01 isolates from the FQR1 and FQR2 lineages from different geographical sources into LA and a rather rapid accumulation of distinct mutations and acquired ARG by the LA isolates.

      https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000355#tab2