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.

中文翻译：

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哥斯达黎加、智利、洪都拉斯和墨西哥艰难梭菌 B1/NAP1/RT027/ST01 菌株的起源、基因组多样性和微进化。


艰难梭菌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，并与严重的疾病表现和死亡率增加有关。流行性 B1/NAP1/RT027/ST01 菌株的两个耐氟喹诺酮 (FQR) 谱系于 20 世纪 90 年代初在美国出现并跨大陆传播（FQR1 和 FQR2）。然而，目前尚不清楚它们何时何地进入拉丁美洲 (LA)，也不清楚来自 LA 的分离株与来自世界其他地区的 B1/NAP1/RT027/ST01 分离株相比是否表现出独特的基因组特征。为了回答第一个问题，我们比较了哥斯达黎加 ( n = 16)、智利 ( n = 5)、洪都拉斯 ( n = 3) 和墨西哥 ( n = 3) 的 25 个 NAP1、RT027 或 ST01 临床分离株的全基因组序列 (WGS)。 n =1) 使用贝叶斯系统发育组学对来自相同基因型的 129 个全球分离株进行全基因组测序。第二个问题是通过对 LA 分离株的突变数量和类型及其移动抗性组的详细分析得到解决的。来自洛杉矶的除两个 B1/NAP1/RT027/ST01 分离株外的所有菌株均属于 FQR2 谱系 ( n =23, 92%)，证实了其广泛分布。对由 154 个 WGS 组成的数据集的分析表明，B1/NAP1/RT027/ST01 菌株被从北美（两次）和欧洲（至少四次）引入 1998 年至 2005 年间分析的四个洛杉矶国家。这些事件发生在 FQR 谱系出现后不久，距离洛杉矶首次报告检测到 B1/NAP1/RT027/ST01 已有十多年。在所有检查的基因组中总共鉴定了 552 个 SNP（3.8-4.3 Mb) 与 R20291 参考基因组的成对比较。此外，成对 SNP 距离是迄今为止在该物种中确定的最小距离之一（0 至 55）。尽管基因组保守性很高，但在感染过程（即slpA ）或抗生素耐药性（即rpoB 、 fusA ）中发挥作用的基因中的 39 个独特 SNP (7 %) 使 LA 分离株脱颖而出。此外，来自智利、洪都拉斯和墨西哥的分离株的抗生素抗性基因（ARG， n = 4）是来自其他地区的相关分离株的两倍。他们独特的 ARG 组包括cfr样基因和tetM ，它们被发现是假定的移动遗传元件的一部分，其序列类似于未描述的整合和接合元件。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 分离株被多次独立引入 LA，并且 LA 分离株相当快速地积累了不同的突变和获得的 ARG。