Phylotypes and Pathotypes of Diarrheagenic <em>Escherichia coli</em> of Gastroenteritis

Hadi Sajid Abdulabbas; Noor Al-Khafaji; Suhad Y. Abed; Hussein Al-Dahmoshi; Huda Najh Al-Baroody

doi:10.5772/intechopen.109860

Abstract

Escherichia coli responsible for wide range of common bacterial infections, the frequent one is gastroenteritis. Bacterial gastroenteritis mainly attributed to diarrheagenic E. coli and accompanied by diarrhea and vomiting. Actually pathogenic E. coli can be classified according to the site of infection whether it be within intestine (called intestinal pathogenic E. coli InPEC) or cause infection outside intestine (called extraintestinal pathogenic E. coli ExPEC). They are assigned to 4 main phylogenetic groups: InPEC include A and B1 while ExPEC have B2 and D groups. Seven Pathotypes have been assigned: Enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enterohemorrhagic (Shiga-toxin producing E. coli (EHEC/STEC), enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), enteroinvasive E. coli (EIEC) and adherent invasive E. coli (AIEC). The patho-phylotyping of diarrheagenic E. coli interaction along with antibiotic resistance and biofilm formation capacity may be valuable insight to know real threat of this pathogen and this is tried to be covered with this chapter. The results revealed that the among DEC, EPEC and ETEC were assigned in high rate to B1 followed by A, B2, D, E, C and F while EAEC show different assignment: D followed by B2, A, B1, C, E and F. The other DEC pathotypes showed different styles.

Keywords

Pathotypes
phylotypes
E. coli
antibiotic resistance
biofilm
InPEC
ExPEC

Author Information

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Hadi Sajid Abdulabbas
- Faculty of Dentistry, University of Al-Ameed, Karbala, Iraq
Noor Al-Khafaji
- Biology Department, College of Science, University of Babylon, Hilla, Iraq
Suhad Y. Abed
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
Hussein Al-Dahmoshi*
- Biology Department, College of Science, University of Babylon, Hilla, Iraq
Huda Najh Al-Baroody
- Department of Microbiology, College of Medicine, University of Al-Ameed, Karbala, Iraq

*Address all correspondence to: dr.dahmoshi83@gmail.com

1. Introduction

Escherichia coli is commensal enterobacteial member emerging as opportunistic pathogen causing numerous of intestinal and extraintestinal infections. Concern Pathotypes of E. coli, they divided in to two main groups: Extraintestinal pathogenic E. coli (ExPEC) and intestinal pathogenic E. coli (InPEC). ExPEC cause range of infections for Human being outside intestine like meningitides as in neonatal meningitis E. coli (NMEC), urinary tract infection as in uropathogenic E. coli (UPEC) and sepsis-associated E. coli (SEPEC) [1, 2, 3]. InPEC includes 8 Pathotypes of diarrheagenic E. coli (DEC) including: enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enteroaggregative E. coli (EAEC), diffusely adherent E. coli (DAEC), enteroinvasive E. coli (EIEC), enterohemorrhagic E. coli (EHEC) (also known as Shiga-toxin-producing E. coli (STEC) or, verotoxin-producing E. coli (VTEC), necrotoxic E. coli (NTEC) and adherent-invasive E. coli (AIEC) [4, 5, 6]. Two systems named as Clermont triplex and quadruplex PCR were used to assign the E. coli isolates to seven phylogroups (A, B1, B2, C, D, E and F) and five clades (clade I, II, III, IV and V) according to presence/absence of six genes: chuA, yjaA, TspE4.C2, arpA, arpAgpEh and trpA(trpAgpC) as mentioned in Table 1 [7, 8, 9].

arpA	chuA	yjaA	TspE4.C2	arpAgpE	trpAgpC	Phylogroups and Clade
+	—	—	—	—	—	A (subgroup A0)
+	—	+	—	—	—	A (subgroup A1)
+	—	—	+	—	—	B1
—	+	+	—	—	—	B2(subgroup B2₂)
—	+	+	+	—	—	B2(subgroup B2₃)
+	—	+	—	—	+	C
+	+	—	—	—	—	D (subgroup D1)
+	+	—	+	—	—	D (subgroup D2)
+	+	—	+	+	—	E
+	+	—	+	+	—	E
—	+	—	—	—	—	F

Table 1.

Genotypic profile for 6 phylogenetic groups and 5 clades of E. coli.

