生物技术通报 ›› 2023, Vol. 39 ›› Issue (12): 287-299.doi: 10.13560/j.cnki.biotech.bull.1985.2023-0578
吴莉丹1(), 冉雪琴2, 牛熙1, 黄世会2, 李升1, 王嘉福1()
收稿日期:
2023-06-16
出版日期:
2023-12-26
发布日期:
2024-01-11
通讯作者:
王嘉福,男,教授,研究方向:生物化学与分子生物学;E-mail: jfwang@gzu.edu.cn作者简介:
吴莉丹,女,硕士研究生,研究方向:微生物学;E-mail: 1848642537@qq.com
基金资助:
WU Li-dan1(), RAN Xue-qin2, NIU Xi1, HUANG Shi-hui2, LI Sheng1, WANG Jia-fu1()
Received:
2023-06-16
Published:
2023-12-26
Online:
2024-01-11
摘要:
不同菌株猪源致病性大肠杆菌的致病力有较大差异,通过着重研究菌株基因组中携带的毒力因子种类和数量,以解析猪源大肠杆菌致病的分子机制。利用二代高通量DNA测序技术测定猪源致病性大肠杆菌的基因组DNA序列,通过生物信息学方法,分析不同毒力菌株的基因组结构特征、进化类型、携带的毒力因子基因及其碱基变异,采用PCR方法对候选毒力因子基因进行验证。猪源致病性大肠杆菌不同毒力菌株的基因组全长范围为4.62-5.3 Mb,含有3 364-3 557个编码基因,菌株的系统进化群和多位点序列分型多属于A群和ST10克隆复合群。6株菌携带112-280个毒力因子基因,强毒菌株的毒力因子基因尤其是毒素基因多于弱毒菌株,且各菌株分泌系统基因的数量变异较大。此外,毒力因子基因中检测到插入缺失、移码突变和无义突变等高影响碱基变异。采用PCR验证了代表性毒力因子基因及其变异。猪源致病性大肠杆菌的毒力与基因组长度、编码基因的数量和变异相关,与GC含量、前噬菌体和CRISPR序列没有必然联系。
吴莉丹, 冉雪琴, 牛熙, 黄世会, 李升, 王嘉福. 猪源致病性大肠杆菌基因组比较与毒力因子分析[J]. 生物技术通报, 2023, 39(12): 287-299.
WU Li-dan, RAN Xue-qin, NIU Xi, HUANG Shi-hui, LI Sheng, WANG Jia-fu. Genome Comparison and Virulence Factor Analysis of Pathogenic Escherichia coli from Porcine[J]. Biotechnology Bulletin, 2023, 39(12): 287-299.
基因类型 Gene type | 检测基因 Gene | 引物序列 Primer sequence(5'-3') | 退火温度 Annealing temperature/℃ | 产物长度 Product size/bp |
---|---|---|---|---|
二型分泌系统 Type II secretory system | gspD | F:TGGTGAAGGCAGCGACAACT | 65 | 273 |
R:TCCGAAGCAGAGGCGTTATCC | ||||
etpD | F:GCCAGACTTGTTACGGAACTGA | 62 | 421 | |
R:GGACCTGAGGACGACGAATATC | ||||
gspE | F:TGCTGCGACTGCTGGACAA | 65 | 334 | |
R:TCACCGACCATCACCACATCC | ||||
三型分泌系统 Type III secretory system | eae | F:ACCAGGCTTCGTCACAGTTG | 63 | 573 |
R:CCATCGTCACCAGAGGAATCG | ||||
eprK | F:TGAGCAGCGGTTAGAGCAATC | 62 | 370 | |
R:CTTCCATAACAGCCAGCAAGTC | ||||
eivF | F:TTGCTGATGCCTTGCCCTTT | 62 | 377 | |
R:GTGTGATGAGGACGAGTAACCA | ||||
espX1 | F:GGTATCTCAACTTCGCCACATT | 59 | 323 | |
R:ACATTCGCTTGTTCTGTCATCA | ||||
espO1-2 | F:TTTCAGGACACACTTGGCATCA | 62 | 213 | |
R:TTGACATCCATGCGACTTCTGA | ||||
六型分泌系统 Type VI secretory system | aec16 | F:AATGCTGCCAACCACTGAACTT | 63 | 218 |
R:CGGAGGTGCCAGATTTGACG | ||||
hcp1 | F:TTGCTCAACGCTTGATTCTGTC | 61 | 336 | |
R:CTCTCCTGTGGTTCCAGTTCTT | ||||
耐热肠毒素类似物 Heat-stabile enterotoxin analogues | east1 | F:TGCCATCAACACAGTATATCCG | 60 | 95 |
R:TGTAGTCCTTCCATGACACGAA | ||||
溶血素Hemolysin | hlyA | F:CAGTGACGCACATACAGGAACA | 62 | 362 |
R:CCGCAGATACAGAACTCAGGAC | ||||
