Uropathogenic Escherichia coli in Iran: Serogroup distributions, virulence factors and antimicrobial resistance properties

Abstract

Background

Urinary tract infections (UTIs) are one of the most common bacterial infections with global expansion. These infections are predominantly caused by uropathogenic Escherichia coli (UPEC).

Methods

Totally, 123 strains of Escherichia coli isolated from UTIs patients, using bacterial culture method were subjected to polymerase chain reactions for detection of various O- serogroups, some urovirulence factors, antibiotic resistance genes and resistance to 13 different antibiotics.

Results

According to data, the distribution of O1, O2, O6, O7 and O16 serogroups were 2.43%, besides O22, O75 and O83 serogroups were 1.62%. Furthermore, the distribution of O4, O8, O15, O21 and O25 serogroups were 5.69%, 3.25%, 21.13%, 4.06% and 26.01%, respectively. Overall, the fim virulence gene had the highest (86.17%) while the usp virulence gene had the lowest distributions of virulence genes in UPEC strains isolated from UTIs patients. The vat and sen virulence genes were not detected in any UPEC strains. Totally, aadA1 (52.84%), and qnr (46.34%) were the most prevalent antibiotic resistance genes while the distribution of cat1 (15.44%), cmlA (15.44%) and dfrA1 (21.95%) were the least. Resistance to penicillin (100%) and tetracycline (73.98%) had the highest while resistance to nitrofurantoin (5.69%) and trimethoprim (16.26%) had the lowest frequencies.

Conclusions

This study indicated that the UPEC strains which harbored the high numbers of virulence and antibiotic resistance genes had the high ability to cause diseases that are resistant to most antibiotics. In the current situation, it seems that the administration of penicillin and tetracycline for the treatment of UTIs is vain.

Background

Urinary tract infections (UTIs) are one of the most frequent infectious diseases around the world. Urinary tract infections comprise ranges of disorders including pyelonephritis (infection of the kidney) and cystitis (infection of the bladder), which are defined by the presence of microorganisms in urinary tract [1]. Foxman (2003) indicated that 40%-50% of women have UTIs throughout their lives [2]. Also, previous report of WHO showed that the UTIs are common causes of febrile illness in 3–8% of girls and 1% of boys [3].

Escherichia coli (E. coli) is the most important cause of UTI [4,5]. Uropathogenic E. coli (UPEC) strains have shown certain virulent properties, including iron uptake systems, adhesins, specific O: K: H serotypes and synthesis of cytotoxins. All of these properties contribute to colonization and invasion of the bacterium [6]. The successful colonization of UPEC in the urinary tract depends on the expression of fimbrial adhesion proteins, which facilitate attachment of the bacterium to the urothelium, and on the presence of specific bacterial genes that encode virulence factors [7-9].

The Escherichia coli strains are normally identified by serological typing of their H (flagellar), O (lipopolysaccharide) and in some cases, K (capsular) surface antigens. Overall, 174 O-serogroups are described for E. coli[10]. The O-serogroups of UPEC strains are related to certain virulence factor profile of each strain. Previous studies reported that O1, O2, O4, O6, O7, O8, O15, O16, O18, O21, O22, O25, O75 and O83 serogroups are preferentially associated with UPEC strains [11-18].

Some of the most important virulence genes of UPEC strains which are associated with severe UTIs are aerobactin (aer), P fimbriae (pap), type 1 fimbriae, afimbrial adhesin I (afaI), hemolysin (hly), cytotoxic necrotizing factor 1 (cnf 1), aerobactin (aer), S fimbriae (sfa), adhesins and fimbriae [19,20]; however, other virulence genes such as kpsMT, ompT, usp, iroN, iha, set 1, astA, group II capsule synthesis; sfa/foc, S and F1C fimbriae; iutA, traT, serum resistance; and fimH, are known to be involved in pathogenicity of this organism [21-23].

The treatment of diseases caused by this bacterium often requires antimicrobial therapy; however, antibiotic-resistant strains of bacteria cause more severe diseases for longer periods of time than their antibiotic-susceptible counterparts. Several studies showed that antibiotic resistance in UPEC is increasing nowadays [24,25]. Because of the high antimicrobial resistances of UPEC strains in Portugal (26%), Italy (25%) and Spain (21%) [26], the identification of bacterial resistance genes seems to be essential to reduce the treatment costs. To our knowledge, the epidemiology and prevalence of serogroups, virulence factors and antimicrobial resistance properties of UPEC strains isolated from patients with UTIs are unknown in Iran. So, the current survey was carried out in order to determine the serogroups, virulence factors and antimicrobial resistance properties of UPEC strains isolated from patients with UTIs in Iran.

