Multidrug resistance in a clinical B. fragilis strain was examined by whole-genome sequencing.
Strain CNM20200260 carried the antimicrobial resistance genes cepA, cfiA2, ant(6\'), erm(F), mef(En2), est(T), tet(Q) and cat(A), along with 82-Phe mutation in gyrA (together with 47 amino acid changes in gyrA/B and parC/parE). bexA/B and other efflux pump genes were also observed. None of the detected insertion sequences was located upstream of cfiA2. The genome-based taxonomy coefficients (average nucleotide identity, DNA-DNA hybridization similarity and difference in genomic G + C%) with respect to genomes of the strains of B. fragilis division II and the novel species Bacteroides hominis (both cfiA-positive) met the criteria for CNM20200260 to belong to either species (>95%, >70% and <1%, respectively). No such similarity was seen with type strain NCTC 9343 or the representative genome FDAARGOS 1225 of B. fragilis (division I, cfiA-negative). Strain CNM20200260 harboured four out of nine Kyoto Encyclopedia of Genes and Genomes orthologues defined for division I and one of two defined for division II.
This is the first description of the co-occurrence of cepA and cfiA in a Bacteroides strain, confirming the complexity of the taxonomy of this species.
方法:通过全基因组测序检查了临床脆弱双歧杆菌菌株的多药耐药性。
结果:菌株CNM20200260携带抗菌药物耐药基因cepA,cfiA2,ant(6\'),erm(F),MEF(En2),est(T),tet(Q)和cat(A),以及gyrA中的82-Phe突变(以及gyrA/B和parC/parE中的47个氨基酸变化)。还观察到bexA/B和其他外排泵基因。没有检测到的插入序列位于cfiA2的上游。基于基因组的分类系数(平均核苷酸同一性,基因组GC%的DNA-DNA杂交相似性和差异)与脆弱芽孢杆菌II和新物种人形拟杆菌(均为cfiA阳性)的基因组符合CNM20200260属于任一物种的标准(>95%,>70%和<1%,分别)。与类型菌株NCTC9343或脆弱芽孢杆菌的代表性基因组FDAARGOS1225没有看到这种相似性(划分I,CFIA阴性)。菌株CNM20200260包含9个京都基因和基因组百科全书中的4个,定义为第I部分,定义为第II部分。
结论:这是对拟杆菌菌株中cepA和cfiA共现的首次描述,证实了该物种分类的复杂性。