铁载体转运系统 Ferric transport system | sitA | F:GCACAACTGATTCTCGCCAATG | 62 | 345 |
R:GGTGACCATCCATCGCTGATT | ||||
菌毛Pilus | cfaB | F:AGGCTCCGCATTGGCAGTA | 63 | 233 |
R:CATCCAGGCTTTGAACCAGTTG | ||||
黏附素Adhesin | eaeH | F:TGTTCCGCAAGACACTAATGGT | 63 | 400 |
R:CGCCGTAGAGCCGAGAGTAA | ||||
aatB | F:GAATGCAGAGCAAGCGTTCAAT | 63 | 402 | |
R:GCCGACTTTAGCCCTCCCATA | ||||
ehaA | F:TGACAGACACGCCATCCATACT | 64 | 241 | |
R:CAGCCGCAAGCACAGGTTAC | ||||
ehaB | F:CGGCATCATGGTCGGTGTT | 59 | 213 | |
R:AGGTCGTTGTTGAAGTGAGAGT | ||||
志贺样毒素 Shiga-toxin | stxB | F:CGACGCCTGATTGTGTAACTG | 61 | 131 |
R:CGCACTGAGAAGAAGAGACTGA | ||||
stx2A | F:TCCATGACAACGGACAGCAG | 62 | 191 | |
R:CGTAAGGCTTCTGCTGTGAC | ||||
耐热肠毒素 Heat-stabile enterotoxin | st | F:TTTCACCTTTCGCTCAGGATG | 60 | 165 |
R:CGGTACAAGCAGGATTACAACA | ||||
热敏肠毒素 Heat-labile enterotoxin | lt | F:CGGGACTTCGACCTGAAATGTT | 62 | 472 |
R:CGGCAGAGGATGGTTACAGATT | ||||
ltB | F:GCTCCCCAGACTATTACAG | 53 | 312 | |
R:CTAGTTTTTCATACTGATTGC | ||||
具有高影响变异的毒力因子基因Virulence factor genes with high impact variation | espY1 | F:CTGGCGGTCACTTCTTTGAG | 59 | 1 116 |
R:TTGTGAAATCATCCCACGCT | ||||
espL4 | F1:CTTTTACGGCTGCATTATGAGA | 58 | 1 980 | |
R1:ATTATTTGCCAGGAGGAGGG | ||||
F2:CTGAACGCCTTACCTAAACTGG | 60 | 909 | ||
R2:GCGCACTACAAAACCGCATA | ||||
espX4 | F:CAGCAGTGTAAAAGGCAAGGG | 59 | 1 957 | |
R:CAACAATCGCATGAAGTGGTAA | ||||
fimD | F1:CTCCAATGGGCGAAAGCA | 62 | 1 281 | |
R1:GCGGGACTGACGAATAGGGT | ||||
F2:CGTGGTACTGCACAGGTCACT | 59 | 1 960 | ||
R2:GTGACAGCAAAATACGAAATGG | ||||
fimI | F:CTAATGCGGATGCGACCTT | 60 | 740 | |
R:ACTGCCAGCAAGCAGAATGT | ||||
rpoS | F:ACCCGCTGCGTTATTTGC | 63 | 1 308 | |
R:CAGGGTTCTGGATTGTGACCAA | ||||
allB | F:GTTTGTCGGCGTCATCGTC | 59 | 1 723 | |
R:AAAGCATATTGCGTGAGCGT |
表1 毒力因子基因检测引物
Table 1 Primers for the detection of virulence factor genes
基因类型 Gene type | 检测基因 Gene | 引物序列 Primer sequence(5'-3') | 退火温度 Annealing temperature/℃ | 产物长度 Product size/bp |
---|---|---|---|---|
二型分泌系统 Type II secretory system | gspD | F:TGGTGAAGGCAGCGACAACT | 65 | 273 |
R:TCCGAAGCAGAGGCGTTATCC | ||||
etpD | F:GCCAGACTTGTTACGGAACTGA | 62 | 421 | |
R:GGACCTGAGGACGACGAATATC | ||||
gspE | F:TGCTGCGACTGCTGGACAA | 65 | 334 | |
R:TCACCGACCATCACCACATCC | ||||
三型分泌系统 Type III secretory system | eae | F:ACCAGGCTTCGTCACAGTTG | 63 | 573 |
R:CCATCGTCACCAGAGGAATCG | ||||
eprK | F:TGAGCAGCGGTTAGAGCAATC | 62 | 370 | |
R:CTTCCATAACAGCCAGCAAGTC | ||||