Methods

Bacterial strains

A total of 123 E. coli strains isolated from patients with symptomatic UTIs were enrolled in the current investigation. The patients were hospitalized or visited the emergence room at Baqiyatallah Hospital in Tehran, Iran. The strains were isolated from pure cultures and identified in the laboratory of Molecular Biology Research Center at Hospital. The strains which were biochemically confirmed as E. coli- positive, were kept in Luria-Bertani /glycerol at −70°C.

DNA isolation

Bacterial strains were subcultured overnight in Luria-Bertani broth (Merck, Germany) and genomic DNA was extracted from typical colonies of E. coli using DNA extraction kit (DNP™, CinnaGen, Iran) according to manufacturer’s instruction.

Detection of uropathogenic E. coli serogroups, virulence factors and antibiotic resistance genes

In the present study various PCR assays were used for detection of serogroups, virulence factors and antimicrobial resistance genes of UPEC E. coli isolates. Table 1 showes the primers applied for detection of UPEC virulence genes, Table 2 indicates the primers used for detection of UPEC serogroups and finally in Table 3 the primers used for detection of antimicrobial resistant genes in uropathogenic E. coli are shown. The amplified products were visualized by ethidium bromide staining after gel electrophoresis of 10 μL of the final reaction mixture in 1.5% agarose.

Table 1.

Primers used for detection of virulence genes in uropathogenic Escherichia coli

Gene	Primer name	Primer sequence (5'-3')	Size of product (bp)	Reference
set-1	set-1-F	GTGAACCTGCTGCCGATATC	147	[21]
	set-1-R	ATTTGTGGATAAAAATGACG
sen	Sen-F	ATGTGCCTGCTATTATTTAT	799	[21]
	Sen-R	CATAATAATAAGCGGTCAGC
astA	astA-F	ATGCCATCAACACAGTATAT	110	[21]
	astA-R	GCGAGTGACGGCTTTGTAGT
sigA	sigA-F	TCCTCGGTATTATTTTATCC	408	[21]
	sigA-R	CGTAACCCCTGTTGTTTCCAC
sap	Sap_f	TACCCTCCACAACAGAGAATG	832	[21]
	Sap-R	TACCCTCCACAACAGAGAATG
pic	Pic-F	ACTGGATCTTAAGGCTCAGGAT	500	[21]
	Pic-R	GACTTAATGTCACTGTTCAGCG
pap	pap3	GCAACAGCAACGCTGGTTGCATCAT	336	[27]
	pap4	AGAGAGAGCCACTCTTATACGGACA
cnf1	cnf1	AAGATGGAGTTTCCTATGCAGGAG	498	[27]
	cnf2	TGGAGTTTCCTATGCAGGAG
hlyA	hly1	AACAAGGATAAGCACTGTTCTGGCT	1177	[27]
	hly2	ACCATATAAGCGGTCATTCCCGTCA
sfa	sfa1	CTCCGGAGAACTGGGTGCATCTTAC	410	[28]
	sfa2	CGGAGGAGTAATTACAAACCTGGCA
afa	afa1	GCTGGGCAGCAAACTGATAACTCTC	750	[28]
	afa2	CATCAAGCTGTTTGTTCGTCCGCCG
iuc	iuc1	ATGAGAATCATTATTGACATAATTG	1482	[29]
	iuc2	CTCACGGGTGAAAATATTTT
fim	fim1	GAGAAGAGGTTTGATTTAACTTATTG	559	[30]
	fim2	AGAGCCGCTGTAGAACTGAGG
papGI	papGJ96-F	TCGTGCTGAGGTCCGGAATTT	461	[31]
	papGJ96-R	TGGCATCCCCCAACATTATCG
papGII	papGIA2-F	GGGATGAGCGGGCCTTTGAT	190	[31]
	papGIA2-R	CGGGCCCCCAAGTAACTCG
papGIII	prsJ96-F	GGCCTGCAATGGATTTACCTGG	258	[31]
	prsJ96-R	CCACCAAATGACCATGCCAGAC
kpsMT	kpsM481F	CCATCGATACGATCATTGCACG	400	[32]
	kpsM481R	ATTGCAAGGTAGTTCAGACTCA
iha	IHA-F	CTGGCGGAGGCTCTGAGATCA	827	[23]
	IHA-R	TCCTTAAGCTCCCGCGGCTGA
iron	IRONEC-F	AAGTCAAAGCAGGGGTTGCCCG	665	[23]
	IRONEC-R	GACGCCGACATTAAGACGCAG
ompT	ompT-F	ATCTAGCCGAAGAAGGAGGC	559	[33]
	ompT-R	CCCGGGTCATAGTGTTCATC
usp	usp -F	ACATTCACGGCAAGCCTCAG	440	[22]
	usp -R	AGCGAGTTCCTGGTGAAAGC
iss	Iss-F	ATCACATAGGATTCTGCCG	309	[34]
	Iss-R	CAGCGGAGTATAGATGCCA
irp2	Irp2-F	AAGGATTCGCTGTTACCGGAC	413	[34]
	Irp2-R	AACTCCTGATACAGGTGGC
tsh	Tsh-F	ACTATTCTCTGCAGGAAGTC	824	[34]
	Tsh-R	CTTCCGATGTTCTGAACGT
vat	Vat-F	TCCTGGGACATAATGGTCAG	981	[34]
	Vat-R	GTGTCAGAACGGAATTGT
cva	Cva-F	TGGTAGAATGTGCCAGAGCAAG	1181	[34]
	Cva-R	GAGCTGTTTGTAGCGAAGCC

