Clonal relationships and extended virulence genotypes among Escherichia coli isolates from women with a first or recurrent episode of cystitis

Multicenter molecular investigation of recurrent Escherichia coli bacteriuria in dogs

Escherichia coli is the most common cause of recurrent urinary tract infection (UTI) in dogs. UTI recurrence comprises of persistent, unresolved E. coli infection or reinfection with a different strain of E. coli. Differentiating between these processes is clinically important but is often impossible with routine diagnostics. We tested the hypothesis that most recurrent canine E. coli bacteriuria is due to recurrence of the same E. coli strain involved in the initial infection. Molecular typing was performed on 98 urinary E. coli isolated from dogs with recurrent bacteriuria from five veterinary diagnostic laboratories in the United States. Of the 42 dogs in this study with multiple E. coli bacteriuria observations, a single strain of E. coli caused recurrent bacteriuria in 26 (62 %) dogs, in some cases on multiple occasions for prolonged periods of time (up to eight months). A single E. coli strain was detected during both subclinical bacteriuria and clinically-apparent UTI in three dogs. Isolates with the P-fimbrial adhesin genes papA and papC were associated with recurrence by the same strain of E. coli. Multiple isolations of a single strain of E. coli associated with recurrent bacteriuria suggests that E. coli may be maintained within the urinary tract of some dogs for prolonged periods of time. In some patients, the same strain can cause both clinical UTI and subclinical bacteriuria. This indicates that in dogs, the urinary bladder may serve as a subclinical, long-term reservoir of E. coli that may cause clinical UTI in the future.

Phenotypic and genotypic characteristics of Escherichia coli strains isolated during a longitudinal follow-up study of chronic urinary tract infections

Worldwide, Urinary Tract Infections (UTIs) are an important health problem with many cases reported annually, women being the most affected. UTIs are relevant because they can become a recurrent condition, associated with different factors that contribute to the chronicity of the disease (cUTI). cUTI can be classified as persistent (peUTI) when the causative agent is the same each time the infection occurs or as reinfection (reUTI) when the associated microorganism is different. The purpose of this work was to characterize Escherichia coli isolates obtained in two prospective studies of patients with cUTI, to define which of them corresponded to peUTI and which to reUTI. A total of 394 isolates of E. coli were analyzed by agglutination with specific sera, antimicrobial susceptibility by diffusion disc test, and the phylogroups and presence of genes associated with virulence by PCR assays. Additionally, in some characterized strains adherence, invasiveness, and biofilm formation were analyzed by in vitro assays. The results showed that the peUTI strains belonged mainly to the classical UPEC serogroups (O25, O75, O6), were included in the B2 phylogroup, carried a great number of virulence genes, and were adherent, invasive, and biofilm-forming. Meanwhile, reUTI strains showed great diversity of serogroups, belonged mainly in the A phylogroup, and carried fewer virulence genes. Both peUTI and reUTI strains showed extensively drug-resistant (XDR) and multidrug-resistant (MDR) profiles in the antimicrobial susceptibility test. In conclusion, it appears that peUTIs are caused principally by classical UPEC strains, while reUTIs are caused by strains that appear to be a part of the common E. coli intestinal biota. Moreover, although both peUTI and reUTI strains presented different serotypes and phylogroups, their antimicrobial resistance profile (XDR and MDR) was similar, confirming the importance of regulating prophylactic treatments and seeking alternatives for the treatment and control of cUTI. Finally, it was possible to establish the features of the E. coli strains responsible for peUTI and reUTI which could be helpful to develop a fast diagnostic methodology.

Comparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing E. coli Isolates from Patients with Recurrent and Sporadic Urinary Tract Infections

The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is a major threat to human health. ESBL-E. coli sequence type (ST) 131 is the dominating clone worldwide, especially its subclade C2. Patients developing recurrent UTI (RUTI) due to ST131 subclade C2 appear to have an increased risk of recurrent infections. We have thus compared the whole genome of ST131 subclade C2 isolates from 14 patients with RUTI to those from 14 patients with sporadic UTI (SUTI). We aimed to elucidate if isolates causing RUTI can be associated with specific genomic features. Paired isolates from patients with RUTI were identical, presenting 2-18 single nucleotide polymorphism (SNP) differences for all six patients investigated. Comparative genomic analyses, including virulence factors, antibiotic resistance, pangenome and SNP analyses did not find any pattern associated with isolates causing RUTI. Despite extensive whole genome analyses, an increased risk of recurrences seen in patients with UTI due to ST131 subclade C2 isolates could not be explained by bacterial genetic differences in the two groups of isolates. Hence, additional factors that could aid in identifying bacterial properties contributing to the increased risk of RUTI due to ESBL-E. coli ST131 subclade C2 remains to be explored.

Clinical and Microbiological Characteristics of Recurrent Escherichia coli Bacteremia

The causative agents of recurrent Escherichia coli bacteremia can be genetically identical or discordant, but the differences between them remain unclear. This study aimed to explore these differences, with regard to their clinical and microbiological features. Patients were recruited from a Japanese tertiary teaching hospital based on blood culture data and the incidence of recurrent E. coli bacteremia. We compared the patients' clinical and microbiological characteristics between the two groups (those with identical or discordant E. coli bacteremia) divided by the result of enterobacterial repetitive intergenic consensus PCR. Among 70 pairs of recurrent E. coli bacteremia strains, 49 pairs (70%) were genetically identical. Patients with genetically identical or discordant E. coli bacteremia were more likely to have renal failure or neoplasms, respectively. The virulence factor (VF) scores of genetically identical E. coli strains were significantly higher than those of genetically discordant strains, with the prevalence of eight VF genes being significantly higher in genetically identical E. coli strains. No significant differences were found between the two groups regarding antimicrobial susceptibility and biofilm formation potential. This study showed that genetically identical E. coli bacteremia strains have more VF genes than genetically discordant strains in recurrent E. coli bacteremia.

IMPORTANCEEscherichia coli causes bloodstream infection, although not all strains are pathogenic to humans. In some cases, this infection reoccurs, and several reports have described the clinical characteristics and/or molecular microbiology of recurrent Escherichia coli bacteremia. However, these studies focused on patients with specific characteristics, and they included cases caused by microorganisms other than Escherichia coli. Hence, little is known about the pathogenicity of Escherichia coli isolated from the recurrent one. The significance of our study is in evaluating the largest cohorts to date, as no cohort studies have been conducted on this topic.

Distinct Characteristics of Escherichia coli Isolated from Patients with Urinary Tract Infections in a Medical Center at a Ten-Year Interval

Escherichia coli causing urinary tract infections (UTIs) are one of the most common outpatient bacterial infections. This study aimed to compare the characteristics of E. coli isolated from UTI patients in a single medical center in 2009-2010 (n = 504) and 2020 (n = 340). The antimicrobial susceptibility of E. coli was determined by the disk diffusion method. PCRs were conducted to detect phylogenetic groups, ST131, K1 capsule antigen, and 15 virulence factors. Phylogenetic group B2 dominated in our 2009-2010 and 2020 isolates. Moreover, no phylogenetic group E strains were isolated in 2020. E. coli isolates in 2020 were more susceptible to amoxicillin, ampicillin/sulbactam, cefuroxime, cefmetazole, ceftazidime, cefoxitin, tetracycline, and sulfamethoxazole/trimethoprim, compared to the isolates in 2009-2010. Extensively drug-resistant (XDR)-E. coli in 2009-2010 were detected in groups B1 (5 isolates), B2 (12 isolates), F (8 isolates), and unknown (1 isolate). In 2020, XDR-E. coli were only detected in groups A (2 isolates), B2 (5 isolates), D (1 isolate), and F (4 isolates). The prevalence of virulence factor genes aer and fimH were higher in E. coli in 2009-2010 compared to those in 2020. In contrast, afa and sat showed higher frequencies in E. coli isolates in 2020 compared to E. coli in 2009-2010.

Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections

Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0-13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.

Escherichia coli urinary tract infections: Host age-related differences in bacterial virulence factors and antimicrobial susceptibility

BACKGROUND

Urinary tract infections (UTIs) caused by uropathogenic Escherichia coli (UPEC) are one of the most common outpatient bacterial infections. Although bacterial and host factors are reported to be associated with UTI pathogenesis, little is known about the host age-related differences in bacterial virulence factors and antimicrobial susceptibility.

METHODS

PCRs were carried out to detect K1 capsule antigen, 15 virulence factors, and phylogenetic groups in E. coli isolates. Antimicrobial susceptibility of selected agents was determined by the disk diffusion method. Isolates were divided into 6 groups based on their host age.

RESULTS

The results showed that virulence factors PapGII, PapGIII, Cnf1, Aer, Usp, Iha, OmpT, HlyA, and Sat, had highest frequencies in the host age group 0-3. Phylogenetic group B2 dominated in our isolates (59.6%) followed by group D (20.7%). In addition, 77.4% of strains isolated from 0 to 3 age group belonged to phylogenetic group B2. Antimicrobial susceptibility tests showed that E. coli strains isolated were significantly more resistant to antimicrobial agents as host age increased. Phylogenetic group B2 isolates were more susceptible to antimicrobial agents, compared to A, B1, and D isolates.

CONCLUSION

We found E. coli isolated from elders were more resistant to antimicrobial agents and had less virulence factors.

Iron Acquisition of Urinary Tract Infection Escherichia coli Involves Pathogenicity in Caenorhabditis elegans

Uropathogenic Escherichia coli (UPEC) is a major bacterial pathogen that causes urinary tract infections (UTIs). The mouse is an available UTI model for studying the pathogenicity; however, Caenorhabditis elegans represents as an alternative surrogate host with the capacity for high-throughput analysis. Then, we established a simple assay for a UPEC infection model with C. elegans for large-scale screening. A total of 133 clinically isolated E. coli strains, which included UTI-associated and fecal isolates, were applied to demonstrate the simple pathogenicity assay. From the screening, several virulence factors (VFs) involved with iron acquisition (chuA, fyuA, and irp2) were significantly associated with high pathogenicity. We then evaluated whether the VFs in UPEC were involved in the pathogenicity. Mutants of E. coli UTI89 with defective iron acquisition systems were applied to a solid killing assay with C. elegans. As a result, the survival rate of C. elegans fed with the mutants significantly increased compared to when fed with the parent strain. The results demonstrated, the simple assay with C. elegans was useful as a UPEC infectious model. To our knowledge, this is the first report of the involvement of iron acquisition in the pathogenicity of UPEC in a C. elegans model.

Genomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms

Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant's symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition.

Does Escherichia coli have pathogenic potential at a low level of bacteriuria in recurrent, uncomplicated urinary tract infection?

BACKGROUND

In recurrent uncomplicated lower urinary tract infection (uLUTI), bacteriuria below 10³ colony-forming units (CFU)/mL is not usually investigated.

OBJECTIVE

To determine the molecular-genetic characteristics of the pathogenic potential of Enterobacteriaceae isolated between episodes of recurrent uLUTI at bacteriuria of 10² CFU/mL.

MATERIALS AND METHODS

Midstream urine samples taken from 169 women between episodes of recurrent uLUTI were examined on six media. Fifteen Enterobacteriaceae strains at a low level of bacteriuria (10² CFU/mL) were analysed by polymerase chain reaction for the presence of the following virulence factor genes (VFGs): papA, papE/F, papGII, afa, bmaE, iutA, feoB, fyuA, kpsMTII and usp.

RESULTS

All 169 patients had leukocyturia and asymptomatic bacteriuria, and 62 of these cases were due to enterobacteria: 10² CFU/mL, 15 strains (24.2%); 10³ CFU/mL, 10 strains (16.1%); and >10³ CFU/mL, 37 strains (59.7%). VFGs were verified in all 15 strains at a low level of bacteriuria (10² CFU/mL): one VFG (papGII) was found in two strains of Klebsiella spp., three VFGs were found in one strain of Enterobacter spp.xst, and between four and nine VFGs were found in the remaining 12 strains. Among the VFGs, papGII (93.3%), usp (86.7%), feoB (80.0%), fyuA (80.0%) and kpsMTII (73.3%) predominated. A significant correlation was found between the presence of papE (P=0.02) and usp (P=0.025) and a relapse rate of more than four recurrences in 1 year. An association was found between leukocyturia and the presence of papE (P=0.031) and papGII (P=0.031).

CONCLUSION

Enterobacteria isolated from the urine of female patients with recurrent uLUTI at a low level of bacteriuria (10² CFU/mL) have a wide spectrum of VFGs, which may play a role in maintaining chronic inflammation of the lower urinary tract.

Bacterial Microcompartment-Mediated Ethanolamine Metabolism in Escherichia coli Urinary Tract Infection

Urinary tract infections (UTIs) are common and in general are caused by intestinal uropathogenic Escherichia coli (UPEC) ascending via the urethra. Microcompartment-mediated catabolism of ethanolamine, a host cell breakdown product, fuels the competitive overgrowth of intestinal E. coli, both pathogenic enterohemorrhagic E. coli and commensal strains. During a UTI, urease-negative E. coli bacteria thrive, despite the comparative nutrient limitation in urine.

Urinary tract infections (UTIs) are common and in general are caused by intestinal uropathogenic Escherichia coli (UPEC) ascending via the urethra. Microcompartment-mediated catabolism of ethanolamine, a host cell breakdown product, fuels the competitive overgrowth of intestinal E. coli, both pathogenic enterohemorrhagic E. coli and commensal strains. During a UTI, urease-negative E. coli bacteria thrive, despite the comparative nutrient limitation in urine. The role of ethanolamine as a potential nutrient source during UTIs is understudied. We evaluated the role of the metabolism of ethanolamine as a potential nitrogen and carbon source for UPEC in the urinary tract. We analyzed infected urine samples by culture, high-performance liquid chromatography, reverse transcription-quantitative PCR, and genomic sequencing. The ethanolamine concentration in urine was comparable to the concentration of the most abundant reported urinary amino acid, d-serine. Transcription of the eut operon was detected in the majority of urine samples containing E. coli screened. All sequenced UPEC strains had conserved eut operons, while metabolic genotypes previously associated with UTI (dsdCXA, metE) were mainly limited to phylogroup B2. In vitro ethanolamine was found to be utilized as a sole source of nitrogen by UPEC strains. The metabolism of ethanolamine in artificial urine medium (AUM) induced metabolosome formation and provided a growth advantage at the physiological levels found in urine. Interestingly, eutE (which encodes acetaldehyde dehydrogenase) was required for UPEC strains to utilize ethanolamine to gain a growth advantage in AUM, suggesting that ethanolamine is also utilized as a carbon source. These data suggest that urinary ethanolamine is a significant additional carbon and nitrogen source for infecting E. coli strains.