2. Diarrheagenic E. coli (DEC) phylotypes

Diarrheagenic E. coli (DEC) is a term referring to 8 or 9 pathotypes of E. coli causing diarrhea in travelers. It accounting for up to 40% of infantile and children diarrhea worldwide [10] and responsible for most of diarrheal outbreaks globally [11]. All DEC Pathotypes categorized according to molecular contents of some virulence genes: eae and bfpA for EPEC [12]; st1a, st1b and ltb1 for ETEC; aggR for EAEC; stx1 and stx2 for EHEC/STEC; ipaH for EIEC; daaD for DAEC [13]. Many studies revealed that, the most prevalent diarrheagenic E. coli were ETEC, EPEC, EAEC, AIEC, EHEC/STEC and DAEC [14, 15, 16, 17]. Concern phylogroups of EPEC, the results gathered from 18 studies for 433 EPEC isolates revealed that: B1 compile (39.3%), A(23.3%), B2(18.2%), D(8.5%), (6.2%, 3.5% and 0.9%) for E, C and F phylogroups respectively (Table 2) [18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]. ETEC phylogroups includes: B1(43.3%), A(28.2%), D(14%), B2(13.4%), C(0.6%), E(0.6%) and F(0.0%) (Table 3) [18, 23, 24, 25, 27, 28, 30, 31, 33, 35, 36, 37]. Concern EAEC phylogroups the results showed that, among 399 EAEC isolates they assigned for D(32.8%), B2(30.5%)A(19.2), B1(16.2%), C(0.8%), E(0.5%) and F(0.0%) (Table 4) [18, 24, 25, 27, 28, 30, 31, 32, 35, 37, 38, 39, 40]. Table 5 showed the phylogroups of EIEC, EHEC/STEC, AIEC and DAEC pathotypes. EIEC phylogroups were A, B1, E, D, B2 and C compile (37.6%, 21.2%, 17.7%, 12.9%, 8.2% and 2.4% respectively). EHEC/STEC phylogroups were C, B1, B2, A, E, D and Fcompile (21.5%, 20.1, 18.7%, 16.2%, 13.4%, 7.7% and 2.4% respectively). AIEC phylogroups were B2, D, A and B1 compile (51.3%, 25.2%, 18.3% and 5.2% respectively) while DAEC phylogroups were A (5/11), B2(3/11) and B1(3/11) [18, 24, 25, 26, 27, 28, 33, 36, 37, 39, 40, 41, 43, 44, 45, 46, 47].

Total isolate no.	ExPEC group		InPEC group					Country	Ref.
Total isolate no.	B2	D	A	B1	C	E	F	Country	Ref.
5	1	0	1	1	1	1	0	South Africa	[18]
53	2	2	9	38	0	0	2	Mexico	[19]
56	25	4	11	12	2	1	1	India	[20]
51	9	2	2	13	8	17	0	Iran	[21]
42	2	6	2	32	0	0	0	Iran	[22]
26	1	4	8	13	0	0	0	Iran	[23]
10	6	0	3	1	0	0	0	Iran	[24]
3	1	0	2	0	0	0	0	Iran	[25]
4	0	0	0	4	0	0	0	Iran	[26]
9	7	0	2	0	0	0	0	Iran	[27]
4	0	0	0	4	0	0	0	Bangladesh	[28]
31	3	0	6	17	0	5	0	Brazil	[29]
25	1	0	18	6	0	0	0	Brazil	[30]
21	3	3	12	3	0	0	0	Brazil	[31]
30	12	5	13	0	0	0	0	Egypt	[32]
32	6	10	6	2	4	3	1	Egypt	[33]
26	0	1	5	20	0	0	0	Italy	[34]
5	0	0	1	4	0	0	0	Switzerland	[35]
Total(433)	79	37	101	170	15	27	4
%	18.2	8.5	23.3	39.3	3.5	6.2	0.9

Table 2.

ExPEC and InPEC phylogroups of EPEC isolates.

Total isolate no.	ExPEC group		InPEC group					Country	Ref.
Total isolate no.	B2	D	A	B1	C	E	F	Country	Ref.
18	4	1	1	8	2	2	0	South Africa	[18]
32	7	7	11	7	0	0	0	Iran	[36]
13	1	1	10	1	0	0	0	Iran	[23]
6	3	0	3	0	0	0	0	Iran	[24]
83	12	16	34	21	0	0	0	Iran	[25]
52	7	7	22	16	0	0	0	Iran	[27]
94	3	9	0	82	0	0	0	Bangladesh	[28]
9	0	4	3	2	0	0	0	Brazil	[30]
19	5	1	9	4	0	0	0	Brazil	[31]
9	3	2	0	4	0	0	0	Egypt	[33]
5	0	0	1	4	0	0	0	Switzerland	[35]
4	1	0	3	0	0	0	0	Mexico	[37]
Total(344)	46	48	97	149	2	2	0
%	13.4	14	28.2	43.3	0.6	0.6	0

Table 3.

ExPEC and InPEC phylogroups of ETEC isolates.

