Virulence factors profile of drug-resistant Escherichia coli isolates from urinary tract infections in Punjab, Pakistan

Genotypic characteristics of Uropathogenic Escherichia coli isolated from complicated urinary tract infection (cUTI) and asymptomatic bacteriuria-a relational analysis

Background

Uropathogenic Escherichia coli (UPEC) is the predominant agent causing various categories of complicated urinary tract infections (cUTI). Although existing data reveals that UPEC harboured numerous virulence determinants to aid its survival in the urinary tract, the reason behind the occurrence of differences in the clinical severity of uninary tract infections (UTI) demonstrated by the UPEC infection is poorly understood. Therefore, the present study aims to determine the distribution of virulence determinants and antimicrobial resistance among different phylogroups of UPEC isolated from various clinical categories of cUTI and asymptomatic bacteriuria (ASB) E. coli isolates. The study will also attempt a relational analysis of the genotypic characteristics of cUTI UPEC and ASB E. coli isolates.

Methods

A total of 141 UPEC isolates from cUTI and 160 ASB E. coli isolates were obtained from Universiti Malaya Medical Centre (UMMC). Phylogrouping and the occurrence of virulence genes were investigated using polymerase chain reaction (PCR). Antimicrobial susceptibility of the isolates to different classes of antibiotics was determined using the Kirby Bauer Disc Diffusion method.

Results

The cUTI isolates were distributed differentially among both Extraintestinal Pathogenic E. coli (ExPEC) and non-ExPEC phylogroups. Phylogroup B2 isolates were observed to possess the highest average aggregative virulence score (7.17), a probable representation of the capability to cause severe disease. Approximately 50% of the cUTI isolates tested in this study were multidrug resistant against common antibiotics used to treat UTI. Analysis of the occurrence of virulence genes among different cUTI categories demonstrated that UPEC isolates of pyelonephritis and urosepsis were highly virulent and had the highest average aggregative virulence scores of 7.80 and 6.89 respectively, compared to other clinical categories. Relational analysis of the occurrence of phylogroups and virulence determinants of UPEC and ASB E. coli isolates showed that 46.1% of UPEC and 34.3% of ASB E. coli from both categories were distributed in phylogroup B2 and had the highest average aggregative virulence score of 7.17 and 5.37, respectively. The data suggest that UPEC isolates which carry virulence genes from all four virulence genes groups studied (adhesions, iron uptake systems, toxins and capsule synthesis) and isolates from phylogroup B2 specifically could predispose to severe UTI involving the upper urinary tract. Therefore, specific analysis of the genotypic characteristics of UPEC could be further explored by incorporating the combination of virulence genes as a prognostic marker for predicting disease severity, in an attempt to propose a more evidence driven treatment decision-making for all UTI patients. This will go a long way in enhancing favourable therapeutic outcomes and reducing the antimicrobial resistance burden among UTI patients.

Antibiotic Resistance Profile, Biofilm Formation Ability, and Virulence Factors Analysis of Three Staphylococcus spp. Isolates From Urine

Background Staphylococcus spp. is one of the most causative agents of urinary tract infections (UTIs). This study aimed to investigate the antibiotic resistance profile and the virulence factors, including the biofilm formation ability of Staphylococcus spp. isolates from urine. Methodology The agar disk diffusion method was used to test the susceptibility of Staphylococcus isolates to ten antibiotics. The biofilm formation ability was determined using the safranin microplate-based method, and the phospholipase, esterase, and hemolysin activities were assessed by the agar plate method. Results During the study period, a prevalence of 18.12% of urinary tract infections caused by the identified Staphylococci was obtained. All the isolated Staphylococcus aureus and S. epidermidis were resistant to cefazolin. Multi-drug resistance (MDR) was recorded in 80.01%, 81.49%, and 76.20% of S. aureus, S. epidermidis, and S. saprophyticus isolates, respectively. Most of the isolates were moderate biofilm formers, while 44.44%, 31.75%, and 30.16% were positive for phospholipase, esterase, and hemolysin activities, respectively. No relevant correlations were observed between the ability of biofilm formation and the resistance to antibiotics or the expression of virulence factors investigated. Conclusion This study shows that Staphylococcus spp. isolates from patients with clinical manifestations of UTIs expressed a high degree of virulence factors, including the ability of biofilm formation, and exhibited multi-drug resistance to the majority of antimicrobials commonly used for the treatment of Staphylococcal infections.