eivF | F:TTGCTGATGCCTTGCCCTTT | 62 | 377 | |
R:GTGTGATGAGGACGAGTAACCA | ||||
espX1 | F:GGTATCTCAACTTCGCCACATT | 59 | 323 | |
R:ACATTCGCTTGTTCTGTCATCA | ||||
espO1-2 | F:TTTCAGGACACACTTGGCATCA | 62 | 213 | |
R:TTGACATCCATGCGACTTCTGA | ||||
六型分泌系统 Type VI secretory system | aec16 | F:AATGCTGCCAACCACTGAACTT | 63 | 218 |
R:CGGAGGTGCCAGATTTGACG | ||||
hcp1 | F:TTGCTCAACGCTTGATTCTGTC | 61 | 336 | |
R:CTCTCCTGTGGTTCCAGTTCTT | ||||
耐热肠毒素类似物 Heat-stabile enterotoxin analogues | east1 | F:TGCCATCAACACAGTATATCCG | 60 | 95 |
R:TGTAGTCCTTCCATGACACGAA | ||||
溶血素Hemolysin | hlyA | F:CAGTGACGCACATACAGGAACA | 62 | 362 |
R:CCGCAGATACAGAACTCAGGAC | ||||
铁载体转运系统 Ferric transport system | sitA | F:GCACAACTGATTCTCGCCAATG | 62 | 345 |
R:GGTGACCATCCATCGCTGATT | ||||
菌毛Pilus | cfaB | F:AGGCTCCGCATTGGCAGTA | 63 | 233 |
R:CATCCAGGCTTTGAACCAGTTG | ||||
黏附素Adhesin | eaeH | F:TGTTCCGCAAGACACTAATGGT | 63 | 400 |
R:CGCCGTAGAGCCGAGAGTAA | ||||
aatB | F:GAATGCAGAGCAAGCGTTCAAT | 63 | 402 | |
R:GCCGACTTTAGCCCTCCCATA | ||||
ehaA | F:TGACAGACACGCCATCCATACT | 64 | 241 | |
R:CAGCCGCAAGCACAGGTTAC | ||||
ehaB | F:CGGCATCATGGTCGGTGTT | 59 | 213 | |
R:AGGTCGTTGTTGAAGTGAGAGT | ||||
志贺样毒素 Shiga-toxin | stxB | F:CGACGCCTGATTGTGTAACTG | 61 | 131 |
R:CGCACTGAGAAGAAGAGACTGA | ||||
stx2A | F:TCCATGACAACGGACAGCAG | 62 | 191 | |
R:CGTAAGGCTTCTGCTGTGAC | ||||
耐热肠毒素 Heat-stabile enterotoxin | st | F:TTTCACCTTTCGCTCAGGATG | 60 | 165 |
R:CGGTACAAGCAGGATTACAACA | ||||
热敏肠毒素 Heat-labile enterotoxin | lt | F:CGGGACTTCGACCTGAAATGTT | 62 | 472 |
R:CGGCAGAGGATGGTTACAGATT | ||||
ltB | F:GCTCCCCAGACTATTACAG | 53 | 312 | |
R:CTAGTTTTTCATACTGATTGC | ||||
具有高影响变异的毒力因子基因Virulence factor genes with high impact variation | espY1 | F:CTGGCGGTCACTTCTTTGAG | 59 | 1 116 |
R:TTGTGAAATCATCCCACGCT | ||||
espL4 | F1:CTTTTACGGCTGCATTATGAGA | 58 | 1 980 | |
R1:ATTATTTGCCAGGAGGAGGG | ||||
F2:CTGAACGCCTTACCTAAACTGG | 60 | 909 | ||
R2:GCGCACTACAAAACCGCATA | ||||
espX4 | F:CAGCAGTGTAAAAGGCAAGGG | 59 | 1 957 | |
R:CAACAATCGCATGAAGTGGTAA | ||||
fimD | F1:CTCCAATGGGCGAAAGCA | 62 | 1 281 | |
R1:GCGGGACTGACGAATAGGGT | ||||
F2:CGTGGTACTGCACAGGTCACT | 59 | 1 960 | ||
R2:GTGACAGCAAAATACGAAATGG | ||||
fimI | F:CTAATGCGGATGCGACCTT | 60 | 740 | |
R:ACTGCCAGCAAGCAGAATGT | ||||
rpoS | F:ACCCGCTGCGTTATTTGC | 63 | 1 308 | |
R:CAGGGTTCTGGATTGTGACCAA | ||||
allB | F:GTTTGTCGGCGTCATCGTC | 59 | 1 723 | |
R:AAAGCATATTGCGTGAGCGT |