Total isolate no.	ExPEC group		InPEC group					Country	Ref.
Total isolate no.	B2	D	A	B1	C	E	F	Country	Ref.
31	9	4	3	10	3	2	0	South Africa	[18]
35	16	8	6	6	0	0	0	Iran	[24]
27	3	6	11	7	0	0	0	Iran	[25]
23	7	14	2	0	0	0	0	Iran	[27]
1	0	0	0	1	0	0	0	Bangladesh	[28]
14	3	0	6	5	0	0	0	Brazil	[30]
31	17	1	13	0	0	0	0	Egypt	[32]
27	0	9	17	1	0	0	0	Brazil	[31]
54	31	19	4	0	0	0	0	Brazil	[38]
8	0	4	3	1	0	0	0	Switzerland	[35]
1	1	0	0	0	0	0	0	Mexico	[37]
9	3	6	0	0	0	0	0	Tunisia	[39]
138	32	60	12	34	0	0	0	India	[40]
Total(399)	122	131	77	65	3	2	0
%	30.5	32.8	19.2	16.2	0.8	0.5	0

Table 4.

ExPEC and InPEC phylogroups of EAEC isolates.

EIEC
Total isolate no.	ExPEC group		InPEC group					Country	Ref.
Total isolate no.	B2	D	A	B1	C	E	F	Country	Ref.
6	0	3	1	2	0	0	0	Iran	[36]
51	1	0	25	9	1	15	0	Brazil	[41]
6	1	1	3	1	0	0	0	Iran	[24]
13	3	4	1	5	0	0	0	Iran	[25]
2	0	2	0	0	0	0	0	Iran	[27]
7	2	1	2	1	1	0	0	Egypt	[33]
Total (42)	7	11	32	18	2	15	0
%	8.2	12.9	37.6	21.2	2.4	17.7	0
EHEC/STEC
5	3	0	0	0	1	1	0	South Africa	[18]
21	2	4	0	15	0	0	0	Iran	[26]
10	1	1	0	8	0	0	0	Bangladesh	[28]
22	5	4	2	3	7	0	1	Egypt	[33]
6	0	0	6	0	0	0	0	Mexico	[37]
5	2	3	0	0	0	0	0	Tunisia	[39]
135	26	4	21	16	37	27	4	Iran	[43]
5	0	0	5	0	0	0	0	Brazil	[44]
Total(209)	39	16	34	42	45	28	5
%	18.7	7.7	16.2	20.1	21.5	13.4	2.4
AIEC
26	14	10	2	0	0	0	0	Spain	[45]
30	22	4	4	0	0	0	0	Spain	[46]
59	23	15	15	6	0	0	0	Korea	[47]
Total(115)	59	29	21	6	0	0	0
%	51.3	25.2	18.3	5.2	0	0	0
DAEC
11	3	0	5	3	0	0	0	Iran	[25]

Table 5.

ExPEC and InPEC phylogroups of EIEC, EHEC/STEC AIEC and DAEC isolates.

3. Uropathogenic E. coli (UPEC) phylotypes

Uropathogenic E. coli (UPEC) is the most common ExPEC causing UTI, one of the most frequent bacterial infections with significant morbidity worldwide, which may convey a sets of virulence factors and belonging to diverse phylogenetic groups [48]. UPEC as ExPEC must be belong to either B2 or D phylogroups. The B2 include 2 phylosubgroups: B2₂ (chuA+, yjaA+, TspE4.C2-, arpA-, arpAgpE-, TrpAgpC-) and B2₃ (chuA+, yjaA+, TspE4.C2+, arpA-, arpAgpE-, TrpAgpC-) while D have 2 phylosubgroups: D1 (chuA+, yjaA-, TspE4.C2-, arpA+, arpAgpE-, TrpAgpC-) and D2 (chuA+, yjaA-, TspE4.C2-, arpA+, arpAgpE-, TrpAgpC+) [49, 50].

Many Iraqi studies studied the assignment of UPEC to phylogroups. Since 2017–2022 only 11 Iraqi studies with valuable no. of UPEC isolates analyze 1119 isolates and assigning them to 7 phylogroups and they are found that: 566(50.6%) for B2, 241(21.5%) for D, 208(18.6%) for A, 60(5.4%) for B1, 23(2.1%) for C, 11(1%) for E and 10(0.8%) for F (Table 6) [51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61]. Concern Iranian studies, 19 study were conducted including 2313 UPEC isolates assigned to phylogroups as follow: 1190(51.4%) for B2, 481(20.8%) for D, 399(17.3%) for A, 190(8.2%) for B1, 26(1.1%) for C, 23(1%) for E and 4(0.2%) for F (Table 7) [25, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79]. Ten studies from Egypt deal with 892 UPEC isolates stated that, B2 compile (38.1%), D (15.2%), A (23.2%), B1 (14.3%), C (3.4%), E (2.8%) and F (2.9%) as mentioned in Table 8 [25, 42, 49, 54, 76, 80, 81, 82, 83, 84]. Nine Turkish studies showed that, among 901 isolated of UPEC, (39.3%) were B2, (31.5%) for D, (2.4%) for A, (6.4%) for B1, (0.1%) for C, (2.1%) for E and (0.1%) for F phylogroups (Table 9) [85, 86, 87, 88, 89, 90, 91, 92, 93].

