Characterization of antibiotic-susceptibility patterns and virulence genes of five major sequence types of Escherichia coli isolates cultured from extraintestinal specimens: a 1-year surveillance study from Iran

Phylogenetic group, antibiotic resistance, virulence gene, and genetic diversity of Escherichia coli causing bloodstream infections in Iran

Escherichia coli is one of the most important pathogens causing bloodstream infections (BSIs) throughout the world. We sought to characterize the phylogroup classification, major human sequence types (STs), antimicrobial resistance, presence of selected antimicrobial resistance and virulence genes, and genetic diversity of E. coli isolated from patients with BSIs at the University Hospital in Iran. A total of 100 E. coli bloodstream isolates were collected between December 2020 and June 2022. This study used PCR to investigate phylogenetic groups (A, B1, B2, C, D, E, and F), four major STs (ST69, ST73, ST95, and ST131), antibiotic resistance genes (ARGs), virulence-associated genes (VAGs), and pathogenicity islands (PAIs). Antimicrobial susceptibility testing was done by disk diffusion method. Genetic diversity was analyzed by repetitive element sequence-based PCR (REP-PCR). The phylogenetic group B2 (32%) predominated, followed by phylogenetic group E (25%). ST131 (28%) was the most prevalent ST and the majority of these isolates (89.3%) were of serotype O25b. Most of E. coli isolates (75%) were categorized as multidrug resistant (MDR) with high rates of resistance (>55%) to ampicillin, trimethoprim-sulfamethoxazole, ciprofloxacin, cefazolin, and ceftriaxone. The most frequent ARGs were bla TEM (66%), sul1 (57%), and sul2 (51%). The most prevalent VAGs and PAIs were fimH (type 1 fimbriae adhesin; 85%), aer (iucC) (aerobactin; 79%), traT (serum resistance; 77%), iutA (aerobactin siderophore receptor; 69%), and PAI IV536 (75%), respectively. The highest rate of ARGs and VAGs was observed in the ST131 isolates. REP-PCR analysis showed high diversity among the studied isolates. The high prevalence of MDR septicemic E. coli with different types of ARGs, VAGs and genotypes is an extremely worrisome sign of BSIs treatment and poses a major threat for hospitalized patients. Active surveillance, stringent prescribing policies, increasing the awareness of ARGs among clinicians and re-defining the infection control measures are essential to curb the dissemination of these strains.

Phylogenetic analysis, biofilm formation, antimicrobial resistance and relationship between these characteristics in Uropathogenic Escherichia coli

BACKGROUND

In the present study, we examine the prevalence of phylogenetic groups, O-serogroups, adhesin genes, antimicrobial resistance, the level of gene expression associated with biofilm formation, and the presence of extended-spectrum beta-lactamase (ESBL) in UPEC strains isolated from both pediatric and adult patients.

METHODS

In this cross-sectional study, 156 UPEC isolates were collected from UTI patients. ESBL-producing isolates were detected using the double-disc synergy (DDS) method, and biofilm formation was assessed through a microplate assay. The presence of O-serogroups, adhesion factors and resistance genes, including ESBLs and PMQR genes, was detected by PCR, and isolates were categorized into phylogenetic groups using multiplex PCR. Additionally, the quantitative real-time PCR method was also used to determine the expression level of genes related to biofilm.

RESULTS

During the study period, 50.6% (79/156) of the samples were obtained from children, and 49.4% (77/156) were from adults. The highest rate of resistance was to NA (91.7%), while FM (10.9%) had the lowest rate of antibiotic resistance. In addition, 67.9% (106/156) of UPEC isolates were ESBL producers. Most of UPEC isolates belonged to phylogenetic group B2 (37.1%). This study revealed that blaCTX-M and qnrS are widely distributed among UPEC isolates. The mean expression levels of fimA genes were significantly higher in non-biofilm producers than in biofilm producers (p < 0.01).

