Tagini Florian, Pillonel Trestan, Croxatto Antony, Bertelli Claire, Koutsokera Angela, Lovis Alban, Greub Gilbert
Institute of Microbiology, Department of Laboratory Medicine, Lausanne University Hospital, Lausanne University, Lausanne, Switzerland.
Division of Pulmonology, Department of Medicine, Lausanne University Hospital, Lausanne, Switzerland.
Front Microbiol. 2018 Aug 17;9:1743. doi: 10.3389/fmicb.2018.01743. eCollection 2018.
is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic infections. Here, a strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel with PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of revealed that the strains CHUV2995, CCUG 5865 and CMCNS703 share a lower average nucleotide identity (ANI) (95.24 to 95.39%) with the NCTC 11397 reference genome than all other genomes (>98.15%). Core genome phylogeny confirmed the presence of two monophyletic clades. Based on these findings, we propose here two new subspecies to replace the lineage denomination used in previous multilocus sequence typing studies: subsp. subsp. nov. (instead of lineage-2), regrouping strains CHUV2995, CCUG 5865, and CMCNS703, and subsp. subsp. nov, regrouping all other in the dataset (instead of lineage-1). Interestingly, members of subspecies displayed a larger genome size than subspecies and were enriched in COG categories related to transport and metabolism of lipids (I) and inorganic ion (P). Conversely, they lacked all genes involved in the synthesis of pili (SpaA-type, SpaD-type and SpaH-type), molybdenum cofactor and of the nitrate reductase. Finally, the CHUV2995 genome is particularly enriched in mobility genes and harbors several prophages. The genome encodes a type II-C CRISPR-Cas locus with 2 spacers that lacks or , which could hamper the acquisition of new spacers and render strain CHUV2995 more susceptible to bacteriophage infections and gene acquisition through various mechanisms of horizontal gene transfer.
是白喉的病原体，白喉是一种由白喉毒素引起的疾病。然而，越来越多的记录报道了非产毒感染。在此，从一名有支气管扩张病史的患者中分离出一株菌株，该患者发展为严重的气管支气管炎，远端气管和主支气管出现多个白色病变。与靶向毒素基因的PCR和Elek试验并行进行的全基因组测序（WGS）在短时间内提供了临床相关结果，表明该分离株不产毒。对新菌株（CHUV2995）与其他56个公开可用的基因组进行比较基因组分析发现，与NCTC 11397参考基因组相比，菌株CHUV2995、CCUG 5865和CMCNS703的平均核苷酸同一性（ANI）较低（95.24%至95.39%），而所有其他基因组的ANI均大于98.15%。核心基因组系统发育证实存在两个单系分支。基于这些发现，我们在此提出两个新的亚种，以取代先前多位点序列分型研究中使用的谱系命名：亚种subsp. nov.（取代谱系2），将菌株CHUV2995、CCUG 5865和CMCNS703归为一组；亚种subsp. nov，将数据集中的所有其他菌株归为一组（取代谱系1）。有趣的是，亚种的成员显示出比亚种更大的基因组大小，并且在与脂质（I）和无机离子（P）的运输和代谢相关的COG类别中富集。相反，它们缺乏所有参与菌毛（SpaA型、SpaD型和SpaH型）、钼辅因子和硝酸盐还原酶合成的基因。最后，CHUV2995基因组特别富含移动基因，并含有多个前噬菌体。该基因组编码一个具有2个间隔区的II-C型CRISPR-Cas位点，该位点缺乏或，这可能会阻碍新间隔区的获得，并使菌株CHUV2995更容易受到噬菌体感染以及通过各种水平基因转移机制获得基因。