Table 2.

Primers used for detection of uropathogenic Escherichia coli serogroups[35]

Serogroup	Target gene	Primer name	Primer sequence (5’-3’)	Size of product (bp)
O1	wzx	wl-14632	GTGAGCAAAAGTGAAATAAGGAACG	1098
		wl-14633	CGCTGATACGAATACCATCCTAC
O6	wzy	wl-14646	GGATGACGATGTGATTTTGGCTAAC	783
		wl-14647	TCTGGGTTTGCTGTGTATGAGGC
O7	wzx	wl-14648	CTATCAAAATACCTCTGCTGGAATC	610
		wl-14649	TGGCTTCGAGATTAAACCTATTCCT
O8	orf469	wl-14652	CCAGAGGCATAATCAGAAATAACAG	448
		wl-14653	GCAGAGTTAGTCAACAAAAGGTCAG
O16	wzx	wl-14654	GGTTTCAATCTCACAGCAACTCAG	302
		wl-14655	GTTAGAGGGATAATAGCCAAGCGG
O21	wzx	wl-14676	CTGCTGATGTCGCTATTATTGCTG	209
		wl-14677	TGAAAAAAAGGGAAACAGAAGAGCC
O75	wzy	wl-17413	GAGATATACATGGGGAGGTAGGCT	511
		wl-17414	ACCCGATAATCATATTCTTCCCAAC
O2	wzy	wl-14636	AGTGAGTTACTTTTTAGCGATGGAC	770
		wl-14637	AGTTTAGTATGCCCCTGACTTTGAA
O4	wzx	wl-14642	TTGTTGCGATAATGTGCATGTTCC	664
		wl-14643	AATAATTTGCTATACCCACACCCTC
O15	wzy	wl-14672	TCTTGTTAGAGTCATTGGTGTATCG	183
		wl-14673	ATAAAACGAGCAAGCACCACACC
O18	wzx	wl-14656	GTTCGGTGGTTGGATTACAGTTAG	551
		wl-14657	CTACTATCATCCTCACTGACCACG
O22	wzx	wl-14660	TTCATTGTCGCCACTACTTTCCG	468
		wl-14661	GAAACAGCCCATGACATTACTACG
O25	wzy	wl-14666	AGAGATCCGTCTTTTATTTGTTCGC	230
		wl-14667	GTTCTGGATACCTAACGCAATACCC
O83	wzx	wl-14668	GTACACCAGGCAAACCTCGAAAG	362
		wl-14669	TTCTGTAAGCTAATGAATAGGCACC
E. coli	16SrRNA	wl-3110	AGAGTTTGATCMTGGCTCAG	919
		wl-3111	CCGTCAATTCATTTGAGTTT

Table 3.