CONCLUSIONS

The high antibiotic resistance rates in this study highlight the significance of local resistance monitoring and investigating underlying mechanisms. Our findings indicate the dominance of phylogroup B2 and group D as the prevailing phylogenetic groups. Consequently, it is imperative to investigate the epidemiological aspects and characterize UPEC isolates across diverse regions and time frames.

Distribution and expression of virulence genes (hlyA, sat) and genotyping of Escherichia coli O25b/ST131 by multi-locus variable number tandem repeat analysis in Tehran, Iran

Escherichia coli ST131 is a pandemic clone with high antibiotic resistance, and it is a major causative agent of urinary tract infection (UTI) and bloodstream infections. This study evaluated the distribution and expression of virulence genes and genotyping of E. coli O25b/ST131 by Multi-locus variable number tandem repeat analysis (MLVA) method among UTI in patients at Tehran hospitals, Iran.A total of 107 E. coli isolates were collected from UTI patients. Polymerase chain reaction (PCR) amplification of the pabB gene was used to identify E. coli O25b/ST131 and the prevalence of sat and hlyA virulence genes was also analyzed. The microtiter method quantified biofilm formation ability in E. coli O25b/ST131. The Real-Time PCR (qRT-PCR) was performed to evaluate the expression of sat and hlyA genes. Finally, MLVA was performed for E. coli O25b/ST131 genotyping by targeting seven tandem repeats. SPSS-16 software was used for statistical analysis. Molecular study showed that 71% of isolates carried the pabB gene and were considered E. coli O25b/ST131 strains. Also, 45.8% and 17.8% of isolates carried sat and hlyA genes, respectively. The 57.9% isolates had biofilm formation ability. Expression of the studied virulence genes showed an increase in strong biofilm producing E. coli O25b/ST131 strains. A total of 76 (100%) E. coli O25b/ST131 strains were typed by the MLVA method.High prevalence of E. coli O25b/ST131 isolates in UTI patients can be a serious warning to the treatment due to the high antibiotic resistance rate, expression of virulence genes, and biofilm formation.

The Molecular Characterization and Risk Factors of ST131 and Non-ST131 Escherichia coli in Healthy Fecal Carriers in Tehran, Iran

Background: Commensal extended-spectrum β-lactamase (ESBL) producing Escherichia coli isolates in the gut can be the reservoir of virulence factors and resistance genes. Objectives: We investigated the molecular feature, risk factors, and quinolone/fluoroquinolone (Q/FQ) resistance in sequence type 131 (ST131) and non-ST131: ESBL-producing E. coli (EPE) isolates in healthy fecal carriers. Methods: A total of 540 fecal samples and its demographic data were collected from healthy adults in Tehran in 2018. ST131 isolates were identified by MLST analysis, and the characteristics of the virulence factor, phylogenic assay, and Q/FQ resistance genes in ST131 and non-ST131 were determined by polymerase chain reaction (PCR). Results: The EPE isolates mainly belonged to the commensal phylogenetic groups A (54.9%) and D (18.1%). The type 1 fimbriae (fimH; 89.6%) gene was the predominant virulence factor, and there was a significant correlation between ferric yersiniabactin uptake (fyuA; 52.9%), aerobactin receptor (iutA; 17.6%), and group II capsule synthesis (kpsMII; 35.3%) with ST131. In Q/FQ-resistant isolates, qnrS (19%) was the predominant gene, and mutations mostly occurred at codon S83 in GyrA The number of mutations in gyrA and parC genes was significantly higher in ST131 isolates than in non-ST131 isolates. There was a significant positive correlation between diabetes, male gender, and living in the south of the city with EPE carriage (P < 0.05). Conclusions: Accumulation of multiple virulence factors and high- level resistance to Q/FQ in some phylogroups (B2 and D), particularly ST131 isolates, require to be considered in detecting resistant isolates in healthy carriers. According to the risk factor for spreading of EPE isolates (diabetes, living in low-income parts of the city, and male gender), the necessary strategies are required to be developed to control the dissemination of antimicrobial-resistant isolates in the community.