The iron hand of uropathogenic Escherichia coli: the role of transition metal control in virulence

The role of iron as a critical nutrient in pathogenic bacteria is widely regarded as having driven selection for iron acquisition systems among uropathogenic Escherichia coli (UPEC) isolates. Carriage of multiple transition metal acquisition systems in UPEC suggests that the human urinary tract manipulates metal-ion availability in many ways to resist infection. For siderophore systems in particular, recent studies have identified new roles for siderophore copper binding as well as production of siderophore-like inhibitors of iron uptake by other, competing bacterial species. Among these is a process of nutritional passivation of metal ions, in which uropathogens access these vital nutrients while simultaneously protecting themselves from their toxic potential. Here, we review these new findings within the current understanding of UPEC transition metal acquisition.

Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections

Urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC) strains. In contrast to many enteric E. coli pathogroups, no genetic signature has been identified for UPEC strains. We conducted a high-resolution comparative genomic study using E. coli isolates collected from the urine of women suffering from frequent recurrent UTIs. These isolates were genetically diverse and varied in their urovirulence, that is, their ability to infect the bladder in a mouse model of cystitis. We found no set of genes, including previously defined putative urovirulence factors (PUFs), that were predictive of urovirulence. In addition, in some patients, the E. coli strain causing a recurrent UTI had fewer PUFs than the supplanted strain. In competitive experimental infections in mice, the supplanting strain was more efficient at colonizing the mouse bladder than the supplanted strain. Despite the lack of a clear genomic signature for urovirulence, comparative transcriptomic and phenotypic analyses revealed that the expression of key conserved functions during culture, such as motility and metabolism, could be used to predict subsequent colonization of the mouse bladder. Together, our findings suggest that UTI risk and outcome may be determined by complex interactions between host susceptibility and the urovirulence potential of diverse bacterial strains.

Pathoadaptive Mutations in Uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) are opportunistic human pathogens that primarily circulate as part of commensal intestinal microbiota. Though they have the ability to survive and proliferate in various urinary tract compartments, the urinary tract is a transient, occasional habitat for UPEC. Because of this, most of the UPEC traits have originally evolved to serve in intestinal colonization and transmission. Some of these bacterial traits serve as virulence factors - they are critical to or assist in survival of UPEC as pathogens, and the structure and/or function may be specialized for the infection. Other traits could serve as anti-virulence factors - they represent liability in the urinary tract and are under selection to be lost or inactivated during the infection. Inactivation, variation, or other changes of the bacterial genes that increase the pathogen's fitness during the infection are called pathoadaptive mutations. This chapter describes examples of pathoadaptive mutations in UPEC and provides rationale for their further in-depth study.

Can MALDI-TOF Mass Spectrometry Reasonably Type Bacteria?

Bacterial typing is crucial to tackle the spread of bacterial pathogens but current methods are time-consuming and costly. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been recently integrated into the microbiology laboratory workflow for a quick and low-cost microbial species identification. Independent research groups have successfully redirected the original function of this technology from their primary purpose to discriminate subgroups within pathogen species. However, identical bacterial subgroups could be identified by unrelated peaks by independent methods, thus limiting their robustness and exportability. We propose several guidelines that could improve the performance of MALDI-TOF MS-based typing methods for use as a first-line epidemiological tool.

Drug and Vaccine Development for the Treatment and Prevention of Urinary Tract Infections

Urinary tract infections (UTI) are among the most common bacterial infections in humans, affecting millions of people every year. UTI cause significant morbidity in women throughout their lifespan, in infant boys, in older men, in individuals with underlying urinary tract abnormalities, and in those that require long-term urethral catheterization, such as patients with spinal cord injuries or incapacitated individuals living in nursing homes. Serious sequelae include frequent recurrences, pyelonephritis with sepsis, renal damage in young children, pre-term birth, and complications of frequent antimicrobial use including high-level antibiotic resistance and Clostridium difficile colitis. Uropathogenic E. coli (UPEC) cause the vast majority of UTI, but less common pathogens such as Enterococcus faecalis and other enterococci frequently take advantage of an abnormal or catheterized urinary tract to cause opportunistic infections. While antibiotic therapy has historically been very successful in controlling UTI, the high rate of recurrence remains a major problem, and many individuals suffer from chronically recurring UTI, requiring long-term prophylactic antibiotic regimens to prevent recurrent UTI. Furthermore, the global emergence of multi-drug resistant UPEC in the past ten years spotlights the need for alternative therapeutic and preventative strategies to combat UTI, including anti-infective drug therapies and vaccines. In this chapter, we review recent advances in the field of UTI pathogenesis, with an emphasis on the identification of promising drug and vaccine targets. We then discuss the development of new UTI drugs and vaccines, highlighting the challenges these approaches face and the need for a greater understanding of urinary tract mucosal immunity.

Population Phylogenomics of Extraintestinal Pathogenic Escherichia coli

The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinal Escherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. An E. coli chromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenic E. coli strains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival of E. coli as a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.

Emergence of Antibiotic Resistance-Associated Clones Among Escherichia coli Recovered From Newborns With Early-Onset Sepsis and Meningitis in the United States, 2008-2009

BACKGROUND

Escherichia coli associated with early-onset sepsis (EOS) have historically been antibiotic-susceptible and K1-encapsulated. In the era of emerging antibiotic resistance, however, the clonal makeup of E coli associated with EOS has not been well characterized.

METHODS

Escherichia coli isolates were collected from 28 cases of EOS and early-onset meningitis (EOM) from April 2008 through December 2009, during a parent study conducted at National Institute of Child Health and Human Development Neonatal Research Network centers from February 2006 through December 2009. Clinical and microbiologic data were collected for the parent study. We applied polymerase chain reaction- and sequence-based molecular techniques to determine clonal, virulence-associated and antibiotic resistance-associated traits of the E coli isolates.

RESULTS

Among 28 E coli strains, phylogroup B2 strains predominated (68%), of which more than half were K1-encapsulated (53%). Phylogroup D strains were prominent as well (18%), but none were K1-encapsulated. Across the strain collection, the rate of ampicillin resistance was high (78%). The sole strain resistant to either extended-spectrum cephalosporins or fluoroquinolones represented ST131 H30-Rx, the multidrug-resistant subclone that has emerged worldwide in the last decade. This strain encoded extended-spectrum β-lactamase CTX-M-15 and carried an IncF plasmid of type F2:A1:B-.

CONCLUSIONS

In this collection of EOS/EOM-associated E coli isolates, we observed a high rate of ampicillin resistance, a low rate of fluoroquinolone resistance, and no aminoglycoside resistance, with resistance to third-generation cephalosporins appearing in only a single strain, from the worldwide emerging ST131 clone. Ongoing surveillance of antibiotic resistance among EOS isolates is warranted, to ensure that standard empiric regimens remain effective.

Biofilm formation, antimicrobial susceptibility, serogroups and virulence genes of uropathogenic E. coli isolated from clinical samples in Iran

BACKGROUND

Uropathogenic Escherichia coli O- Serogroups with their virulence factors are the most prevalent causes of UTIs. The present research performed to track common uropathogenic E.coli serogroups, antibiotic resistance pattern of strains and prevalence of virulence genes in isolations having the ability to constitute biofilm.