Primers used for detection of antimicrobial resistant genes in uropathogenic Escherichia coli

Antimicrobial agent	Resistance gene	Sequence	Size (bp)	References
Streptomycin	aadA1	(F) TATCCAGCTAAGCGCGAACT	447	[36]
		(R) ATTTGCCGACTACCTTGGTC
Gentamicin	aac(3)-IV	(F) CTTCAGGATGGCAAGTTGGT	286	[36]
		(R) TCATCTCGTTCTCCGCTCAT
Sulfonamide	sul1	(F) TTCGGCATTCTGAATCTCAC	822	[36]
		(R) ATGATCTAACCCTCGGTCTC
Beta-lactams	blaSHV	(F) TCGCCTGTGTATTATCTCCC	768	[36]
		(R) CGCAGATAAATCACCACAATG
Beta-lactams	CITM	(F) TGGCCAGAACTGACAGGCAAA	462	[36]
		(R) TTTCTCCTGAACGTGGCTGGC
Chloramphenicol	cat1	(F) AGTTGCTCAATGTACCTATAACC	547	[36]
		(R) TTGTAATTCATTAAGCATTCTGCC
Chloramphenicol	cmlA	(F) CCGCCACGGTGTTGTTGTTATC	698	[36]
		(R) CACCTTGCCTGCCCATCATTAG
Tetracycline	tet(A)	(F) GGTTCACTCGAACGACGTCA	577	[37]
		(R) CTGTCCGACAAGTTGCATGA
Tetracycline	tet(B)	(F) CCTCAGCTTCTCAACGCGTG	634	[37]
		(R) GCACCTTGCTGATGACTCTT
Trimethoprim	dfrA1	(F) GGAGTGCCAAAGGTGAACAGC	367	[38]
		(R) GAGGCGAAGTCTTGGGTAAAAAC
Quinolones	qnr	(F) GGGTATGGATATTATTGATAAAG	670	[39]
		(R) CTAATCCGGCAGCACTATTTA

Antimicrobial susceptibility testing

Antimicrobial susceptibility tests was performed by the Kirby–Bauer disc diffusion method using Mueller–Hinton agar (HiMedia Laboratories, Mumbai, India, MV1084), according to the Clinical and Laboratory Standards Institute guidelines [40]. After incubating the inoculated plates aerobically at 37°C for 18–24 h in an aerobic atmosphere, the susceptibility of the E. coli isolates to each antimicrobial agent was measured and the results were interpreted in accordance with interpretive criteria provided by CLSI (2006). E. coli ATCC 25922 was used as quality control organisms in antimicrobial susceptibility determination.

Statistical analysis

The data were analyzed using SPSS software (Version 17.SPSS Inc, United States) to find any significant correlation between incidences of virulence factors and antibiotics resistance genes of uropathogenic E. coli serogroups isolated from patients with urinary tract infection. Statistical significance was regarded at a P value < 0.05.

Ethical issues

In the current study we tried to protect the life, health, dignity, integrity, rights to self-determination, privacy, and confidentiality of personal information of research subjects. We conform to generally accepted scientific principles, be based on a thorough knowledge of the scientific literature, other relevant sources of information, and adequate laboratory and, as appropriate, animal experimentation. All samples were taken from volunteer patients for this research. All ethical issues were considered and this research was performed with hospitals’ permission. The name and characters, personal information and even patients’ illnesses and their medical information remained secret. In addition, in this cooperation agreement we stated that this research will help urology and microbiology and is able to clarify the epidemiology and prevalence of stereotypes, virulence factors and antimicrobial resistance of UPEC strains isolated from patients with urinary tract infection. All of the patients showed their satisfaction in order to use their sample in this investigation especially to determine antibiotic resistance in UPEC strains.

Results and discussion

Our results revealed high distribution of UPEC serogroups isolated from patients with urinary tract infection (Table 4). Totally, O25 (26.01%), O15 (21.13%) and O16 (10.56%) had the highest while O18 (0.81%), O75 (1.62%), O22 (1.62%) and O83 (1.62%) had the lowest distributions of UPEC serogroups isolated from patients with UTIs (Table 4). Besides, the serogroups of 13.82% UPEC strains isolated from these patients could not be detected and were diagnosed as non-detected serogroups (Table 4).