Demonstrating the utility of Escherichia coli asymptomatic bacteriuria isolates’ virulence profile towards diagnosis and management—A preliminary analysis

Asymptomatic bacteriuria (ASB) caused by Escherichia coli (E. coli) is a significant condition associated with pregnancy and is considered as prognostic for the development of symptomatic urinary tract infection (UTI). However, treating all ASB increases the use of antibiotics and leads to the development of multidrug resistance (MDR). Therefore, this study aimed to identify the distribution of UPEC associated virulence genes and antibiotic susceptibility among phylogroups of E. coli isolated from ASB in pregnancy. Moreover, the gene expression of selected virulence genes was also compared among two E. coli isolates (with different pathogenic potential) to determine its pathogenicity. One hundred and sixty E. coli isolates from midstream urine samples of pregnant women with ASB were subjected to PCR-based detection for its phylogroups and virulence genes. The antibiotic susceptibility of isolated strains was determined by the disc diffusion method. Expression of the virulence genes were determined through microarray analysis and quantitative Real-Time PCR. The prevalence of ASB in this study was 16.1%. Within ASB isolates, the occurrence of phylogroup B2 was the highest, and isolates from this group harboured most of the virulence genes studied. Overall, the most identified virulence genes among all phylogroups in descending order were fimH, chuA, kpsMTII, usp, fyuA, hlyA, iroN, cnf, papC, sfa, ompT, and sat. In this study, higher resistance to antibiotics was observed for ampicillin (77.5%), amoxicillin-clavulanate (54.4%), trimethoprim-sulfamethoxazole (46.9%) and amikacin (43.8%) compared to the other tested antibiotics and 51.9% of the tested isolates were MDR. Furthermore, hierarchical clustering and gene expression analysis demonstrated extreme polarization of pathogenic potential of E. coli causing ASB in pregnancy necessitating the need for bacterial isolate focused approach towards treatment of ASB.

Surface-Enhanced Raman Scattering for Rapid Detection and Characterization of Antibiotic-Resistant Bacteria

As the prevalence of antibiotic-resistant bacteria continues to rise, biosensing technologies are needed to enable rapid diagnosis of bacterial infections. Furthermore, understanding the unique biochemistry of resistance mechanisms can facilitate the development of next generation therapeutics. Surface-enhanced Raman scattering (SERS) offers a potential solution to real-time diagnostic technologies, as well as a route to fundamental, mechanistic studies. In the current review, SERS-based approaches to the detection and characterization of antibiotic-resistant bacteria are covered. The commonly used nanomaterials (nanoparticles and nanostructured surfaces) and surface modifications (antibodies, aptamers, reporters, etc.) for SERS bacterial detection and differentiation are discussed first, and followed by a review of SERS-based detection of antibiotic-resistant bacteria from environmental/food processing and clinical sources. Antibiotic susceptibility testing and minimum inhibitory concentration testing with SERS are then summarized. Finally, recent developments of SERS-based chemical imaging/mapping of bacteria are reviewed.

Genotypic Characterization of Virulence Factors in Escherichia coli Isolated from Patients with Acute Cystitis, Pyelonephritis and Asymptomatic Bacteriuria

INTRODUCTION

Urinary Tract Infections (UTIs) caused by Uropathogenic Escherichia coli (UPEC) are among the most common infections worldwide. It is well-documented that the pathogenesis of UPEC is mediated by the production of a wide variety of Virulence Factors (VFs). Thus, detection of these VFs and evaluation of their association with different clinical types of UTIs could help to understand the role of these factors in pathogenesis of UPEC isolates.

AIM

To investigate the genotypic characteristics of UPEC isolates and to examine the relationship between VFs and different clinical symptoms of UTI.