METHODS

In this research 130 E.coli isolation from patients having UTI symptoms were collected and antimicrobial resistance pattern was performed by Kirby-Bauer method. Polymerase chain reaction was done using primer pairs to identify common serogroups of uropathogenic E.coli and studying virulence genes in isolations creating biofilm.

RESULTS

Among 130 E.coli isolates, 80 (61.53 %) were able to make biofilm that 15 isolates (18.75 %) indicated strong reaction, 20 (25 %) of medium and 45 (56.25 %) of weak biofilm reaction. Among isolations creating biofilm, the highest resistance reported to Ampicillin (87.5 %) and the lowest to Nitrofurantoin (3.75 %). The frequency of fimH, pap, sfa and afa genes in isolations having the ability to create strong biofilm reported 93.33 %, 86.66 %, 86.66 % and 66.66 %, respectively.

CONCLUSIONS

The findings indicated the importance of virulence genes in serogroups producing uropathogenic E.coli biofilm. It is recommended that strains producing biofilm before antibiotic use should be studied.

Escherichia coli ST131, an intriguing clonal group

In 2008, a previously unknown Escherichia coli clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. coli lineage among extraintestinal pathogenic E. coli (ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coli isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coli ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131.

[Distribution of phylogenetic groups and virulence factors in CTX-M-15 β-lactamase-producing uropathogenic Escherichia coli strains isolated from patients in the community of Mérida, Venezuela]

In this study, the distribution of phylogenetic groups and the genetic detection of virulence factors in CTX-M-15 β-lactamase-producing uropathogenic Escherichia coli (UPEC) strains were analyzed. Twenty eight strains were isolated between January 2009 and July 2011 from patients with urinary tract infection (UTI) who attended the Public Health Laboratory at Mérida, Venezuela. Determination of phylogenetic groups and detection of six virulence genes, fimH, fyuA, kpsMTII, usp, PAI and papAH, were performed by PCR amplification. Fifteen of the 28 isolates were mainly located in the phylogenetic group A, followed by B2 (12/28) and D (1/28). No direct relationship between the severity or recurrence of UTI and the distribution of phylogroups was observed. All studied virulence factors were found in group B2 strains with the highest frequency. The prevalent virulence profile included the combination of three main genes: fimH, kpsMTII and fyuA and, to a lesser extent, the presence of other determinants such as usp, PAI and/or papAH. These results indicate that virulent UPEC incorporated three important properties: adhesion, iron uptake and evasion of phagocytosis, which favored the production of recurrent UTI. This is the first report describing the association of phylogenetic groups with the potential virulence of CTX-M-15 β-lactamase producing UPEC strains in Venezuela.

Virulence determinants in Escherichia coli associated with recurrent cystitis in sexually active women

More than a quarter of women who experience acute cystitis develop recurrence but information on specific urovirulent genetic profile of uropathogenic Escherichia coli associated with recurrent cystitis is still limited. In this prospective cohort study, index episode E. coli from a cohort of 46 sexually active women with acute cystitis who reported recurrence during followup were grouped into repeat infection (RI) and single infection (SI) isolates, based on enterobacterial repetitive intergenic consensus (ERIC) PCR profile comparison with subsequent E. coli isolated from same women. PCR for phylogrouping and 15 virulence genes along with test for biofilm formation were done. Virulence score was calculated for each isolate as number of virulence genes detected. Among 46 index E. coli, 22 were RI, and 24 were SI isolates. RI isolates had phylogroup B2 as majority (54.5%) which is typically described as more virulent phylogroup and virulence score for RI isolates was also significantly higher compared to SI isolates. Virulence gene malX (p = 0.03) was significantly associated with RI isolates. 68.2% RI isolates were strong to moderate biofilm producers in comparison to 33.3% SI isolates, an important survival strategy to reside in bladder and or vagina. Overall, E. coli associated with recurrent cystitis appear to be more virulent and malX seems to have a role in causing repeat infection.

Extraintestinal isolates ofEscherichia coli: identification and prospects for vaccine development

Extraintestinal pathogenic Escherichia coli (ExPEC) cause a wide variety of infections that are responsible for significant morbidity, mortality and costs to our healthcare system. Thereby, the development of an efficacious ExPEC vaccine will minimize disease and may be cost-effective in selected patient groups. Surface polysaccharides, such as capsule, have been traditional targets for vaccine development. Considering that significant antigenic heterogeneity exists among surface polysaccharides present in various ExPEC strains, their use as vaccine candidates will be challenging. Therefore, alternative vaccine candidates/approaches are being identified and evaluated and are discussed in this review. The authors envision that an efficacious ExPEC vaccine will consist of either a polyvalent subunit vaccine or a genetically engineered killed whole-cell vaccine.

Isolation of generalized transducing bacteriophages for uropathogenic strains of Escherichia coli

The traditional genetic procedure for random or site-specific mutagenesis in Escherichia coli K-12 involves mutagenesis, isolation of mutants, and transduction of the mutation into a clean genetic background. The transduction step reduces the likelihood of complications due to secondary mutations. Though well established, this protocol is not tenable for many pathogenic E. coli strains, such as uropathogenic strain CFT073, because it is resistant to known K-12 transducing bacteriophages, such as P1. CFT073 mutants generated via a technique such as lambda Red mutagenesis may contain unknown secondary mutations. Here we describe the isolation and characterization of transducing bacteriophages for CFT073. Seventy-seven phage isolates were acquired from effluent water samples collected from a wastewater treatment plant in Madison, WI. The phages were differentiated by a host sensitivity-typing scheme with a panel of E. coli strains from the ECOR collection and clinical uropathogenic isolates. We found 49 unique phage isolates. These were then examined for their ability to transduce antibiotic resistance gene insertions at multiple loci between different mutant strains of CFT073. We identified 4 different phages capable of CFT073 generalized transduction. These phages also plaque on the model uropathogenic E. coli strains 536, UTI89, and NU14. The highest-efficiency transducing phage, ΦEB49, was further characterized by DNA sequence analysis, revealing a double-stranded genome 47,180 bp in length and showing similarity to other sequenced phages. When combined with a technique like lambda Red mutagenesis, the newly characterized transducing phages provide a significant development in the genetic tools available for the study of uropathogenic E. coli.

Magnetic Nanoparticles Immobilization and Functionalization for Biosensor Applications

We describe an approach forE. colibacteria detection using an electrochemical immunosensor. The immunosensor was based on functionalized magnetic nanoparticles immobilized onto bare gold electrode. Cyclic voltammetry and impedance spectroscopy was performed before and after magnetic nanoparticles deposition. The magnetic nanoparticles functionalized with anti-E. colipolyclonal antibody were used for bacteria detection. Lytic T4-phage was used to confirm the success recognition of bacteria with the developed immunosensor. The specificity of the immunosensor was tested againstEnterococcus faeciumbacteria. A limit detection of 103 CFU/mLE. colibacteria was obtained with a good reproducibility.