Table 4.

Distribution of virulence genes in uropathogenic Escherichia coli serogroups isolated from urinary tract infections in Iran

Gene	O1 (3)	O6 (13)	O7 (3)	O8 (4)	O16 (3)	O21 (5)	O75 (2)	O2 (3)	O4 (7)	O15 (26)	O18 (1)	O22 (2)	O25 (32)	O83 (2)	Non detect (17)
set1 (98)	3	12	3	4	3	3	-	1	4	25	-	2	28	-	10
astA (26)	-	3	1	1	-	1	-	-	-	8	-	-	10	-	2
sigA (26)	1	5	-	-	1	-	1	1	1	-	1	1	11	1	2
sap (32)	-	-	-	3	2	1	-	-	1	10	1	-	14	-	-
pic (16)	2	8	1	-	-	-	1	-	-	4	-	-	-	-	-
sfa (66)	1	8	1	-	3	4	1	2	5	10	1	-	23	-	7
afa (10)	-	-	-	-	-	-	1	-	-	3	-	-	4	-	2
cnf1 (62)	1	4	-	2	1	4	-	-	4	15	1	-	30	-	-
hlyA (62)	-	8	2	-	-	2	-	2	4	21	-	1	9	1	10
iuc (13)	-	-	-	-	-	-	-	-	-	3	-	-	10	-	-
fim (106)	3	10	3	3	1	5	2	3	7	23	1	2	30	2	11
kspMT (5)	-	1	-	1	-	-	-	1	-	2	-	-	-	-
ompT (6)	-	-	-	-	-	-	-	1	-	1	-	-	3	-	1
usp (2)	-	-	-	-	-	-	-	-	-	1	-	-	-	-	1
iss (10)	-	2	-	-	-	1	-	-	2	3	-	-	2	-	-
irp2 (14)	-	-	-	-	1	-	-	-	-	1	-	-	10	-	1
vat (12)	1	-	1	2	-	-	1	2	-	-	1	-	3	1	-
cva (6)	-	6	-	-	-	-	-	-	-	-	-	-	-	-	-
pap (62)	1	3	1	2	1	3	1	1	4	20	-	1	20	1	3
papGI (10)	-	1	1	-	-	1	-	-	-	4	-	1	-	1	1
papGII (19)	-	-	-	-	-	-	1	1	4	3	-	-	8	-	2
papGIII (62)	1	2	1	2	1	2	1	1	2	19	-	-	19	-	11
iha (22)	-	2	-	1	-	1	-	-	-	3	1	1	10	1	2
iron (52)	-	2	1	1	3	1	-	1	2	10	1	-	21	2	7

Overall, fim and set1 had the highest distributions of virulence genes while usp, kpsMT, cva and ompT had the lowest (Table 4). As it was shown in Table 4, we were not able to identify the distributions of sen and tsh virulence genes of UPEC in our population. Table 5 shows the distributions of antibiotic resistance genes of UPES isolated from patients with UTIs. It was recognized that aadA1 (52.84%) and qnr (46.34%) had the highest while cat1 (15.44%) and cmlA (15.44%) had the lowest distributions of antibiotic resistance genes (Table 5). Also, the distributions of tetA, tet B, dfrA1, dfrA1, aac(3)-IV, sul1, blaSHV and CITM antibiotic resistance genes were 43.80%, 36.58%, 21.95%, 22.76%, 36.58%, 27.64% and 39.83%, respectively (Table 5).

Table 5.

Distribution of antimicrobial resistance genes in uropathogenic Escherichia coli serogroups isolated from urinary tract infections in Iran

