Characterization of E. coli Phylogroups Causing Catheter-Associated Urinary Tract Infection

Figures & data

Table 1 Sequences of the Primers and the Size of Amplicon in Base Pair (Bp) Used in Multiplex PCR for Detection of UPEC Strains Phylogroups and PAIs

Target	Primer Sequence	Amplicon (Bp)	Reference
PAI I536	TAATGCCGGAGATTCATTGTC AGGATTTGTCTCAGGGCTTT	1800	[^Citation21]
PAI II536	CATGTCCAAAGCTCGAGCC CTACGTCAGGCTGGCTTTG	1000	[^Citation21]
PAI III536	CGGGCATGCATCAATTATCTTTG TGTGTAGATGCAGTCACTCCG	200	[^Citation21]
PAI IV536	AAGGATTCGCTGTTACCGGAC TCGTCGGGCAGCGTTTCTTCT	300	[^Citation21]
PAI ICFT073	GGACATCCTGTTACAGCGCGCA TCGCCACCAATCACAGCGAAC	930	[^Citation21]
PAI IICFT073	ATGGATGTTGTATCGC ACGAGCATGTGGATCTGC	400	[^Citation21]
PAI IJ96	TCGTGCTCAGGTCCGGAATTT TGGCATCCCACATTATCG	400	[^Citation21]
PAI IIJ96	GGATCCATGAAAACATGGTTAATGGG GATATTTTTGTTGCCATTGGTTACC	2300	[^Citation21]
ChuA	GACGAACCA ACGGTCAGGAT TGCCGCCAGTACC AAAGACA	279	[^Citation11]
YjaA	TGAAGTGTCAGGAGACGCT G ATGGAGAATGCGTTCCTCAAC	211	[^Citation11]
TspE4C2	GAGTAATGTCGGGGCATTCA CGCGCCAACAAAGTATTACG	154	[^Citation11]

Table 2 Comparison of the Phylogenetic Groups, PAIs, Antibiotic Resistance Pattern and Biofilm Formation of UPEC Isolated from CAUTI and Com-UTI

	CAUTI (No = 45) No/%	Com-UTI (No = 45) No/%	P value
Phylogenetic Groups
A	24 (53.3%)	22 (48.9%)	(0.40)
B1	5 (11.1%)	3 (6.7%)
B2	11 (24.4%)	14 (31.1%)
D	5 (11.1%)	6 (13.3%)
PAIs
PAI III536	2 (4.4%)	0 (0%)	(0.49)
PAI IV536	32 (71.1%)	33 (73.3%)	(0.81)
PAI IICFT073	21 (46.7%)	19 (42.2%)	(0.60)
PAI IJ96	4 (8.9%)	2 (4.4%)	(0.67)
PAI ICFT073	3 (6.7%)	2 (4.4%)	(1)
No PAI	5 (11.1%)	6 (13.3%)	(0.74)
1PAI	22 (48.9%)	23 (51.1%)	(0.83)
2 PAIs	14 (31.1%)	15 (33.3%)	(0.82)
3 PAIs	4 (8.9%)	1 (2.2%)	(0.36)
Antimicrobial agents
Gentamicin	12 (26.7%)	9 (20%)	(0.45)
Amikacin	2 (4.4%)	1 (2.2%)	(1)
Piperacillin-tazobactam	8 (17.8%)	6 (13.3%)	(0.56)
Meropenem	3 (6.7%)	2 (4.4%)	(1)
Cefuroxime	39 (86.7%)	38 (84.4%)	(0.76)
Cefotaxime	22 (48.9%)	21 (46.7%)	(0.83)
Ceftazidime	25 (55.6%)	21 (46.7%)	(0.39)
Cefepime	21 (46.7%)	17 (37.8%)	(0.39)
Ciprofloxacin	32 (71.1%)	30 (66.7%)	(0.64)
Trimethoprim-Sulfamethoxazole	30 (66.7%)	28 (62.2%)	(0.66)
Aztreonam	24 (53.3%)	21 (46.7%)	(0.52)
Ampicillin	45 (100%)	45 (100%)	NA
Amoxicillin-Clavulanate	39 (86.7%)	33 (73.3%)	(0.11)
Nitrofurantoin	12 (26.7%)	14 (31.1%)	(0.64)
Norfloxacin	32 (71.1%)	27 (60%)	(0.26)
Tetracycline	34 (75.6%)	34 (75.6%)	(1)
MDR	36 (80%)	32 (71.1%)	(0.32)
ESBL	22 (48.9%)	15 (33.3%)	(0.13)
Biofilm	31 (68.9%)	20 (44.4%)	(0.01)*

Note: *P value ≤ 0.05 was considered significant.