Prevalence of common carbapenemase genes and multidrug resistance among uropathogenic Escherichia coli phylogroup B2 isolates from outpatients in Wasit Province/ Iraq

Carbapenems are the last resort antimicrobials for the treatment of extended spectrum β-lactamases (ESBLs) producing Enterobacteriaceae. Emergence of carbapenems resistant group B2 uropathogenic E. coli (UPEC) is a major concern because of their high virulence. Prevalence of these enzymes and multidrug resistance (MDR) among B2 UPEC isolates from Iraqi outpatients with acute urinary tract infection (UTI) was evaluated in this research. Urine cultures were performed and the isolates were identified biochemically. Escherichia coli isolates were tested for phylogroup reference by quadraplex PCR, then B2 isolates were detected for antimicrobial resistance by disc diffusion test and carbapenemase genes by PCR. Escherichia coli was the most prevalent among Gram-negative isolates (66.6%) and B2 was the most detected phylogroup among E. coli isolates (33.9%). Most of B2 isolates showed high resistance rates to tested antimicrobials, especially β-lactams with MDR revealed in 100% of them. Whereas, low resistance rates were noted against carbapenems, aminoglycosides and nitrofurantoin. Carbapenemase genes were detected in 76.3% of B2 isolates. Of which, blaOXA-48 was the most frequent (57.8%), followed by blaPER (47.3%), blaKPC (15.7%), blaVEB and blaVIM (10.5%, for each). Whereas, blaGES and blaIMP genes were not found. Coproduction of these genes occurred among 17 isolates. The combination of blaOXA-48 and blaPER was the most frequent (41.1%). All carbapenemase producing isolates were MDR. These results revealed high prevalence of carbapenemase genes and MDR among B2 UPEC recovered in this study. In the study area. it is strongly advised to use aminoglycosides and nitrofurantoin for empirical treatment of UPEC.

Molecular epidemiology of blaCTX-M gene-producing uropathogenic Escherichia coli among Iranian kidney transplant patients: clonal dissemination of CC131 and CC10

Background

This study aimed to investigate the phylogenetic characterization and virulence traits of uropathogenic Escherichia coli (UPEC) isolated from kidney transplant patients (KTPs) as well as non-KTPs and analyze the clonal distribution of Extended spectrum β-lactamases (ESBLs)-producing UPEC containing bla_CTX-M gene.

Methods

To this end, we determined virulence marker and the phylogenetic characterization of UPEC in non-KTPs (n = 65) and KTPs (n = 46). The non-KTPs were considered the control group of the study. Also, according to the Achtman scheme, we performed multilocus sequence typing to assess the relationship between twenty-nine of ESBL-producing isolates containing bla_CTX-M gene.

Results

According to the results of PCR assay, the prevalence of virulence factor genes ranged from 0% (cnf and papG III) to 93.7% (fimH). Also, KTP isolates significantly differed from non-KTP isolates only in terms of the prevalence of pap GI elements. Moreover, the most frequent UPEC isolates were in phylogenetic group B₂, followed by group D (18.9%), and group A (13.5%). Furthermore, except for phylogenetic group C, there was no significant correlation between phylogenetic distribution in KTPs and non-KTPs. Additionally, MLST analysis of bla_CTX-M carrying isolates identified 18 unique sequence types (ST) the most common of which was ST131 (24.1%), followed by ST1193 (10.3%), while fourteen STs were detected only once.

Conclusions

The results further revealed significant differences between the UPEC isolates from KTPs and non-KTPs regarding the phylogroups C and PAI gene. Based on MLST analysis, we also observed a relatively high diversity in UPEC isolates obtained from KTPs and non-KTPs. Moreover, clonal complex (CC) 131 and ST131 were found to be the most prevalent clones and ST types, respectively. Besides, for the first time, ST8503 were reported in KTPs. These results suggested regular studies on characterization of UPEC isolates among KTPs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-021-00470-7.