UPEC Serogroup	Antibiotic resistance genes
	aadA1	tetA	tetB	dfrA1	qnr	aac(3)-IV	sul1	blaSHV	CITM	cat1	cmlA
O1 (3)	1	1	1	1	1	1	1	1	1	-	-
O6 (13)	6	6	3	4	5	1	11	7	7	1	1
O7 (3)	1	-	2	2	2	1	2	-	2	-	-
O8 (4)	1	2	-	2	-	1	1	1	2	-	-
O16 (3)	2	1	1	1	-	1	1	1	3	1	-
O21 (5)	-	3	2	1	2	2	1	1	-	1	1
O75 (2)	1	1	1	1	-	1	-	2	1	-	1
O2 (3)	1	2	1	1	1	1	2	2	-	2	-
O4 (7)	1	4	2	-	6	4	-	3	2	2	1
O15 (26)	8	10	9	11	6	10	10	4	10	-	1
O18 (1)	-	-	1	1	1	2	1	-	-	1	-
O22 (2)	1	1	-	1	-	1	1	2	1	-	-
O25 (32)	31	18	14	1	28	1	1	1	17	10	14
O83 (2)	1	-	-	-	3	1	2	2	2	-	-
Non detected (17)	10	4	8	-	2	-	11	7	1	1	-
Total (123)	65 (52.84%)	53 (43.8%)	45 (36.58%)	27 (21.95%)	57 (46.34%)	28 (22.76%)	45 (36.58%)	34 (27.64%)	49 (39.83%)	19 (15.44%)	19 (15.44%)

The disk diffusion method indicated that the UPEC serogroups had maximum resistance to penicillin (100%) and tetracycline (73.98%) antibiotics while resistance to nitrofurantoin (5.69%) was minimum (Table 6). Besides, the UPEC serogroups had 53.65%, 25.20%, 30.89%, 33.33%, 29.26%, 20.32% and 36.58% resistances to streptomycin, chloramphenicol, sulfamethoxazol, enrofloxacin, enrofloxacin, lincomycin, cephalothin and ampicillin antibiotics, respectively. Totally, resistance to gentamycin, ciprofloxacin and trimethoprim were minimal (17.07%, 19.51% and 16.26%), respectively (Table 6).

Table 6.

Antimicrobial resistance properties in uropathogenic Escherichia coli serogroups isolated from urinary tract infections in Iran

UPEC Serogroup	P10 (%)	TE30 (%)	S10 (%)	C30 (%)	SXT (%)	GM10 (%)	NFX5 (%)	L2 (%)	CF30 (%)	CIP5 (%)	TMP5 (%)	F/M300 (%)	AM10 (%)
O1 (3)	3	2	2	-	1	-	-	1	-	-	1	-	1
O6 (13)	13	8	6	2	10	1	2	10	6	5	4	2	6
O7 (3)	3	-	2	-	2	1	2	1	-	-	1	-	2
O8 (4)	4	2	2	-	1	1	-	1	-	-	1	-	2
O16 (3)	3	2	1	-	-	-	-	1	-	-	1	-	2
O21 (5)	5	4	2	1	1	1	1	1	-	2	-	1	-
O75 (2)	2	2	-	1	-	-	-	-	1	-	-	-	1
O2 (3)	3	3	-	2	1	-	-	-	1	-	-	1	-
O4 (7)	7	6	5	2	-	4	1	2	3	6	-	-	2
O15 (26)	26	19	14	-	10	10	6	15	4	5	10	1	10
O18 (1)	1	-	-	1	-	1	-	-	-	-	1	-	-
O22 (2)	2	1	-	-	1	1	-	-	2	-	1	-	1
O25 (32)	32	30	18	22	-	1	27	4	-	6	-	-	17
O83 (2)	2	-	-	-	1	-	2	-	1	-	-	-	1
Non detected (17)	17	12	14	-	10	-	-	-	7	-	-	2	-
Total (123)	123 (100%)	91 (73.98%)	66 (53.65%)	31 (25.20%)	38 (30.89%)	21 (17.07%)	41 (33.33%)	36 (29.26%)	25 (20.32%)	24 (19.51%)	20 (16.26%)	7 (5.69%)	45 (36.58%)

In this table P10 = penicillin (10 u/disk); TE30 = tetracycline (30 μg/disk); S10 = streptomycin (10 μg/disk); C30 = chloramphenicol (30 μg/disk); SXT = sulfamethoxazol (25 μg/disk); GM10 = gentamycin (10 μg/disk); NFX5 = enrofloxacin (5 μg/disk); L2 = lincomycin (2 μg/disk); CF30 = cephalothin (30 μg/disk); CIP5 = ciprofloxacin (5 μg/disk); TMP5 = trimethoprim (5 μg/disk); F/M300 = nitrofurantoin (300 μg/disk); AM10 = ampicillin (10 u/disk).