MATERIALS AND METHODS

In this cross-sectional study conducted at Pasteur Institute of Iran, a total of 156 UPEC isolated from outpatients and inpatients (symptomatic and asymptomatic UTI patients) visiting general and private hospitals in Tehran, Iran between March 2014 and February 2015 were included. Among them, 49 patients experienced at least one episode of recurrent UTI. A Polymerase Chain Reaction (PCR) assay was developed to detect the presence of different VFs in the isolates. Moreover, Pulsed-Field Gel Electrophoresis (PFGE) was used to characterize clonal relationships among UPEC isolates.

RESULTS

The prevalence of virulence genes ranged from 0% for cdtB to 100% for fimH. The papEF, hlyA and aer genes were found to be significantly more frequent in UPEC isolated from patients with pyelonephritis, while the afa gene, the only indicator of recurrent UTIs, was more prevalent in UPEC isolated from patients with cystitis. In the present study, 34 PFGE clonal groups were found in the UPEC genome.

CONCLUSION

Our findings showed that from outpatients and patients with pyelonephritis, isolates were more virulent than those isolated from inpatients and cystitis patients, respectively. PFGE displayed a large diversity in the UPEC isolates that could be considered as an evolutionary strategy in the survival of the bacteria.

Zinc-triggered hydrogelation of self-assembled small molecules to inhibit bacterial growth

There is a significant need to develop antibacterial materials that could be applied locally and directly to the places surrounded by large amount of bacteria, in order to address the problems of bacterial antibiotic-resistance or irreversible biofilm formation. Hydrogels are thought to be suitable candidates due to their versatile applications in biomedical field. Among them, small molecular hydrogels have been paid lots of attention because they are easy to design and fabricate and often sensitive to external stimuli. Meanwhile, the antibacterial activity of metal ions are attracting more and more attention because resistance to them are not yet found within bacteria. We therefore designed the zinc ion binding peptide of Nap-GFFYGGGHGRGD, who can self-assemble into hydrogels after binds Zn(2+) and inhibit the growth of bacteria due to the excellent antibacterial activity of Zn(2+). Upon the addition of zinc ions, solutions containing Nap-GFFYGGGHGRGD transformed into supramolecular hydrogels composed of network of long nano-fibers. Bacterial tests revealed an antibacterial effect of the zinc triggered hydrogels on E. coli. The studied small molecular hydrogel shows great potential in locally addressing bacterial infections.

Virulence factors, serogroups and antimicrobial resistance properties of Escherichia coli strains in fermented dairy products

Background

From a clinical perspective, it is essential to know the microbial safety of fermented dairy products. Doogh and kashk are fermented dairies. These products are used by millions of people but their microbial qualities are unknown. Shiga toxin producing Escherichia coli (STEC) is one of the most commonly detected pathogens in the cases of food poisoning and food-borne illnesses. The present investigation was carried out in order to study the molecular characterization and antimicrobial resistance properties of STEC strains isolated from fermented dairy products.

Methods

Six hundred fermented dairy samples were collected and immediately transferred to the laboratory. All samples were cultured immediately and those that were E. coli-positive were analyzed for the presence of O157 , O26, O103, O111, O145, O45, O91, O113, O121 and O128 STEC serogroups, tetA, tetB, blaSHV, CITM, cmlA, cat1, aadA1, dfrA1, qnr, aac (3)-IV, sul1 and ereA antibiotic resistance genes and stx1, stx2, eaeA, ehly, cnf1, cnf2, iutA, cdtB, papA, traT, sfaS and fyuA virulence factors using PCR. Antimicrobial susceptibility testing was performed also using disk diffusion methodology with Mueller–Hinton agar.

Results

Fifty out of 600 (8.33%) dairy samples harbored E. coli. In addition, yoghurt was the most commonly contaminated dairy. O157 (26%) and O26 (12%) were the most commonly detected serogroups. A significant difference was found between the frequency of Attaching and Effacing E. coli and Enterohaemorrhagic E. coli (P <0.05). Stx1 (44%), eae (36%), papA (32%) stx2 (30%), and ehly (28%) were the most commonly detected virulence factors. The genes encode resistance against tetracycline (tetA and tetB) (76% and 70%, respectively), cephalothin (blaSHV) (38%), ampicillin (CITM) (36%) and gentamicin (aac (3)-IV) (32%) were the most commonly detected. High resistance levels to tetracycline (84%), penicillin (46%), ampicillin (38%) and streptomycin (36%) were observed.