Figure 1 Detection of UPEC phylogroups using multiplex PCR¹¹ targeting the genes chuA (279bp) and yjaA (211bp) and the DNA fragment TspE4.C2 (154bp). Lane M: 100 bp DNA Ladder. Lane 1: Distilled water as negative control, Lane 2: phylogroup A, Lane 3: phylogroup B1, Lane 4,5: phylogroup A, Lane 6: phylogroup B1, Lane 7: phylogroup B2, Lane 8: phylogroup A, Lane 9: phylogroup A, Lane 10: phylogroup D, Lane 11: phylogroup A, Lane 12: phylogroup B2 and Lane 13: phylogroup A.

Figure 2 Detection of UPEC PAIs using multiplex PCR A to detect PAI III536 (200 bp), PAI IV536 (300 bp) and PAI IICFT073 (400 bp). Lane M: 100 pb DNA ladder. Lane 1: UPEC strains with PAI IICFT073, Lane 2: UPEC strains with no PAI, Lane 3: UPEC strains with PAI IV536 and PAI IICFT073, Lane 4: UPEC strains with no PAI and Lane 5: UPEC strains with PAI IV536.

Figure 3 (A and B) Detection of UPEC PAIs using multiplex PCR B to detect 5 PAIs; PAI IJ96 (400 bp), PAI ICFT073 (930 bp), PAI II536 (1000 bp), PAI I536 (1800 bp) and PAI IIJ96 (2300 bp). (A); Lane M: 100 pb DNA ladder. Lanes 1–5: UPEC strains with PAI ICFT073. (B); Lane M: 100 pb DNA ladder. Lanes 1–6,8: UPEC strains with no PAI and Lanes 7,9 UPEC strains with PAI IJ96.

Table 3 Antibiotic Resistance Pattern and Biofilm Formation of Different UPEC Phylogroups Isolated from CAUTI and Com-UTI

Antimicrobial Agents	CAUTI					Com-UTI
	A (24)	B1 (5)	B2 (11)	D (5)	P value	A (22)	B1 (3)	B2 (14)	D (6)	P value
Gentamicin	7 (29.2%)	3 (60%)	2 (18.2%)	0 (0%)	0.067	5 (22.7%)	1 (33.3%)	1 (7.1%)	2 (33.3%)	0167
Amikacin	2 (8.3%)	0 (0%)	0 (0%)	0 (0%)	0.790	1 (4.5%)	0 (0%)	0 (0%)	0 (0%)	0.864
Piperacillin-Tazobactam	6 (25%)	0 (0%)	2 (18.2%)	0 (0%)	0.327	4 (18.2%)	1 (33.3%)	0 (0%)	1 (16.7%)	0.283
Meropenem	3 (12.5%)	0 (0%)	0 (0%)	0 (0%)	0.691	1 (4.5%)	0 (0%)	1 (7.1%)	0 (0%)	0.207
Cefuroxime	22 (91.7%)	5 (100%)	8 (72.7%)	4 (80%)	0.444	19 (86.4%)	1 (33.3%)	13 (92.8%)	5 (83.3%)	0.430
Cefotaxime	17 (70.8%)	0 (0%)	0 (0%)	5 (100%)	0.0001*	15 (68.2%)	1 (33.3%)	2 (14.3%)	3 (50%)	0.202
Ceftazidime	18 (75%)	1 (20%)	1 (9.1%)	5 (100%)	0.0001**	14 (63.6%)	1 (33.3%)	3 (21.4%)	3 (50%)	0.244
Cefepime	17 (70.8%)	0 (0%)	2 (18.2%)	2 (40%)	0.243	11 (50%)	1 (33.3%)	3 (21.4%)	2 (33.3%)	0.421
Ciprofloxacin	16 (66.7%)	5 (100%)	7 (63.6%)	4 (80%)	0.485	18 (81.8%)	2 (66.7%)	5 (35.7%)	5 (83.3%)	0.068
Trimethoprim-Sulfamethoxazole	14 (58.3%)	5 (100%)	8 (72.7%)	3 (60%)	0.211	14 (63.6%)	2 (66.7%)	7 (50%)	5 (83.3%)	0.112
Aztreonam	15 (62.5%)	0 (0%)	5 (45.4%)	4 (80%)	0.033^†	13 (59.1%)	2 (66.7%)	4 (28.6%)	2 (33.3%)	0.378
Ampicillin	24 (100%)	5 (100%)	11 (100%)	5 (100%)	NA	22 (100%)	3 (100%)	14 (100%)	6 (100%)	NA
Amoxicillin-Clavulanate	23 (95.8%)	5 (100%)	7 (63.6%)	4 (80%)	0.488	19 (86.4%)	2 (66.7%)	8 (57.1%)	4 (66.7%)	0.489
Nitrofurantoin	8 (33.3%)	2 (40%)	0 (0%)	2 (40%)	0.149	8 (36.4%)	2 (66.7%)	1 (7.1%)	3 (50%)	0.101
Norfloxacin	17 (70.8%)	5 (100%)	6 (54.5%)	4 (80%)	0.398	16 (72.7%)	2 (66.7%)	5 (35.7%)	4 (66.7%)	0.221
Tetracycline	17 (70.8%)	5 (100%)	9 (81.8%)	3 (60%)	0.120	19 (86.4%)	3 (100%)	7 (50%)	5 (83.3%)	0.183
MDR	21 (87.5%)	5 (100%)	6 (54.5%)	4 (80%)	0.358	20 (91%)	2 (66.7%)	5 (35.7%)	5 (83.3%)	0.080
ESBL	19 (79.2%)	0 (0%)	2 (18.2%)	1 (20%)	0.471	9 (41%)	1 (33.3%)	3 (21.4%)	2 (33.3%)	0.375
Biofilm	15 (62.5%)	4 (80%)	8 (72.7%)	4 (80%)	0.455	10 (45.4%)	1 (33.3%)	6 (42.8%)	3 (50%)	0.376