菌株名 Strain | Scaffolds数目 Number of scaffolds | 基因组总长度 Genomic length/Mb | GC含量 GC content/% | N50/kb | L50 | 对参考基因组的覆盖度 Genomic coverage/% | 重复序列占比 Duplication ratio/% |
---|---|---|---|---|---|---|---|
S10670 | 148 | 5.30 | 50.31 | 160.71 | 9 | 87.45 | 1 |
E24190 | 171 | 4.96 | 50.54 | 91.86 | 15 | 90.87 | 1.01 |
P555 | 113 | 4.84 | 50.70 | 125.71 | 13 | 91.55 | 1.01 |
P211 | 107 | 4.75 | 50.63 | 120.03 | 15 | 89.80 | 1 |
P32 | 191 | 4.99 | 50.33 | 158.35 | 10 | 91.98 | 1 |
P111 | 108 | 4.62 | 50.90 | 110.78 | 15 | 89.86 | 1 |
表2 菌株基因组组装质量分析
Table 2 Quality analysis of the assembly genomes in E. coli strains
菌株名 Strain | Scaffolds数目 Number of scaffolds | 基因组总长度 Genomic length/Mb | GC含量 GC content/% | N50/kb | L50 | 对参考基因组的覆盖度 Genomic coverage/% | 重复序列占比 Duplication ratio/% |
---|---|---|---|---|---|---|---|
S10670 | 148 | 5.30 | 50.31 | 160.71 | 9 | 87.45 | 1 |
E24190 | 171 | 4.96 | 50.54 | 91.86 | 15 | 90.87 | 1.01 |
P555 | 113 | 4.84 | 50.70 | 125.71 | 13 | 91.55 | 1.01 |
P211 | 107 | 4.75 | 50.63 | 120.03 | 15 | 89.80 | 1 |
P32 | 191 | 4.99 | 50.33 | 158.35 | 10 | 91.98 | 1 |
P111 | 108 | 4.62 | 50.90 | 110.78 | 15 | 89.86 | 1 |
菌株名 Strain | 编码基因数Number of encoded genes | CDS个数Number of CDS | GC含量 GC content/% | tRNA数目Nu-mber og tRNAs | rRNA数目Nu-mber of rRNAs | 前噬菌体数目Nu-mber of prophages | CRISPR序列/可能存在的CRISPR序列数目Number of Crispr/PCrispr |
---|---|---|---|---|---|---|---|
K-12(Ref) | 3 459 | 4 305 | 51.86 | 88 | 22 | 2 | 2/3 |
S10670 | 3 519 | 5 040 | 51.37 | 96 | 9 | 3 | 1/4 |
E24190 | 3 497 | 4 732 | 51.63 | 85 | 11 | 0 | 2/6 |
P555 | 3 428 | 4 531 | 51.71 | 85 | 11 | 0 | 2/8 |
P211 | 3 434 | 4 483 | 51.70 | 83 | 11 | 2 | 4/4 |
P32 | 3 557 | 4 837 | 51.39 | 98 | 14 | 2 | 1/4 |
P111 | 3 364 | 4 308 | 51.93 | 85 | 12 | 1 | 3/8 |
表3 基因组注释分析
Table 3 Genome annotation
菌株名 Strain | 编码基因数Number of encoded genes | CDS个数Number of CDS | GC含量 GC content/% | tRNA数目Nu-mber og tRNAs | rRNA数目Nu-mber of rRNAs | 前噬菌体数目Nu-mber of prophages | CRISPR序列/可能存在的CRISPR序列数目Number of Crispr/PCrispr |
---|---|---|---|---|---|---|---|
K-12(Ref) | 3 459 | 4 305 | 51.86 | 88 | 22 | 2 | 2/3 |
S10670 | 3 519 | 5 040 | 51.37 | 96 | 9 | 3 | 1/4 |
E24190 | 3 497 | 4 732 | 51.63 | 85 | 11 | 0 | 2/6 |
P555 | 3 428 | 4 531 | 51.71 | 85 | 11 | 0 | 2/8 |
P211 | 3 434 | 4 483 | 51.70 | 83 | 11 | 2 | 4/4 |
P32 | 3 557 | 4 837 | 51.39 | 98 | 14 | 2 | 1/4 |
P111 | 3 364 | 4 308 | 51.93 | 85 | 12 | 1 | 3/8 |
菌株 Strain | MLST分型 MLST typing | 系统进化群 Phylogenetic group | 血清型 Serotype |