Arrangements of Mobile Genetic Elements among Virotype E Subpopulation of Escherichia coli Sequence Type 131 Strains with High Antimicrobial Resistance and Virulence Gene Content

Escherichia coli sequence type 131 (ST131) is known for its contribution to multidrug resistance and the worldwide spread of this clone has become a global problem. Understanding the trends among ST131 clades will help design strategies to prevent its rapid dissemination. In this study, 72 ST131 strains were subjected to comparative genomic analysis and 64 clade C strains were compared with clade C strains reported from other regions using publicly available whole-genome sequencing data. C1 (n = 31 [48.4%]) and C2 (n = 33 [%51.5]) strains had the same prevalence in our collection, and C1-M27 (n = 22) strains were closely related, carried a unique plasmid type (F1:A2:B20), and exhibited virotype C. Removal of 11 C2 strains with varied virotype patterns and the heterogeneous IncF type identified 22 closely related virotype E/F strains with replicon type F31/F36:A4:B1, forming what we denote as the “C2-subset.” In a global context, the C2-subset constituted a distinct cluster with international virotype E strains and harbored a genomic island, GI-pheU. Association of cnf1/hlyCABD genes with 1 to 7 mobile genetic elements, mostly IS682/ISKpn37 combination within GI-pheU was identified. The C2-subset accounted for excess resistance/virulence of subclade C2 relative to C1 strains. In addition, a conserved chromosomal IS26-mediated composite transposon (IS15DIV-ISEcp1-bla_CTX-M-15-WbuC cupin fold metalloprotein-Tn2-IS15DIV) was observed in the C2-subset. The local spread of the C2-subset in the hospital studied, with the carriage of higher virulence/resistance markers and a peculiar F-type plasmid, demonstrates the potential for diversification of the ST131 lineage and the emergence of subpopulations with higher survival potential to cause health care-associated outbreaks.

IMPORTANCEEscherichia coli sequence type 131 (ST131) is a globally dominant multidrug-resistant clone that is commonly associated with extraintestinal infections. Specific sublineages have been shown to have emerged and spread within ST131, highlighting the complex nature of ST131 epidemiology. This study systematically compared the Iranian ST131 population to those reported from other countries and found a subpopulation harboring virotype E, a homogeneous profile of plasmid Inc-F type F31/F36:A4:B1 harboring cnf1/hemolysin genes on the genomic island GI-pheU, and up to seven mobile genetic elements (MGEs) flanking cnf1/hemolysin virulence markers. The results of this study highlight the importance of MGEs for virulence gene acquisition and the formation of new subpopulations among pandemic clones such as E. coli ST131.

Expansion of a Subset Within the C2 Subclade of Escherichia coli Sequence Type 131 (ST131) Is Driving the Increasing Rates of Aminoglycoside Resistance

Background

Sequence type 131 (ST131) of Escherichia coli is a pandemic clone that drives the increasing rates of antibiotic resistance. While the pervasiveness of ST131 clade C, especially subclades C2 and C1-M27, has been demonstrated in numerous global surveys, no report about the ST131 clades and their virotypes has been published from Iran so far.

Methods

A collection of 73 consecutive ST131 isolates from extraintestinal specimens was investigated for determination of virotypes, antibiotic susceptibility patterns, resistance/virulence determinants, and clade subsets.

Results

Most of the isolates belonged to subclade C2 (33/73; 45.2%), which had the highest virulence factor (VF) scores and resistance rates, followed by C1-M27 (18; 24.6%), C1-non-M27 (14; 19.1%), and A (8; 10.9%). The distinctive profiles of subclade C2 virulence genes were revealed by principle coordinates analysis testing. The distribution of the hlyA virulence gene among subclade C2 was not uniform, so that positive strains (21; 63.6%) showed significantly higher rates of resistance (bla_CTX-M-15, bla_OXA-1, aac(6’)-Ib-cr, aac(6’)-Ib, aac(3)-IIa) and virulence (hra, tia/hek, K5, cnf, papGII, papC) markers and gentamicin/tobramycin resistance. Virotype C as the most common virotype (34; 46.5%) was predominant among the subclade C1 population, while virotypes E and F (21; 28.7%) were detected among subclade C2, which had the highest VF scores and aminoglycoside resistance rates.