Conclusion

Fermented dairy products can easily become contaminated by antibiotic resistant STEC strains. Our findings should raise awareness about antibiotic resistance in Iran. Clinicians should exercise caution when prescribing antibiotics, especially in veterinary treatments.

Association of some virulence genes with antibiotic resistance among uropathogenic Escherichia coli isolated from urinary tract infection patients in Alexandria, Egypt: A hospital-based study

Uropathogenic Escherichia coli (UPEC) is the infecting agent most frequently involved in urinary tract infections (UTIs) worldwide. UPEC resistance to commonly used antibiotics represents a major health problem all over the world. Several factors have been associated with UPEC resistance to antibiotics. The present study deployed a molecular approach to explore the association between some UPEC virulence genes and antibiotic resistance among patients with UTI in Alexandria, Egypt. The study revealed a significant association between presence of the pap gene and resistance to gentamicin; however, it was not significantly associated with resistance to β-lactam antibiotics, quinolones, aminoglycosides, nitrofurantoin and trimethoprim/sulfamethoxazole. The genes sfa, aer and cnf1 were not significantly associated with UPEC resistance to any of the tested antibiotics. In conclusion, resistance of UPEC isolates in the present study could be attributed to other virulence factors.

The influence of antibiotic resistance gene carriage on biofilm formation by two Escherichia coli strains associated with urinary tract infections

Urinary tract infections (UTI) caused by uropathogenic Escherichia coli are one of the most common forms of human disease. In this study, the effect of the presence of newly acquired antibiotic resistance genes on biofilm formation of UTI-associated E. coli strains was examined. Two clinical UTI-associated E. coli strains (SMC18 and SMC20) carrying different combinations of virulence genes were transformed with pGEM-T, pGEM-T::KmΔAmp, or pGEM-T::Km to construct ampicillin-resistant (KmSAmpR), kanamycin-resistant (KmRAmpS), or ampicillin- and kanamycin-resistant (KmRAmpR) strains. Transformed and wild-type strains were characterized for biofilm formation, bacterial surface hydrophobicity, auto-aggregation, morphology, and attachment to abiotic surfaces. Transformation with a plasmid carrying an ampicillin resistance gene alone decreased (p < 0.05) biofilm formation by SMC18 (8 virulence marker genes) but increased (p < 0.05) biofilm formation by SMC20 (5 virulence marker genes). On the other hand, transformation with a plasmid carrying a kanamycin resistance gene alone or both ampicillin and kanamycin resistance genes resulted in a decrease (p < 0.05) in biofilm formation by SMC18 but did not affect (p > 0.05) the biofilm formation by SMC20. Our results suggest that transformation of UTI-associated E. coli with plasmids carrying different antibiotic resistance gene(s) had a significant impact on biofilm formation and that these effects were both strain dependent and varied between different antibiotics.

Serogroups, virulence genes and antibiotic resistance in Shiga toxin-producing Escherichia coli isolated from diarrheic and non-diarrheic pediatric patients in Iran

Background

From a clinical perspective, it is important to know which serogroups, virulence genes and antibiotic resistance patterns are present in Shiga toxin-producing Escherichia coli strains in pediatric patients suffering from diarrheic and non-diarrheic infections. This is the first study in Iran that has comprehensively investigated the Shiga toxin-producing Escherichia coli -related infection characteristics in diarrheic and non-diarrheic pediatric patients of 0–60 months of age.

Methods

Two-hundred and twenty four diarrheic and 84 non-diarrheic stool specimens were collected from the Baqiyatallah hospital of Tehran, Iran. The stool samples were cultured immediately and those that were E. coli-positive were analyzed for the presence of antibiotic resistance genes and bacterial virulence factors using PCR. Antimicrobial susceptibility testing was performed using disk diffusion method.