---|---|---|---|
K-12(Ref) | ST10(ST10 Cplx) | A | O16∶H48 |
S10670 | ST11(ST11 Cplx) | D | O157∶H7 |
E24190 | ST4(ST10 Cplx) | A | O6∶H16 |
P555 | ST209(ST10 Cplx) | A | H4 |
P211 | 新类型 | A | O4∶H45 |
P32 | ST34(ST10 Cplx) | A | O9∶H4 |
P111 | ST542 | A | O26∶H30 |
表4 系统进化群、血清型及MLST分型
Table 4 Phylogenetic groups, serotypes and MLST typing
菌株 Strain | MLST分型 MLST typing | 系统进化群 Phylogenetic group | 血清型 Serotype |
---|---|---|---|
K-12(Ref) | ST10(ST10 Cplx) | A | O16∶H48 |
S10670 | ST11(ST11 Cplx) | D | O157∶H7 |
E24190 | ST4(ST10 Cplx) | A | O6∶H16 |
P555 | ST209(ST10 Cplx) | A | H4 |
P211 | 新类型 | A | O4∶H45 |
P32 | ST34(ST10 Cplx) | A | O9∶H4 |
P111 | ST542 | A | O26∶H30 |
菌株Strain | 分泌系统Secretory system | 毒素Toxin | 鞭毛Flagellum | 铁摄取Iron uptake | 生物膜Biofilm | 其他Other | 合计Total |
---|---|---|---|---|---|---|---|
K-12(Ref) | 16 | 1 | 86 | 15 | 3 | 6 | 127 |
S10670 | 140 | 12 | 92 | 25 | 1 | 10 | 280 |
E24190 | 27 | 5 | 109 | 15 | 5 | 9 | 170 |
P555 | 26 | 1 | 85 | 15 | 1 | 6 | 134 |
P211 | 24 | 1 | 96 | 20 | 14 | 6 | 161 |
P32 | 38 | 1 | 86 | 15 | 3 | 6 | 149 |
P111 | 7 | 1 | 80 | 15 | 3 | 6 | 112 |
表5 菌株基因组中毒力因子分析
Table 5 Virulence factors in genomes of strains
菌株Strain | 分泌系统Secretory system | 毒素Toxin | 鞭毛Flagellum | 铁摄取Iron uptake | 生物膜Biofilm | 其他Other | 合计Total |
---|---|---|---|---|---|---|---|
K-12(Ref) | 16 | 1 | 86 | 15 | 3 | 6 | 127 |
S10670 | 140 | 12 | 92 | 25 | 1 | 10 | 280 |
E24190 | 27 | 5 | 109 | 15 | 5 | 9 | 170 |
P555 | 26 | 1 | 85 | 15 | 1 | 6 | 134 |
P211 | 24 | 1 | 96 | 20 | 14 | 6 | 161 |
P32 | 38 | 1 | 86 | 15 | 3 | 6 | 149 |
P111 | 7 | 1 | 80 | 15 | 3 | 6 | 112 |
图1 六株菌的分泌系统基因簇比较 A:二型分泌系统的基因分布;B:三型分泌系统二的基因分布;C:六型分泌系统的基因分布
Fig. 1 Comparison of the secretion system gene cluster from six strains A: Genes of T2SS. B: Genes of ETT2. C: Genes of T6SS
图2 23个毒力因子基因PCR扩增分析
Fig. 2 PCR amplification of 23 virulence factor genes A: S10670. B: E24190. C: P555. D: P211. E: P32. F: P111. 0: GN3K DNA marker; 1: gspD/etpD; 2: gspE; 3: eae; 4: eprK; 5: eivF; 6: espX1; 7: espO1-2; 8: aec16; 9: hcp1/tssD1; 10: east1; 11: hlyA; 12: sitA; 13 : cfaB; 14: eaeH; 15: aatB; 16: ehaA; 17: ehaB; 18: stxB; 19: stx2A; 20: st; 21: lt; 22: ltB
基因Gene | S10670 | E24190 | P555 | P211 | P32 | P111 |
---|---|---|---|---|---|---|
etpD | + | . | . | . | . | . |
gspD | . | + | . | . | . | . |
gspE | . | + | . | . | + | . |
eae | + | . | . | . | . | . |