Notes: *Cefotaxime: P value between phylogroups A and B1 equals 0.007 (Significant) and P value between phylogroups A and B2 equals 0.0001 (Significant). P value between phylogroups D and B1 equals 0.008 (Significant). P value between phylogroups D and B2 equals 0.0001 (Significant). **Ceftazidime: P value between phylogroups A and B1 equals 0.034 (Significant) and P value between phylogroups A and B2 equals 0.0001 (Significant). P value between phylogroups D and B1 equals 0.048 (Significant). P value between phylogroups D and B2 equals 0.001 (Significant). ^†Aztreonam: P value between phylogroups A and B1 equals 0.017 (Significant). P value between phylogroups D and B1 equals 0.048 (Significant).

Table 4 Prevalence of PAIs in Different UPEC Phylogroups Isolated from CAUTI and Com-UTI

	PAIs	PAI III536 (No/%)	PAI IV536 (No/%)	PAI IICFT073 (No/%)	PAI IJ96 (No/%)	PAI ICFT073 (No/%)	No PAI (No/%)	1 PAI (No/%)	2 PAIs (No/%)	3 PAIs (No/%)	Total PAIs (No/%)
	Phylogroups (No)
CAUTI UPEC	A (24)	2 (8.3%)	15 (62.5%)	13 (54.2%)	2 (8.3%)	0 (0%)	4 (16.7%)	9 (37.5%)	10 (41.7%)	1 (4.2%)	20 (83.3%)
	B1 (5)	0 (0%)	5 (100%)	0 (0%)	1 (20%)	0 (0%)	0 (0%)	4 (80%)	1 (20%)	0 (0%)	5 (100%)
	B2 (11)	0 (0%)	10 (91%)	6 (54.5%)	1 (9.1%)	3 (27.3%)	0 (0%)	5 (45.5%)	3 (27.3%)	3 (27.3%)	11 (100%)
	D (5)	0 (0%)	2 (40%)	2 (40%)	0 (0%)	0 (0%)	1 (20%)	4 (80%)	0 (0%)	0 (0%)	4 (80%)
Com-UTI UPEC	A (22)	0 (0%)	18 (81.8%)	7 (31.8%)	2 (9.1%)	1 (4.5%)	3 (13.6%)	10 (45.4%)	9 (41%)	0 (0%)	19 (86.4%)
	B1 (3)	0 (0%)	2 (66.7%)	2 (66.7%)	0 (0%)	0 (0%)	0 (0%)	2 (66.7%)	1 (33.3%)	0 (0%)	3 (100%)
	B2 (14)	0 (0%)	9 (64.3%)	7 (50%)	0 (0%)	1 (7.1%)	2 (14.3%)	8 (57.1%)	3 (21.4%)	1 (7.1%)	12 (85.7%)
	D (6)	0 (0%)	4 (66.7%)	3 (50%)	0 (0%)	0 (0%)	1 (16.7%)	3 (50%)	2 (33.3%)	0 (0%)	5 (83.3%)

SabateM, MorenoE, PerezT, AndreuA, PratsG. Pathogenicity island markers in commensal and uropathogenic Escherichia coli isolates. Clin Microbiol Infect. 2006;12(9):880–886. doi:10.1111/j.1469-0691.2006.01461.x16882293

 PubMed Web of Science ®Google Scholar

ClermontO, BonacorsiS, BingenE. Rapid and simple determination of the Escherichia coli Phylogenetic Group. Appl Environ Microbiol. 2000;66(10):4555–4558. doi:10.1128/AEM.66.10.4555-4558.200011010916

 PubMed Web of Science ®Google Scholar