Results

One-hundred and fifty four out of 224 (68.75%) diarrheic stools and 31 out of 84 (36.90%) non-diarrheic stools harbored E. coli. In addition, children in 13–24 month-old age group had the highest incidence of infection with this bacterium (77.63%). A significant difference was found between the frequency of Attaching and Effacing Escherichia coli and Enterohaemorrhagic Escherichia coli (P =0.045). The genes encoding Shiga toxins and intimin were the most commonly detected virulence factors. Among all serogroups studied, O26 (27.04%) and O111 (18.85%) had the highest incidences in the diarrheic and non-diarrheic patients. The incidence of genes encoding resistance against sulfonamide (sul1), gentamicin (aac(3)-IV), trimethoprim (aadA1), cephalothin (blaSHV) and tetracycline (tetA) were 82.78%, 68.03%, 60.65%, 56.55% and 51.63%, respectively. High resistance levels against penicillin (100%), tetracycline (86.88%), gentamicin (62.29%) and streptomycin (54.91%) were observed. Marked seasonality in the serogroup distributions was evident, while STEC infections were more common in summer (P =0.041).

Conclusions

Our findings should raise awareness about antibiotic resistance in diarrheic pediatric patients in Iran. Clinicians should exercise caution when prescribing antibiotics, especially during the warmer months of the year.

Shiga toxin-producing Escherichia coli isolated from chicken meat in Iran: serogroups, virulence factors, and antimicrobial resistance properties

The aim of the current study was to determine the virulence factors, serogroups, and antibiotic resistance properties of Shiga toxin-producing Escherichia coli isolated from chicken meat samples. A total of 422 chicken meat samples were collected from 5 townships of Iran. Specimens were immediately transferred to the laboratory in a cooler with an ice pack. Samples were cultured, and the positive culture samples were analyzed by PCR assays. Finally, the antimicrobial susceptibility test was performed using the disk diffusion method in Mueller-Hinton agar. According to the results, out of 422 samples, 146 (34.59%) were confirmed to be E. coli positive and among E. coli-positive samples, 51 (34.93%) and 31 (21.23%) were from attaching and effacing E. coli (AEEC) and enterohemorrhagic E. coli (EHEC) subgroups, respectively. All of the EHEC-positive samples had all stx1, eaeA, and ehly virulence genes, whereas only 5 (9.80%) of AEEC subgroup had all stx1, stx2, and eaeA genes. As the data revealed, O157 was the most prevalent and O111 was the least prevalent strains in the Shiga toxin-producing E. coli (STEC) population. Among STEC strains, sulI and blaSHV had the highest and lowest incidence rate, respectively. There was a high resistance to tetracycline (76.82%), followed by chloramphenicol (73.17%) and nitrofurantoin (63.41%), but there was low resistance to cephalotine (7.31%) antibiotics in isolated strains. Results shows that the PCR technique has a high performance for detection of serogroups, virulence genes, and antibiotic resistance genes in STEC strains. This study is the first prevalence report of detection of virulence genes, serogroups, and antibiotic resistance properties of STEC strains isolated from chicken meat samples in Iran. Based on the results, chicken meat is one of the main sources of STEC strains and its virulence factors in Iran, so an accurate meat inspection would reduce disease outbreaks.

Incidence of Shiga toxin-producing Escherichia coli serogroups in ruminant's meat

To assess the presences of Escherichia coli, its serogroups, virulence factors and antibiotic resistance properties in ruminant's meat, a total of 820 raw meat samples were collected and then evaluated using culture, PCR and disk diffusion methods. Totally, 238 (29.02%) samples were positive for presence of Escherichia coli. All of the isolates had more than one virulence gene including Stx1, Stx2, eaeA and ehly. All investigated serogroups were found in beef and sheep and all except O145, O121 and O128 were found in goat. The O91, O113, O111, O103, O26 and O157 serogroups were found in camel. Totally, aadA1-blaSHV combination was the most predominant antibiotic resistance gene. The highest resistance of STEC strains was seen against penicillin while resistance to nitrofurantoin and ciprofloxacin was minimal. These findings showed that health care and meat inspection should be reconsidered in Iranian slaughterhouses and butchers.