Virulence potential of Escherichia coli isolates from skin and soft tissue infections

Escherichia coli strains frequently are isolated from skin and soft tissue infections (SSTI); however, their virulence potential has not yet been extensively studied. In the present study, we characterized 102 E. coli SSTI strains isolated mostly from surgical and traumatic wounds, foot ulcers, and decubitus. The strains were obtained from the Institute of Microbiology and Immunology, University of Ljubljana, Slovenia. Phylogenetic backgrounds, virulence factors (VFs), and antibiotic resistance profiles were determined. Correlations between VFs and phylogenetic groups were established and analyzed with regard to patient factors. Further, the associations of the three most prevalent antibiotic resistance patterns with virulence potential were analyzed. Our results showed that the majority of the studied strains (64%) [corrected] belonged to the B2 phylogenetic group. The most prevalent VF was ompT (80%), while toxin genes cnf1 and hlyA were found with prevalences of 32 and 30%, respectively. None of the investigated bacterial characteristics were significantly associated with patient gender, age, type of infection, or immunodeficiency. The most prevalent antibiotic resistance pattern was resistance to ampicillin (46%), followed by resistance to tetracycline (25%) and fluoroquinolones (21%). Strains resistant to ciprofloxacin exhibited a significantly reduced prevalence of cnf1 (P < 0.05) and usp (P < 0.01). Our study revealed that E. coli isolates from SSTIs exhibit a remarkable virulence potential that is comparable to that of E. coli isolates from urinary tract infections and bacteremia.

Plasmids imparting sulfonamide resistance in Escherichia coli: implications for persistence

Sulfonamide resistance remains prevalent among clinical isolates of Escherichia coli in the United Kingdom, despite a dramatic (>97%) national decline in the rate of prescription of sulfonamides in the 1990s. To investigate potential mechanisms accounting for this persistence, we characterized plasmids carrying sul2, the most prevalent determinant of sulfonamide resistance. Among 33 conjugative and 5 nonconjugative plasmids carrying sul2, resistance to other antimicrobial agents was common, but the spectrum of resistance profiles was diverse: 82%, 74%, and 45% carried resistance to ampicillin, streptomycin, and trimethoprim, respectively. Resistance to mercury was carried by 33% of the plasmids, but none conferred significant resistance to silver or to any of three disinfectants tested. The potential virulence genes iutA (aerobactin system) and traT (serum survival) were carried by 21% and 36% of the plasmids, respectively. The 33 conjugative plasmids belonged to five different incompatibility groups, FIB, B/O, I1, K/B, and P (42%, 33%, 9%, 3% and 3%, respectively), with 3 plasmids being unassigned, and to 19 similarity groups on the basis of their restriction profiles. The sequences flanking sul2 were diverse and suggested more than one mechanism of genetic mobility. The five nonconjugative plasmids were all related to p9123 (pBP1), which was previously found to confer a fitness advantage on its host. We propose that the persistence of sul2, despite the reduced rate of prescription of sulfonamides, is due to a combination of coselection by antibiotics still in common use, a lack of a selective disadvantage in sul2 carriage, and the genetic mobility of sul2.

Extraintestinal pathogenic Escherichia coli-induced acute necrotizing pneumonia in cats

Extraintestinal pathogenic Escherichia coli (ExPEC) are pathogens involved in several disease conditions, ranging from urinary tract infection to meningitis in humans and animals. They comprise epidemiologically and phylogenetically distinct strains, affecting most species and involving any organ or anatomical site. Here, we report fatal cases of necrotizing pneumonia in cats. Over a 1-week period, 13 cats from an animal shelter in Stamford, Connecticut were presented for necropsy. All had a clinical history of acute respiratory disease. The gross and microscopic findings for all the cats were consistent. Escherichia coli was uniformly isolated from the lungs of all the tested cats. All the isolates were haemolytic, genetically related as determined by enterobacterial repetitive intergenic consensus PCR, and harboured genes encoding for cytotoxic necrotizing factor-1 and fimbriae and adhesions that are characteristic of ExPEC, implying a point source clonal outbreak. As cats are common household pets, this report raises concerns regarding zoonotic potential (in either direction) for these ExPEC strains.

A prospective, longitudinal study of the behavior of serologically classified isolates of Escherichia coli in women with recurrent urinary tract infections

OBJECTIVE

This study characterizes further the behavior of serologically classified isolates of Escherichia coli in women with recurrent urinary tract infections (UTIs).

METHODS

A prospective, longitudinal study of 203 young to middle-aged women with UTIs was conducted. Seven hundred and sixty-one UTIs due to E. coli were identified in the 203 women during observation periods of 1.1-19.4 years. Isolates from urine were routinely serologically classified. Clusters of UTIs and rates per year of infections with the same serogroup were defined to quantify further UTIs.

RESULTS

One hundred and forty-eight (73%) of the 203 women experienced 2-42 UTIs with E. coli. Fifteen percent of recurrences occurred within 1 month of the previous infection; 57%, 6 months; and 70%, 1 year. During the first four months, recurrences with the same serogroup accounted for 81-50% of recurrences; thereafter, recurrences with a different serogroup were more frequent. Clusters of UTIs occurred in 52% of the 148 women and ranged in size from 2-5 infections. Multiple recurrences with the same serogroup were more frequently caused by a few common serogroups.

CONCLUSIONS

Isolates of a few common serogroups of E. coli were associated with the great majority of both index and recurrent UTIs. Some isolates of both common and less common serogroups were associated with multiple recurrences with the same serogroup. The wide range in rates/year among recurrences with isolates of different serogroups in individual women were consistent with the hypothesis that these differences were more likely to be due to differences in virulence of the isolates than to host factors.

Implication of biofilm formation in the persistence of urinary tract infection caused by uropathogenic Escherichia coli

Escherichia coli is the most frequent microorganism involved in urinary tract infection (UTI). Acute UTI caused by uropathogenic E. coli (UPEC) can lead to recurrent infection, which can be defined as either re-infection or relapse. E. coli strains causing relapse (n = 27) and re-infection (n = 53) were analysed. In-vitro production of biofilm, yersiniabactin and aerobactin was significantly more frequent among strains causing relapse. Biofilm assays may be helpful in selecting patients who require a therapeutic approach to eradicate persistent biofilm-forming E. coli strains and prevent subsequent relapses.

Expression of the Escherichia coli IrgA homolog adhesin is regulated by the ferric uptake regulation protein

The IrgA homolog adhesin (Iha) is an adherence-conferring outer membrane protein of Escherichia coli associated with enterohemorrhagic and uropathogenic strains. Here, we used primer extension analysis to identify iha promoters in O157:H7 and uropathogenic E. coli strains. Transcriptional fusions demonstrated that iha transcription is repressed by iron. Gel shifts using purified ferric uptake regulator protein (Fur) demonstrated that repression involves a direct interaction between Fur and the iha promoter. We identified strain-dependent differences in iha expression and determined that single nucleotide polymorphisms upstream of the iha promoter, in particular position -85, contribute to differences in expression levels.

Subtyping of uropathogenic Escherichia coli according to the pathogenicity island encoding uropathogenic-specific protein: Comparison with phylogenetic groups

BACKGROUND

Phylogenetic analysis has been used widely to characterize extraintestinal pathogenic Escherichia coli in molecular epidemiological studies. We have recently reported a putative pathogenicity island (PAI), carrying uropathogenic-specific protein (usp) and a unique mosaic structure of small open reading frames following usp, providing four subtypes of PAIusp classified from their sequential patterns.

METHODS

A total of 427 E. coli isolates from uncomplicated urinary tract infections (194 cystitis, 76 pyelonephritis, and 107 prostatitis) and 50 fecal isolates were examined for phylogenetic grouping and PAIusp subtyping as well as the prevalence of virulence factors (VF) and O serogroups.