eprK | + | . | . | + | + | . |
eivF | + | . | . | . | . | . |
espX1 | + | + | + | + | . | + |
espO1-2 | + | . | . | . | . | . |
aec16 | + | . | + | . | . | . |
hcp1/tssD1 | . | + | + | . | + | . |
east1 | . | + | . | . | . | . |
hlyA | + | . | . | . | . | . |
sitA | . | . | . | + | . | . |
cfaB | . | . | . | + | . | . |
eaeH | + | + | + | . | + | . |
aatB | . | + | . | . | . | . |
ehaA | + | . | . | . | . | . |
ehaB | + | + | + | + | + | + |
stx2A | + | . | . | . | . | . |
stxB | + | . | . | . | . | . |
ST | . | + | . | . | . | . |
LT | . | + | . | . | . | . |
LTB | . | + | . | . | . | . |
表6 23个毒力因子基因验证汇总分析
Table 6 Summary of 23 validated virulence factor genes
基因Gene | S10670 | E24190 | P555 | P211 | P32 | P111 |
---|---|---|---|---|---|---|
etpD | + | . | . | . | . | . |
gspD | . | + | . | . | . | . |
gspE | . | + | . | . | + | . |
eae | + | . | . | . | . | . |
eprK | + | . | . | + | + | . |
eivF | + | . | . | . | . | . |
espX1 | + | + | + | + | . | + |
espO1-2 | + | . | . | . | . | . |
aec16 | + | . | + | . | . | . |
hcp1/tssD1 | . | + | + | . | + | . |
east1 | . | + | . | . | . | . |
hlyA | + | . | . | . | . | . |
sitA | . | . | . | + | . | . |
cfaB | . | . | . | + | . | . |
eaeH | + | + | + | . | + | . |
aatB | . | + | . | . | . | . |
ehaA | + | . | . | . | . | . |
ehaB | + | + | + | + | + | + |
stx2A | + | . | . | . | . | . |
stxB | + | . | . | . | . | . |
ST | . | + | . | . | . | . |
LT | . | + | . | . | . | . |
LTB | . | + | . | . | . | . |
菌株 Strain | 变异类型 Types of variation | 变异影响 Effects of variation | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
单核核苷酸多态性SNP | 多核苷酸多态性MNP | 插入INS | 缺失DEL | 多核苷酸多态性和插入缺失MIXED | 高影响HIGH | 中度影响MODERATE | 低影响LOW | 调控 REGULATION | |||
S10670 | 47 276 | 8 026 | 180 | 202 | 195 | 293 | 8 809 | 41 164 | 574 640 | ||
E24190 | 16 584 | 2 577 | 73 | 94 | 45 | 101 | 3 272 | 14 025 | 202 712 | ||
P211 | 28 783 | 4 556 | 123 | 146 | 98 | 78 | 2 507 | 9 972 | 147 791 | ||
P555 | 11 690 | 2 196 | 52 | 60 | 58 | 130 | 5 503 | 24 572 | 352 584 | ||
P444 | 16 737 | 2 919 | 82 | 92 | 71 | 66 | 2 461 | 10 530 | 147 261 | ||
P32 | 12 133 | 2 225 | 54 | 56 | 44 | 81 | 3 488 | 14 268 | 204 157 | ||
P111 | 19 650 | 3 181 | 97 | 86 | 72 | 93 | 3 925 | 16 694 | 242 466 |
表7 各菌株的基因组变异位点
Table 7 Variation sites in the genome of each strain
菌株 Strain | 变异类型 Types of variation | 变异影响 Effects of variation | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