Our results revealed that the UPEC strains were able to be one of the major causative agents of UTIs in Iran and this finding was in accordance with the previous study which mentioned that 150 million people are diagnosed as UTI- positive annually [41]. Also, The UPEC strains are isolated from the uterine contents in the majority (82–100%) of clinical pyometra cases [42,43]. Therefore, such a high prevalence of serogroups, virulence factors and antibiotic resistance genes in UPEC strains exhibits that there is a high risk of developing incurable diseases.

Several investigations have been performed on the prevalence of UPEC strains in UTI cases in Iran [44,45]. Kalantar et al. [44] showed that the E. coli was the most frequent occurring pathogen (54.80%) in patients with severe UTIs. Esmaeili [45] demonstrated that the E. coli was the most common cause of UTI in human. Also, previous study has been reported that the incidence of UTI has been increased recently [46].

Another study in Iran showed that 140 out of 244 patients with UTIs (57.37%) had the high levels of E. coli infection which was lower than our percentage (66.12%) [47]. Ghorashi et al. [48] declared that 77% of patients with UTIs were positive for E. coli which was higher than our results. Several investigations have been performed on the prevalence of UPEC strains in UTI cases around the world including Brazil [49], United States [50], Europe, and Canada [51].

Our results indicated that there were several serogroups of E. coli in UTI positive patients. There was statistical significant differences between the presence of O25 and O18 serogroups (P < 0.01), O25 and O83, O75, O22, O7, O2 and O1 (P < 0.05). Totally, O25 and O15 were the most prevalent serogroups. Since 1980 [52], many investigators reported that several O-serogroups were found with variable frequencies in UTIs patients. Similar results have been reported recently too [12,53]. The previous survey showed that the majority of uropathogenic E. coli strains such as O4, O6, O14, O22, O75 and O83 were HlyA + CNF1+ and expressed P-fimbriae or MRHA type III, whereas O18 serogroup strains were HlyA + CNF1− and P-fimbriated [14] which was in accordance with those of us.

Based on our results, there were significant differences about (P < 0.01) between the presence of fim, tsh and sen virulence genes as well as set1, tsh and sen genes (P < 0.05) and also between fim and usp genes of isolated E. coli strains (P < 0.05). Therefore, fim and set1 were the most common virulence genes. Arabi et al. [54] showed the similar results of UPEC virulence genes in Iran. Arabi et al. [54] indicated that the fim and sfa fimbriae genes were observed in 92.7% of isolates, separately. Also, Asadi Karam et al. [55] showed that the fim genes were the most prevalent virulence genes of UPES strains. Karimian et al. [56] proved that fimH gene with the frequency rate of 79.67% was the most and tsh and usp genes with the frequency rate of 0.0% and 1.62% respectively were the least common virulence genes in E. coli strains isolated from patients with urinary tract infections. Also, Karimian et al. [56] showed that the presence of cnf1, hlyA, pap, iroN, afa, iuc, iha, ompT and irp2 virulence genes were 50.4, 50.4, 50.4, 42.27, 8.13, 10.56, 17.88, 4.87 and 11.38%, respectively. Other virulence genes of UPEC strains like aatA, aggR and stbA[47] and stx1 and stx2[57] have been reported from Iran previously. Another investigation announced that the prevalence rate of fimH, fyuA, kpsMTII and iucD genes were above 75% likewise papC, papG, sat, iron, usp and traT were between 35-65% [12].

Our results contrary to other studies indicated that there are the possibilities of the existence of multiple virulence genes in UPEC strains isolated from UTIs patients [58,59]. The importance of UPEC strains’ sfa gene in patients with severe UTIs has been reported previously [59,60] while Abe et al. [11] and Santo et al. [59] reported lower prevalence of sfa gene among UPEC. Another study indicated that usp and iha virulence genes were present in 63.7% and 34.1% of all E. coli isolates [22] which both were higher than our findings.

The statistical analyses were significant among aadA1, cat1 and cmlA antibiotic resistance genes (P < 0.05). This correlation was demonstrated among tetracycline and nitrofuration (P < 0.05) and also penicillin, trimethoprim and gentamycin (P < 0.05) too. High frequency of resistant UPEC strains to one or more antimicrobials was observed in the present work and it was in agreement with previous studies [61,62].