RESULTS

Both phylogenetic group B2 and usp-positive strains were equally predominant in cystitis, pyelonephritis and prostatitis (B2, 80.9%, 86.8%, and 86.9%; usp, 79.4%, 93.4%, and 88.8%, respectively). Furthermore, each PAIusp subtype was shown to be closely associated with several VF genes as well as several common O serogroups of uropathogenic E. coli.

CONCLUSIONS

In molecular epidemiological studies, PAIusp subtyping will provide additional informative findings of E. coli strains belonging to phylogenetic group B2.

Iha from an Escherichia coli urinary tract infection outbreak clonal group A strain is expressed in vivo in the mouse urinary tract and functions as a catecholate siderophore receptor

Virulence factors of pathogenic Escherichia coli belonging to a recently emerged and disseminated clonal group associated with urinary tract infection (UTI), provisionally designated clonal group A (CGA), have not been experimentally investigated. We used a mouse model of ascending UTI with CGA member strain UCB34 in order to identify genes of CGA that contribute to UTI. iha was identified to be expressed by strain UCB34 in the mouse kidney using selective capture of transcribed sequences. iha from strain UCB34 demonstrated a siderophore receptor phenotype when cloned in a catecholate siderophore receptor-negative E. coli K-12 strain, as shown by growth promotion experiments and uptake of (55)Fe complexed to enterobactin or its linear 2, 3-dihydroxybenzoylserine (DHBS) siderophore derivatives. Siderophore-mediated growth promotion by Iha was TonB dependent. Growth and iron uptake were more marked with linear DHBS derivatives than with purified enterobactin. The reported phenotype of adherence to epithelial cells conferred by expressing iha from a multicopy cloning vector in a poorly adherent E. coli K-12 host strain was confirmed to be specific to iha, in comparison with other siderophore receptor genes. iha expression was regulated by the ferric uptake regulator Fur and by iron availability, as shown by real-time reverse transcriptase PCR. In a competitive infection experiment using the mouse UTI model, wild-type strain UCB34 significantly outcompeted an isogenic iha null mutant. Iha thus represents a Fur-regulated catecholate siderophore receptor that, uniquely, exhibits an adherence-enhancing phenotype and is the first described urovirulence factor identified in a CGA strain.

Differential genome contents of nontypeable Haemophilus influenzae strains from adults with chronic obstructive pulmonary disease

Haemophilus influenzae is an important cause of otitis media in children and lower respiratory infection in adults with chronic obstructive pulmonary disease (COPD). Patients with COPD experience periodic exacerbations that are associated with acquisition of new bacterial strains. However, not every strain acquisition is associated with exacerbation. To test the hypothesis that genetic differences among strains account for differences in pathogenic potential, a microarray consisting of 4,992 random 1.5- to 3-kb genomic fragments of an exacerbation strain was constructed. Competitive hybridization was performed using six strains associated with exacerbation as well as five strains associated with asymptomatic colonization. Seven sequences that were absent in all five colonization strains and present in at least two exacerbation strains were identified. One such sequence was a previously unreported gene with high homology to the meningococcal immunoglobulin A (IgA) protease gene, which is distinct from the previously described H. influenzae IgA protease. To assess the distribution of the seven sequences among well-characterized strains of H. influenzae, 59 exacerbation strains and 73 asymptomatic colonization strains were screened by PCR for the presence of these sequences. The presence or absence of any single sequence was not significantly associated with exacerbations of COPD. However, logistic regression and subgroup analysis identified combinations of the presence and absence of genes that are associated with exacerbations. These results indicate that patterns of genes are associated with the ability of strains of H. influenzae to cause exacerbations of COPD, supporting the concept that differences in pathogenic potential are based in part on genomic differences among infecting strains, not merely host factors.

Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis

The evolutionary origins of extraintestinal pathogenic Escherichia coli (ExPEC) remain uncertain despite these organisms' relevance to human disease. A valid understanding of ExPEC phylogeny is needed as a framework against which the observed distribution of virulence factors and clinical associations can be analyzed. Accordingly, phylogenetic relationships were defined by multi-locus sequence analysis among 44 representatives of selected ExPEC clonal groups and the E. coli Reference (ECOR) collection. Recombination, which significantly obscured the phylogenetic signal for several strains, was dealt with by excluding strains or specific sequences. Conflicting overall phylogenies, and internal phylogenies for virulence-associated phylogenetic group B2, were inferred depending on the specific dataset (i.e., how extensively purged of recombination), outgroup (Salmonella enterica and/or Escherichia fergusonii), and analysis method (neighbor joining, maximum parsimony, maximum likelihood, or Bayesian likelihood). Nonetheless, the major E. coli phylogenetic groups A, B1, and B2 were consistently well resolved, as was a major sub-component of group D and an ECOR 37-O157:H7 clade. Moreover, nine important ExPEC clonal groups within groups B2 and D, characterized by serotypes O6:K2:H1, O18:K1:H7, O6:H31, and O4:K+:H+ (from group B2), and O1:K1:H-, O7:K1:H-, O157:K+:H (non-7), O15:K52:H1, and O11/17/77:K52:H18 ("clonal group A") (from group D), were consistently well resolved, regardless of clinical background (cystitis, pyelonephritis, neonatal meningitis, sepsis, or fecal), host group, geographical origin, and virulence profile. Among the group B2-derived clonal groups the O6:K2:H1 clade appeared basal. Within group D, "clonal group A" and the O15:K52:H1 clonal group were consistently placed with ECOR 47 and ECOR 44, respectively, as nearest neighbors. These findings clarify phylogenetic relationships among key ExPEC clonal groups but also emphasize that recombination appears to obscure the oldest evolutionary relationships, despite extensive targeted sequencing and use of a wide range of analysis techniques.

[Recurrent urinary tract infections in women. Virulence of pathogens and host reaction]

The interactions of host-specific and microbial factors are responsible for recurrent urinary tract infections (rUTI). The anatomical properties of the female urogenital tract favor colonization by uropathogens. Local factors such as glucose concentration of the urine, stability of the lactobacilli population, the influence of estrogens, the activity of Tamm-Horsfall protein or of defensins, and disturbance of the systemic defense mechanisms dictate the course of an infection. The most prominent uropathogen is E. coli. It expresses various virulence factors including adhesions, toxins, iron uptake systems, and a capsule. It is still unclear if there are virulence factors characteristic for E. coli strains causing rUTI. The formation of intracellular reservoirs by invasion of uroepithelial cells by E. coli could be another, as yet little noticed cause for rUTI. Therefore, in cases of rUTI the application of intracellularly active antibiotics should be considered.

Bacterial characteristics in relation to clinical source of Escherichia coli isolates from women with acute cystitis or pyelonephritis and uninfected women

Characteristics differentiating Escherichia coli strains that cause cystitis or pyelonephritis from fecal E. coli remain incompletely defined, particularly among adult women in the United States. Accordingly, phylogenetic group, O antigens, and virulence factors (VFs) were analyzed among 329 E. coli isolates from the mid-to-late 1990s from women in the United States with acute pyelonephritis (n = 170), cystitis (n = 83), or no infection (fecal; n = 76). Compared with fecal and cystitis isolates, pyelonephritis isolates exhibited a greater prevalence of phylogenetic group B2, most virulence-associated O antigens, and most VFs and had higher VF scores. In contrast, cystitis and fecal isolates differed minimally. By stepwise multivariable logistic regression, significant (P < or = 0.015) predictors of cystitis and/or pyelonephritis (versus fecal) included afa/dra (Dr-binding adhesins), ibeA (invasion of brain endothelium), iha (putative adhesin-siderophore), malX (pathogenicity island marker), the O75 antigen, papEF (P fimbriae), papG allele II (P adhesin variant), group B2, and sfa/foc (S and F1C fimbriae). However, virulence profiles overlapped considerably among source groups and varied greatly within each group. E. coli "clonal group A" (CGA) and the O2:K5/K7:H1 and O75:K+ clonal groups were significantly associated with cystitis and/or pyelonephritis. These findings identify potential vaccine targets, suggest that urovirulence is multiply determined, and confirm the urovirulence of specific E. coli clonal groups, including recently recognized CGA.