Conclusions

The appearance of virotypes E and F among subclade C2 strains with higher rates of aminoglycoside resistance/virulence gene content shows the shifting dynamics of this pandemic clone in response to antibiotic selection pressure by establishing subsets with higher survival potential.

Prevalence of E. coli ST131 among Uropathogenic E. coli Isolates from Iraqi Patients in Wasit Province, Iraq

The emergence of Escherichia coli sequence type 131 (E. coli ST131) clone represents a major challenge to public health globally, since this clone is reported as highly virulent and multidrug-resistant, thus making it successfully disseminated worldwide. In Iraq, there is no previous study dealing with this important clone, so this project was suggested to investigate its presence within uropathogenic E. coli (UPEC) from Iraqi patients in Wasit Province. A total of 112 UPEC isolates from cases of acute urinary tract infection (UTI) were analysed for phylogenetic groups by quadruplex PCR; then, these isolates were investigated for E. coli ST131 clone by both conventional and real-time PCR procedures. The antibiotic susceptibility test was performed by the disk diffusion method. The results revealed that, out of 112 UPEC isolates, 38 (33.9%) belonged to phylogroup B2. For conventional PCR, 92.1% (35/38) of B2 E. coli isolates were positive for E. coli ST131, of which 34 were O25b-ST131 strain and 1 was O16-ST131 strain. However, serogroups O25b and O16 represented 17.1% and 2.8%, respectively. By RT-PCR assay, 15.1% (17/112) and 44.7% (17/38) of total and B2 E. coli isolates were confirmed as being E. coli ST131, respectively. The highest resistance rates of E. coli ST131 isolates were against the β-lactams, while low resistance rates were against amikacin, nitrofurantoin, and gentamicin. Fortunately, all isolates were susceptible to carbapenems. Moreover, 52.9% (9 out of 17) of E. coli ST131 isolates were MDR. In conclusion, the presence of E. coli ST131 among UPEC isolates from Iraqi patients is confirmed with high resistance to most antimicrobials included in this study.

The emergence of the hypervirulent Klebsiella pneumoniae (hvKp) strains among circulating clonal complex 147 (CC147) harbouring blaNDM/OXA-48 carbapenemases in a tertiary care center of Iran

Background

Klebsiella pneumoniae is a public health concern because of its ability to develop multidrug resistance and hypervirulent genotypes, of those capsular types K1 and K2 cause community and nosocomial life-threatening infections. This study aimed to determine the antibiotic susceptibility patterns and genotypic traits of a collection of Klebsiella spp. isolates. Furthermore, the clonal relatedness of bla_NDM producing strains was investigated.

Methods

During a 19-months  surveillance study, 122 Klebsiella spp. isolates were cultured from extraintestinal specimens of patients admitted to the tertiary referral hospital in Semnan, Iran. Isolates were identified using biochemical tests and subjected to determination of phylogroups, capsular types and virulence/resistance genes content. Hypervirulent K. pneumoniae (hvKp) strains were detected genotypically, and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting was used to determine the clonality of bla_NDM producing strains.

Results

Multidrug resistant phenotype was detected in 75 (61.5%) isolates and amikacin was found as the most potent antibiotic with the susceptibility rate of 85.2%. The carbapenemase genes were detected in 45 (36.8%) strains, including 21 (17.2%) bla_OXA-48, 7 (5.6%) bla_NDM-1, 14 (11.4%) bla_NDM-1/OXA-48 and 3 (2.4%) bla_IMP- carrying strains, while 55 (45.08%) isolates showed carbapenem resistant phenotype. The first bla_NDM-1 carrying strain was cultured from a sputum specimen on March 2015, while the last positive one was recovered from blood culture on September 2016. Most of the isolates (80.3%) belonged to phylogroup I, and bla_NDM-1 was identified among all three phylogroups. The ERIC-PCR clustered the 101 bla_NDM negative and 21 bla_NDM-1 positive isolates into 25 and five clusters, respectively, and the latter group belonged to clonal complex 147 (CC147). One K1 and 15 K2 bla_NDM-1 negative isolates were detected, of those three strains were identified as hvKp. Five K2 positive strains, including four bla_OXA-48 producer and one hvKp sequence type 86 (ST86) were carbapenem resistant. Among carbapenem resistant isolates, CC147 strains harboured higher rates of siderophores iutA and ybtS.

