Abstract：
Bacteroides fragilis, an anaerobic gut bacterium and opportunistic pathogen, comprises two genetically divergent groups (or divisions) at the species level. Differences exist both in the core and accessory genomes and the beta-lactamase genes, with the cephalosporinase gene cepA represented only in division I and the carbapenemase gene cfiA only in division II.
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.
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.
摘要：
背景：脆弱拟杆菌，厌氧肠道细菌和机会病原体，在物种水平上包括两个遗传上不同的群体（或分裂）。核心和辅助基因组以及β-内酰胺酶基因都存在差异，头孢菌素酶基因cepA仅在第I部分中代表，碳青霉烯酶基因cfiA仅在第II部分中代表。
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。
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。