(Patho-)Genomics of Escherichia coli

Escherichia coli represents a versatile and diverse enterobacterial species which can be subdivided into (i) nonpathogenic, commensal, (ii) intestinal pathogenic and (iii) extraintestinal pathogenic strains. This classification is mainly based on the presence or absence of DNA regions which are frequently associated with certain pathotypes. In most cases, this genetic information has been horizontally acquired and belongs to the flexible E. coli genome, such as plasmids, bacteriophages and genomic islands. These genomic regions contribute to the rapid evolution of E. coli variants as they are frequently subject to rearrangements, excision and transfer as well as further acquisition of additional DNA thus contributing to the creation of new (pathogenic) variants. Genetic diversity and genome plasticity of E. coli has been underestimated. The accumulating amount of sequence information generated in the era of "genomics" helps to increase our understanding of factors and mechanisms that are involved in diversification of this bacterial species as well as in those that may direct host specificity.

Genetic analysis of enteropathogenic and enterohemorrhagic Escherichia coli serogroup O103 strains by molecular typing of virulence and housekeeping genes and pulsed-field gel electrophoresis

We investigated the genetic relationships of 54 Escherichia coli O103 strains from humans, animals, and meat by molecular typing of housekeeping and virulence genes and by pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing (MLST) of seven housekeeping genes revealed seven profiles, I through VII. MLST profiles I plus III cover 45 Shiga toxin-producing E. coli (STEC) O103:H2 strains from Australia, Canada, France, Germany, and Northern Ireland that are characterized by the intimin (eae) epsilon gene and carry enterohemorrhagic E. coli (EHEC) virulence plasmids. MLST profile II groups five human and animal enteropathogenic E. coli (EPEC) O103:H2 strains that were positive for intimin (eae) beta. Although strains belonging to MLST groups II and I plus III are closely related to each other (92.6% identity), major differences were found in the housekeeping icdA gene and in the virulence-associated genes eae and escD. E. coli O103 strains with MLST patterns IV to VII are genetically distant from MLST I, II, and III strains, as are the non-O103 E. coli strains EDL933 (O157), MG1655 (K-12), and CFT073 (O6). Comparison of MLST results with those of PFGE and virulence typing demonstrated that E. coli O103 STEC and EPEC have recently acquired different virulence genes and DNA rearrangements, causing alterations in their PFGE patterns. PFGE typing was very useful for identification of genetically closely related subgroups among MLST I strains, such as Stx2-producing STEC O103 strains from patients with hemolytic uremic syndrome. Analysis of virulence genes contributed to grouping of E. coli O103 strains into EPEC and STEC. Novel virulence markers, such as efa (EHEC factor for adherence), paa (porcine adherence factor), and cif (cell cycle-inhibiting factor), were found widely associated with E. coli O103 EPEC and STEC strains.

The IrgA homologue adhesin Iha is an Escherichia coli virulence factor in murine urinary tract infection

The role of the Escherichia coli iron-regulated gene homologue adhesin (Iha) in the pathogenesis of urinary tract infections (UTIs) is unknown. We performed a series of complementary analyses to confirm or refute the hypothesis that Iha is a virulence factor in uropathogenic E. coli. Fecal E. coli isolates exhibited significantly lower prevalences of iha (range, 14 to 22%) than did clinical isolates from cases of pediatric cystitis or pyelonephritis, adult pyelonephritis or urosepsis, or bacteremia (range, 38 to 74%). Recombinant Iha from E. coli pyelonephritis isolate CFT073 conferred upon nonadherent E. coli ORN172 the ability to adhere to cultured T-24 human uroepithelial cells. In a well-established mouse model of ascending UTI, CFT073 and its derivative UPEC76 (a pap [P fimbriae] mutant version of strain CFT073) each significantly outcompeted their respective iha deletion mutants in CBA/J mice 48 h after bladder challenge (P < 0.03 for urine, both kidneys, and bladders of both constructs, except for bladders of mice challenged with UPEC76 and its deletion mutant, where P = 0.11). These data suggest that Iha(CFT073) is a virulence factor and might be a target for anti-UTI interventions.

Highly resistant metabolically deficient dwarf mutant of Escherichia coli is the cause of a chronic urinary tract infection

We present the case of a 68-year-old diabetic woman who has been suffering from chronic urinary tract infections, recurring over a period of at least 5 years, caused by a slowly growing metabolically deficient dwarf mutant (MDD) of Escherichia coli. This MDD strain was auxotrophic for histidine, was resistant to multiple antibiotics, and showed atypical growth behavior. Colonies were tiny on routine media but were able to revert to normal growth after extended incubation. This strain was identified as E. coli by 16S ribosomal DNA sequencing, and virulence factor profiles were determined by PCR. Seven MDD isolates collected over the 5-year period were grown from midstream urine to significant colony counts and shown to belong to the same clonal group by pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus PCR. These MDDs were repeatedly misidentified by biochemical methods due to their slow growth and atypical colony morphology. This case highlights the importance of recognizing MDDs of Enterobacteriaceae in patients with chronic infections. To our knowledge this is the first report of an MDD of E. coli causing a chronic urinary tract infection.

Rapid identification of Escherichia coli pathotypes by virulence gene detection with DNA microarrays

One approach to the accurate determination of the pathogenic potential (pathotype) of isolated Escherichia coli strains would be through a complete assessment of each strain for the presence of all known E. coli virulence factors. To accomplish this, an E. coli virulence factor DNA microarray composed of 105 DNA PCR amplicons printed on glass slides and arranged in eight subarrays corresponding to different E. coli pathotypes was developed. Fluorescently labeled genomic DNAs from E. coli strains representing known pathotypes were initially hybridized to the virulence gene microarrays for both chip optimization and validation. Hybridization pattern analysis with clinical isolates permitted a rapid assessment of their virulence attributes and determination of the pathogenic group to which they belonged. Virulence factors belonging to two different pathotypes were detected in one human E. coli isolate (strain H87-5406). The microarray was also tested for its ability to distinguish among phylogenetic groups of genes by using gene probes derived from the attaching-and-effacing locus (espA, espB, tir). After hybridization with these probes, we were able to distinguish E. coli strains harboring espA, espB, and tir sequences closely related to the gene sequences of an enterohemorrhagic strain (EDL933), a human enteropathogenic strain (E2348/69), or an animal enteropathogenic strain (RDEC-1). Our results show that the virulence factor microarray is a powerful tool for diagnosis-based studies and that the concept is useful for both gene quantitation and subtyping. Additionally, the multitude of virulence genes present on the microarray should greatly facilitate the detection of virulence genes acquired by horizontal transfer and the identification of emerging pathotypes.