Conclusion

The present findings showed a hospital circulation of CC147 bla_NDM-1 or bla_NDM-1/OXA-48 producing strains, disseminated in different wards. The hvKp/ST86 strain expressing K2 capsular type and carbapenem resistant phenotype wasn’t reported from Iran so far. So, it seems that we must be aware of the emergence and spread of new K. pneumoniae clones associated with resistant and hypermucoviscous phenotypes.

Antibiotic Resistance Among Uropathogenic Escherichia coli

Urinary tract infections (UTIs) belong to the most common community-acquired and nosocomial infections. A main etiological factor of UTIs is uropathogenic Escherichia coli (UPEC). This review describes the current state of knowledge on the resistance of UPEC to antibiotics recommended for the treatment of UTIs based on the available literature data. Nitrofurantoin and fosfomycin are recommended as first-line therapy in the treatment of uncomplicated cystitis, and the resistance to these antimicrobial agents remains low between UPEC. Recently, in many countries, the increasing resistance is observed to trimethoprim-sulfamethoxazole, which is widely used as the first-line antimicrobial in the treatment of uncomplicated UTIs. In European countries, the resistance of UPEC to this antimicrobial agent ranges from 14.6% to 60%. The widespread use of fluoroquinolones (FQs), especially ciprofloxacin, in the outpatients is the cause of a continuous increase in resistance to these drugs. The resistance of UPEC to FQs is significantly higher in developing countries (55.5–85.5%) than in developed countries (5.1–32.0%). Amoxicillin-clavulanic acid is recommended as first line-therapy for pyelonephritis or complicated UTI. Resistance rates of UPEC to amoxicillin-clavulanic acid are regionally variable. In European countries the level of resistance to this antimicrobial ranges from 5.3% (Germany) to 37.6% (France). Increasing rates of UPEC resistance to antimicrobials indicate that careful monitoring of their use for UTI treatment is necessary.

Clonal diversity, virulence genes content and subclone status of Escherichia coli sequence type 131: comparative analysis of E. coli ST131 and non-ST131 isolates from Iran

BACKGROUND

The Escherichia coli sequence type 131 (ST131) is a well established clone causing significant extraintestinal infections worldwide. However, no studies have been reported the phenotypic and molecular traits of ST131 isolates in comparison to other clones of E. coli from Iran. So, we determined the differences between 69 ST131 strains collected during a one year surveillance study and 84 non-ST131 isolates, including 56 clinical fluoroquinolone resistant and 28 broiler colibacillosis isolates in terms of clonality and genetic background.

RESULTS

ST131 isolates were associated with phylogroup B2 (68 out of 69 isolates, 98.4%), while clinical non-ST131 and fluoroquinolone resistant broiler isolates mainly belonged to phylogroup A. The highest virulence score was observed in ST131 clone, while they showed less diversity in virulence profiles than other clinical isolates. Almost all of the ST131 isolates (95.6%) were ExPEC and had the highest virulence scores, but their resistance scores were less than clinical non-ST131 isolates. Broiler isolates showed higher prevalence of ExPEC-associated virulence genes and CTX-M-G1/G9 resistance determinants as compared to clinical non-ST131 isolates. While bla_OXA-48/NDM carbapenemases were mostly found in ST131 clone, resistance rate against ertapenem was higher among clinical non-ST131 strains. According to ERIC-based fingerprinting, the ST131 strains were more genetically similar, followed by non-ST131 and broiler isolates.

CONCLUSIONS

ST131 isolates possess the ability to make a balance between clonality and extent of resistance/virulence genes content, so this phenomenon gives a fitness advantage over other E. coli clones. The broilers E. coli population poses a potential zoonotic risk which could be transmitted to the community through the food chain. A number of factors are involved in the dissemination of and infections due to ST131 clone.