Shiga toxin-producing Escherichia coli isolated from bovine mastitic milk: serogroups, virulence factors, and antibiotic resistance properties

The aim of this study was to detect the virulence factors, serogroups, and antibiotic resistance properties of Shiga toxin-producing Escherichia coli, by using 268 bovine mastitic milk samples which were diagnosed using California Mastitis Test. After E. coli identification, PCR assays were developed for detection of different virulence genes, serogroups, and antibiotic resistance genes of Escherichia coli. The antibiotic resistance pattern was studied using disk diffusion method. Out of 268 samples, 73 (27.23%) were positive for Escherichia coli, and, out of 73 positive samples, 15 (20.54%) were O26 and 11 (15.06%) were O157 so they were the highest while O111 was not detected in any sample so it was the lowest serogroup. Out of 73 STEC strains, 11 (15.06%) and 36 (49.31%) were EHEC and AEEC, respectively. All of the EHEC strains had stx1, eaeA, and ehly, virulence genes, while in AEEC strains stx1 had the highest prevalence (77.77%), followed by eaeA (55.55%). Totally, aadA1 (65.95%) had the highest while blaSHV (6.38%) had the lowest prevalence of antibiotic resistance genes. The disk diffusion method showed that the STEC strains had the highest resistance to penicillin (100%), followed by tetracycline (57.44%), while resistance to cephalothin (6.38%) was the lowest.

Molecular characterization of Shiga toxin-producing Escherichia coli isolated from ruminant and donkey raw milk samples and traditional dairy products in Iran

The aims of the current study were to detect the virulence factors and antibiotic resistance of Shiga toxin-producing E. coli, in animal milk and dairy products in Iran. After E. coli dentification with culture method, PCR assay were developed for detection of pathogenic genes, serotypes and antibiotic resistance genes of E. coli. Results showed that out of 719 samples, 102 (14.18%) were confirmed to be positive for E. coli and out of 102 positive samples, 17.64% were O26 and 13.72% were O157 and 1.96% were O91 and 1.96% were O145 serotypes. Totally, the prevalence of stx1 and papA genes were the highest while the prevalence of sfaS and fyuA were the lowest in the positive samples. PCR results showed that tetA, tetB were the highest (64.70%) and aac(3)-IV were the lowest (27.45%) antibiotic resistant genes in E. coli positive samples. Our study indicated that the isolated E. coli trains in these regions had a highest antibiotic resistance to tetracycline (58.82%) and the lowest to nitrofurantoin (3.92%). tetA gene and E. coli O157 serotype had highest and aac(3)-IV gene, and E. coli O145 serotype had a lowest frequency rates of antibiotics resistance genes, in the region.

Relationship between urinary tract infection categorization and pathogens' antimicrobial susceptibilities

BACKGROUND

Urinary tract infections (UTIs) can be hard to treat and treatment plans need to include accurate categorization such as uncomplicated or complicated UTI, or catheterized or uncatheterized UTI. We investigated the antibiotic susceptibilities of representative uropathogens in UTI categories.

METHODS

We isolated uropathogens and analyzed their antimicrobial susceptibilities according to UTI categorization such as: (1) urology outpatients, urology inpatients, or other department inpatients; (2) uncomplicated or complicated UTIs; (3) upper or lower UTIs, and (4) non-catheterized or catheterized UTIs.

RESULTS

Escherichia coli, Enterococcus faecalis, and Pseudomonas aeruginosa were representative uropathogens. Susceptibilities to levofloxacin (LVFX) in E. coli in urology outpatients (p = 0.0179), those to ceftadizime in E. coli in other department inpatients (p = 0.0327), and those to LVFX in E. faecalis in complicated UTI (p = 0.0137) significantly decreased in these 3 years compared with the previous 3 years. Susceptibilities of upper UTI to LVFX in E. coli were significantly lower in the recent 4 years compared to lower UTI (p = 0.0452) and those of catheterized UTI to LVFX in E. faecalis were significantly lower than in non-catheterized UTI (p = 0.0153).

CONCLUSIONS

Data demonstrated different tendencies of uropathogens' antibiotic susceptibilities according to UTI categorizations and they could be useful for planning UTI treatments.