单核核苷酸多态性SNP | 多核苷酸多态性MNP | 插入INS | 缺失DEL | 多核苷酸多态性和插入缺失MIXED | 高影响HIGH | 中度影响MODERATE | 低影响LOW | 调控 REGULATION | |||
S10670 | 47 276 | 8 026 | 180 | 202 | 195 | 293 | 8 809 | 41 164 | 574 640 | ||
E24190 | 16 584 | 2 577 | 73 | 94 | 45 | 101 | 3 272 | 14 025 | 202 712 | ||
P211 | 28 783 | 4 556 | 123 | 146 | 98 | 78 | 2 507 | 9 972 | 147 791 | ||
P555 | 11 690 | 2 196 | 52 | 60 | 58 | 130 | 5 503 | 24 572 | 352 584 | ||
P444 | 16 737 | 2 919 | 82 | 92 | 71 | 66 | 2 461 | 10 530 | 147 261 | ||
P32 | 12 133 | 2 225 | 54 | 56 | 44 | 81 | 3 488 | 14 268 | 204 157 | ||
P111 | 19 650 | 3 181 | 97 | 86 | 72 | 93 | 3 925 | 16 694 | 242 466 |
基因Gene | 基因长度Total length/bp | 菌株Mutagenic bacteriaum | 位置Location | 突变类型Mutation type |
---|---|---|---|---|
espY1 | 651 | S10670、P555 | 579 | 移码突变(G--GG) |
espL4 | 2 187 | E24190、P211、P32、P111 P555 P111 | 1 140 564-1 352 654 | 缺失(612 bp), 非参考基因序列 插入(>900 bp) |
espX4 | 1 581 | S10670 P555 | 177、261 841 | 移码突变(G--GA)、移码突变(ATT--TA) 插入(>900 bp) |
fimD | 2 637 | E24190 | 1 971 | 无义突变(G--T) |
fimI | 540 | P32 | 470 | 移码突变(TG-T) |
allB | 1 362 | S10670 | 888 | 无义突变(G--T) |
rpoS | 993 | E24190 | 525-526 | 插入(771 bp) |
表8 七个具有高影响变异的毒力因子基因
Table 8 Seven virulence factor genes with high impact variants
基因Gene | 基因长度Total length/bp | 菌株Mutagenic bacteriaum | 位置Location | 突变类型Mutation type |
---|---|---|---|---|
espY1 | 651 | S10670、P555 | 579 | 移码突变(G--GG) |
espL4 | 2 187 | E24190、P211、P32、P111 P555 P111 | 1 140 564-1 352 654 | 缺失(612 bp), 非参考基因序列 插入(>900 bp) |
espX4 | 1 581 | S10670 P555 | 177、261 841 | 移码突变(G--GA)、移码突变(ATT--TA) 插入(>900 bp) |
fimD | 2 637 | E24190 | 1 971 | 无义突变(G--T) |
fimI | 540 | P32 | 470 | 移码突变(TG-T) |
allB | 1 362 | S10670 | 888 | 无义突变(G--T) |
rpoS | 993 | E24190 | 525-526 | 插入(771 bp) |
图3 毒力因子基因的高影响变异位点 A:espY1的移码突变;B:菌株E24190、P211、P32的espL4基因的缺失变异;C:菌株S10670的espX4基因移码突变;D:菌株E24190的FimD基因中的无义突变;E:菌株S10670的allB基因中的无义突变;F:菌株P32的FimI基因中的移码突变
Fig. 3 High-impact variant loci in virulence factor genes A: Frame-shift mutation in espY1. B: Variation sites of espL4 gene in E24190, P211, and P32 strains. C: Frame-shift mutation sites of espX4 gene in strain S10670. D: Nonsense mutation sites of the FimD gene in strain E24190. E: Nonsense mutation site of allB gene in strain S10670. F: Frame-shift mutation site of FimI gene in strain P32
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