Functional relationships of the sialyltransferases involved in expression of the polysialic acid capsules of Escherichia coli K1 and K92 and Neisseria meningitidis groups B or C

Polysialic acid (PSA) capsules are cell-associated homopolymers of alpha2,8-, alpha2,9-, or alternating alpha2,8/2,9-linked sialic acid residues that function as essential virulence factors in neuroinvasive diseases caused by certain strains of Escherichia coli and Neisseria meningitidis. PSA chains structurally identical to the bacterial alpha2,8-linked capsular polysaccharides are also synthesized by the mammalian central nervous system, where they regulate neuronal function in association with the neural cell adhesion molecule (NCAM). Despite the structural identity between bacterial and NCAM PSAs, the respective polysialyltransferases (polySTs) responsible for polymerizing sialyl residues from donor CMP-sialic acid are not homologous glycosyltransferases. To better define the mechanism of capsule biosynthesis, we established the functional interchangeability of bacterial polySTs by complementation of a polymerase-deficient E. coli K1 mutant with the polyST genes from groups B or C N. meningitidis and the control E. coli K92 polymerase gene. The biochemical and immunochemical results demonstrated that linkage specificity is dictated solely by the source of the polymerase structural gene. To determine the molecular basis for linkage specificity, we created chimeras of the K1 and K92 polySTs by overlap extension PCR. Exchanging the first 52 N-terminal amino acids of the K1 NeuS with the C terminus of the K92 homologue did not alter specificity of the resulting chimera, whereas exchanging the first 85 or reciprocally exchanging the first 100 residues did. These results demonstrated that linkage specificity is dependent on residues located between positions 53 and 85 from the N terminus. Site-directed mutagenesis of the K92 polyST N terminus indicated that no single residue alteration was sufficient to affect specificity, consistent with the proposed function of this domain in orienting the acceptor. The combined results provide the first evidence for residues critical to acceptor binding and elongation in polysialyltransferase.

Identification of urovirulence traits in Escherichia coli by comparison of urinary and rectal E. coli isolates from dogs with urinary tract infection

Spontaneously occurring urinary tract infection (UTI) in dogs was exploited as an experiment of nature to gain insights into UTI pathogenesis in humans. Concurrent urinary and rectal Escherichia coli isolates from 37 dogs with UTI were compared with respect to phylogenetic background, O antigens, and extended virulence genotype. In 54% of the UTI episodes, the dog's urinary and rectal isolates represented the same strain. Urinary isolates differed dramatically from rectal-only isolates in that they derived predominantly from E. coli phylogenetic group B2, expressed typical (human) UTI-associated O antigens, and possessed many virulence-associated genes, most notably pap elements (P fimbriae), papG (adhesin) allele III, sfa/foc and sfaS (S fimbriae), hly (hemolysin), fyuA (yersiniabactin), iroN (siderophore), and ompT (outer membrane protease T). The 20 urinary isolates that corresponded with the host's predominant rectal strain were no less virulent according to the markers analyzed than were the 17 urinary isolates that differed from the host's predominant rectal strain. These findings suggest that UTI pathogenesis is similar in dogs and humans, provide added support for the special-pathogenicity over the prevalence hypothesis of UTI pathogenesis, and identify numerous specific virulence-associated factors as significant correlates of urovirulence.

Urinary tract infections: what's new?

PURPOSE

This review provides practicing urologists with important basic information about urinary tract infections (UTIs) that can be applied to everyday clinical problems.

MATERIALS AND METHODS

A review is presented of provocative and controversial concepts in the current literature.

RESULTS

Bacterial virulence mechanisms are critical for overcoming the normal host defenses. Increasing antimicrobial resistance of uropathogens has led to reconsideration of traditional treatment recommendations in many areas. For effective patient management the first issue is to define complicating urological factors. Managing complicated urinary tract infections, particularly in urology, is determined by clinical experience to define the pertinent anatomy and to determine the optimal interventions. New clinical data are summarized on UTIs in long-term care patients, behavioral risks for UTI in healthy women and anatomical differences associated with an increased risk for UTI. The rationale is presented for UTI prophylaxis using cranberry juice, immunization and bacterial interference. Current treatment trends for UTI include empiric therapy (without urine culture and sensitivity testing), short-course therapy, patient-administered (self-start) therapy and outpatient therapy for uncomplicated pyelonephritis.

CONCLUSIONS

Recommendations for treating patients with UTIs have changed based on basic science and clinical experience.

Conserved filamentous prophage in Escherichia coli O18:K1:H7 and Yersinia pestis biovar orientalis

Microbial virulence is known to emerge by horizontal gene transfer mechanisms. Here we describe the discovery of a novel filamentous prophage, designated CUS-1, which is integrated into the chromosomal dif homologue of the high-virulence clone Escherichia coli O18:K1:H7. An homologous chromosomal element (CUS-2) in Yersinia pestis biovar orientalis is integrated at the same relative location as CUS-1; both lysogenic E. coli and Y. pestis strains produce particles with properties expected of single-stranded DNA virions. CUS(phi) is epidemiologically correlated with the emergence of K1 strains with increased virulence and with the Y. pestis biovar responsible for the current (third) plague pandemic.

Recurrent urinary tract infection in the female

PURPOSE OF REVIEW

Recurrent urinary tract infection is a common problem and can affect women of all ages, particularly the elderly and pregnant women. Obstetricians and gynaecologists need to have up-to-date knowledge of the diagnosis, pathophysiology and management of this condition.

RECENT FINDINGS

The diagnosis of urinary tract infection is made on the basis of symptoms and bacteriuria of more than 103 bacteria per ml. Host and bacterial virulence factors are important in the pathogenesis of recurrent urinary tract infections. General host factors predisposing to recurrent infection are genetic factors, ageing, the menopause, urogenital dysfunction, sexual behaviour, and previous pelvic surgery. Urinary tract infection is common in pregnancy, and recent studies have suggested an association with mental retardation and developmental delay. Women with recurrent urinary tract infection in pregnancy should be considered for long-term antibiotic prophylaxis. Intravaginal oestrogens and cranberry juice have been found to be effective for prevention, although more research is required. Women with recurrent urinary tract infection should have at least a 3-day course of trimethoprim or cotrimoxazole, or a 5-day course of beta-lactams or nitrofurantoin, with perhaps a 10-day course in the elderly. Women with frequent urinary tract infection (more than three episodes per year) should be offered prophylactic antibiotics, which can be patient-initiated, postcoital, or long-term low-dose therapy. In the future, vaccines against specific uropathogenic bacteria may be useful in urinary tract infection prophylaxis.

SUMMARY

More research is required, by all medical disciplines, on various aspects of urinary tract infection.

Concurrent fecal colonization with extraintestinal pathogenic Escherichia coli in a homosexual man with recurrent urinary tract infection and in his male sex partner

A 72-year-old homosexual man experienced frequent recurrences of symptomatic urinary tract infection (UTI) putatively due to the same strain of extraintestinal pathogenic Escherichia coli, despite receiving repeated courses of seemingly appropriate antibiotic therapy. Both the patient and his male sex partner were found to have fecal colonization with the strain recovered from the patient's urine, which exhibited characteristics of the E. coli O1/O2:K1:H7 clonal group (which is associated with urosepsis), whereas genetically distinct E. coli strains were recovered from a jar of petroleum jelly used by the couple during sexual activity.