Total isolate no.	ExPEC group		InPEC group					Ref.
Total isolate no.	B2	D	A	B1	C	E	F	Ref.
57	38	3	6	7	1	0	2	[51]
88	46	7	11	0	13	11	0	[52]
50	18	14	4	14	0	0	0	[53]
42	18	15	8	1	0	0	0	[54]
50	18	21	9	0	0	0	0	[55]
395	172	113	96	14	0	0	0	[56]
103	38	20	27	9	5	0	4	[57]
100	91	6	1	2	0	0	0	[58]
56	43	4	4	5	0	0	0	[59]
72	26	16	20	2	4	0	4	[60]
105	57	22	22	4	0	0	0	[61]
Total(1119)	566	241	208	60	23	11	10
%	50.6	21.5	18.6	5.4	2.1	1	0.8

Table 6.

Distribution of phylogenetic groups among UPEC isolates in Iraq.

Total isolate no.	ExPEC group		InPEC group					Ref.
Total isolate no.	B2	D	A	B1	C	E	F	Ref.
93	55	4	1	7	9	13	4	[62]
100	52	28	14	6	0	0	0	[63]
232	135	42	37	18	0	0	0	[64]
113	50	35	23	5	0	0	0	[65]
251	92	79	40	40	0	0	0	[66]
77	55	22	0	0	0	0	0	[67]
90	47	12	4	0	17	10	0	[68]
160	75	48	25	12	0	0	0	[69]
50	24	10	15	1	0	0	0	[70]
104	26	20	32	26	0	0	0	[25]
100	55	22	17	6	0	0	0	[71]
60	50	6	3	1	0	0	0	[72]
261	144	28	61	28	0	0	0	[73]
93	26	29	29	9	0	0	0	[74]
144	106	23	7	8	0	0	0	[75]
90	25	11	46	8	0	0	0	[76]
100	55	22	17	6	0	0	0	[77]
90	53	18	13	6	0	0	0	[78]
105	65	22	15	3	0	0	0	[79]
Total(2313)	1190	481	399	190	26	23	4
%	51.4	20.8	17.3	8.2	1.1	1	0.2

Table 7.

Distribution of phylogenetic groups among UPEC isolates in Iran.

Total isolate no.	ExPEC group		InPEC group					Ref.
Total isolate no.	B2	D	A	B1	C	E	F	Ref.
175	113	33	19	10	0	0	0	[80]
42	18	15	8	1	0	0	0	[54]
59	42	0	0	0	0	0	17	[49]
103	24	17	56	6	0	0	0	[81]
22	7	9	4	2	0	0	0	[82]
144	40	12	15	38	15	17	7	[42]
105	32	17	26	30	0	0	0	[83]
104	26	20	32	26	0	0	0	[25]
90	25	11	46	8	0	0	0	[76]
48	13	2	1	7	15	8	2	[84]
Total(892)	340	163	207	128	30	25	26
%	38.1	15.2	23.2	14.3	3.4	2.8	2.9

Table 8.

Distribution of phylogenetic groups among UPEC isolates in Egypt.

Total isolate no.	ExPEC group		InPEC group					Ref.
Total isolate no.	B2	D	A	B1	C	E	F	Ref.
97	20	37	29	11	0	0	0	[85]
50	22	13	11	4	0	0	0	[86]
153	58	48	41	6	0	0	0	[87]
45	19	4	1	0	1	19	1	[88]
146	52	43	36	15	0	0	0	[89]
69	16	31	15	7	0	0	0	[90]
43	18	2	23	0	0	0	0	[91]
156	95	48	8	5	0	0	0	[92]
142	54	58	20	10	0	0	0	[93]
Total(901)	354	284	184	58	1	19	1
%	39.3	31.5	2.4	6.4	0.1	2.1	0.1

Table 9.

Distribution of phylogenetic groups among UPEC isolates in Turkey.

4. Conclusion

Data analysis of current study revealed that the among DEC, EPEC and ETEC were assigned in high rate to B1 followed by A, B2, D, E, C and F while EAEC show different assignment: D followed by B2, A, B1, C, E and F. The other DEC pathotypes showed different styles.

Conflict of interest

There is no ‘conflict of interest’ for this work.

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Phylotypes and Pathotypes of Diarrheagenic Escherichia coli of Gastroenteritis

Antimicrobial Stewardship - New Insights [Working Title]