The most common antibacterial drugs in UTIs’ treatment are trimethoprim-sulfamethoxazole, cephalosporins, semi-synthetic penicillins with or without beta-lactamase inhibitors and quinolones [62,63]; however, our results proved that resistance to penicillin, sulfamethoxazole, trimethoprim and cephalotin were 100%, 30.89%, 16.26% and 20.32%, respectively. Oliveira et al. from Brazil [61] reported that 90% of UPEC strains possessed at least one of the resistant genes, the prevalence of them were as follows: traT (76%), aer (41%), PAI (32%), sfa (26%), pap (25%), cnf1 (18%), afa (6%), and hly (5%) and the most common were ampicillin (51%) and trimethoprim-sulfamethoxazole (44%). According to Idrees Muhammad et al. [64] results, there were high prevalence of class 1 integrons (43.56%), sulfamethoxazole resistance genes sul1 (45.54%) and sul2 (51.48%) as well as quinolone resistance genes in multi drug resistance UPEC isolates in Pakistan. Farshad et al. [65] showed the high prevalence of resistance genes to ampicillin (80.2%), co-trimoxazole (76%) and tetracycline (70.8%) in Iran.

Recently, trimethoprim-sulfamethoxazole was used as a standard antibiotic for a calculated UTIs therapy and due to the increased resistance of UPEC strains to this class of antibiotics, fluoroquinolones as broad-spectrum antimicrobial agents have been used with increasing frequency in complicated as well as uncomplicated UTIs [66], but after a short time resistance to fluoroquinolones was emerged [67]. Previous study showed that more than 10% of the E. coli isolated in 2000–2002 from intensive care unit patients in European and North American were resistant to ciprofloxacin [68], while this amount of resistance was increased significantly in our evaluation.

Gulsun et al. [69] reported that the sensitivity of the UPEC strains to the norfloxacin, ciprofloxacin, netilmicin, amikacin, ceftriaxone, gentamicin, nitrofurantoin, amoxicillin-clavulanate, trimethoprim/sulfamethoxazole and ampicillin were 89%, 85%, 80%, 78%, 74%, 72%, 71%, 58%, 45%, 35%, respectively which was somewhat similar to our progeny. In a study carried out in India, the highest resistance have been shown against amoxicillin (67.3%) and least against nitrofurantoin (57.3%) [70] which was similar to our findings. On the other hand our results revealed that in the current situations the nitrofurantoin is a choice drug due its lowest antibiotic resistance in UPEC strains. Eighty five to ninety two percent of UPEC strains were sensitive to nitrofurantoin in previous study [53].

Our results showed that resistance to chloramphenicol was 25.5% but chloramphenicole is a forbidden antibiotic and the high antibiotic resistance to this drug in our study indicated the irregular and unauthorized use of this drug in medicine treatments. Unfortunately, not only in medicine, but also veterinarians in many fields of veterinary such as large animal internal medicine, poultry and even aquaculture, use this antibiotic as a basic one. Therefore, in a very short period of time, antibiotic resistance will appear.

Conclusions

Based on our results, O25 serotype, fim virulence gene, aadA1 antibiotic resistance gene and finally resistance to penicillin had highest frequencies in UPEC strains isolated from UTIs patients. The results of our study revealed the high presence of UPEC strains in patients with UTIs in Iran. To our knowledge, our study is the first report of direct detection of serogroups, virulence factors and antimicrobial resistance properties of uropathogenic E. coli strains in Iran. Due to the high prescription of antibiotics in humans and even animals, antibiotics resistance has been increased in UPEC strains and we recommend using antibiotics only in severe conditions and applying strong antibiotics and multi antibiotic descriptions.

Competing interests

The authors declare that they have no competing interests.

Authors’ contributions

HM carried out the molecular genetic studies, participated in the primers sequence alignment and drafted the manuscript. AK and MS carried out the sampling and culture method. RR participated in the primers sequence alignment. FSD, MM and NS participated in the design of the study, performed the statistical analysis and writing the manuscript. All authors read and approved the final manuscript.

Acknowledgement

The authors would like to thank Dr. E. Tajbakhsh, and Mr. M. Momeni at the Biotechnology Research Center of the Islamic Azad University of Shahrekord for their important technical and clinical support. This work was supported by the Islamic Azad University, Shahrekord Branch-Iran grant 90/9025.