Persistence of Escherichia coli clones and phenotypic and genotypic antibiotic resistance in recurrent urinary tract infections in childhood

Antimicrobial Resistance in Uropathogenic Escherichia coli Strains Isolated from Relapses from Recurrent Urinary Tract Infections

Little is known about the characteristics of uropathogenic Escherichia coli (UPEC) associated with recurrent urinary tract infections (RUTIs). The present study aimed to analyze the phenotypic antimicrobial resistance of recurrent UPEC isolates attributable to either relapse or reinfection. A total of 140 E. coli strains were isolated from 70 outpatients with RUTIs. All isolates were analyzed by random amplified polymorphic DNA-polymerase chain reaction to evaluate genetic similarity between the first and second isolates. We found that 64.2% (45/70) of outpatients had a relapse with the primary infecting E. coli strain and 35.7% (25/70) had reinfection with a new E. coli strain. Compared with reinfecting strains, relapse UPEC isolates exhibited much higher antimicrobial resistance; 89% of these isolates were multidrug-resistant and 46.6% were extended-spectrum β-lactamase producers. Our study provides evidence that RUTIs are mainly driven by the persistence of the original strain in the host (relapses) despite appropriate antibiotic treatments, and only RUTIs attributed to relapses seem to favor multidrug resistance in UPEC isolates.

In house-development of a rapid immunochromatographic test for the detection of Escherichia coli in urine samples

Urinary tract infections (UTIs) are a common health concern. Urine culture is the "gold standard" for UTI diagnosis but takes 48h. Rapid methods like dipstick tests are used as point-of-care tests. However, their sensitivity and specificity are variable. In this work, a rapid immunochromatographic test (IT) for detecting Escherichia coli in urine was developed, and its performance was evaluated in urine samples from patients with suspected UTI. The "universal lateral flow assay kit" was employed using an E. coli capture antibody. One hundred and five (105) urine samples were analyzed using the IT, dipstick test, and urine culture. The sensitivity of the IT was 74.5%, specificity 88.9%, positive predictive value (PPV) 86.3%, and negative predictive value (NPV) 78.7%. The combination of the IT with the dipstick test increases sensitivity to 94.1%, specificity to 66.7%, PPV to 72.7%, and NPV to 92.3%. Using the IT for detecting E. coli in urine could be a valuable technique for UTI screening, showing better specificity and diagnostic precision but lower sensitivity than the dipstick test. Based on these results, we propose that the combined use of both screening techniques would allow a rapid and more precise diagnosis of UTI, rationalizing the indication for empirical antibiotics.

Top-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas

Control of hospital-associated Enterococcus faecium infection is a strenuous task due to the difficulty of identifying transmission routes and the persistence of this nosocomial pathogen despite the implementation of infection control measures that have been successful with other important nosocomial pathogens. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June 2018 and May 2019. In the top-down approach used in this study, we employed, in addition to the 106 E. faecium UAMS isolates, a filtered set of 2,167 E. faecium strains from the GenBank database to assess the current population structure of E. faecium species and, consequently, to identify the lineages associated with our clinical isolates. We then evaluated the antibiotic resistance and virulence profiles of hospital-associated strains from the species pool, focusing on antibiotics of last resort, to establish an updated classification of high-risk and multidrug-resistant nosocomial clones. Further investigation of the clinical isolates collected from UAMS patients using whole-genome sequencing analytical methodologies (core genome multilocus sequence typing [cgMLST], core single nucleotide polymorphism [coreSNP] analysis, and phylogenomics), with the addition of patient epidemiological data, revealed a polyclonal outbreak of three sequence types occurring simultaneously in different patient wards. The integration of genomic and epidemiological data collected from the patients increased our understanding of the relationships and transmission dynamics of the E. faecium isolates. Our study provides new insights into genomic surveillance of E. faecium to assist in monitoring and further limiting the spread of multidrug-resistant E. faecium. IMPORTANCE Enterococcus faecium is a member of the gastrointestinal microbiota. Although its virulence is low in healthy, immunocompetent individuals, E. faecium has become the third leading cause of health care-associated infections in the United States. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from cancer patients at the University of Arkansas for Medical Sciences (UAMS). We employed a top-down analytical approach (from population genomics to molecular biology) to classify our clinical isolates into their genetic lineages and thoroughly evaluate their antibiotic resistance and virulence profiles. The addition of patient epidemiological data to the whole-genome sequencing analytical methodologies performed in the study allowed us to increase our understanding of the relationships and transmission dynamics of the E. faecium isolates. This study provides new insights into genomic surveillance of E. faecium to help monitor and further limit the spread of multidrug-resistant E. faecium.

Genome profiling of uropathogenic E. coli from strictly defined community-acquired UTI in paediatric patients: a multicentric study

BACKGROUND

Urinary tract infection (UTI) in children is a common bacterial infection. The emergence of extended-spectrum beta-lactamases (ESBLs) poses a major challenge against the treatment of uropathogens. We aimed to characterize the E. coli isolates recovered from children with UTI for their resistance profile and circulating sequence types (ST).

METHODS

Children (> 1.5-18 years of age) from different community health centres of India with symptoms of UTI were enrolled. Isolates causing significant bacteriuria were identified by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility by the automated system, VITEK-2 (Biomeriux, Durhum, US). Nineteen E. coli isolates (15 ESBL positive and 4 ESBL negative) were sequenced in Oxford Nanopore platform followed by core-genome phylogeny, accessory genome cluster analysis, identification of sequence types, mobile genetic elements, genetic antimicrobial resistance markers. The correlation between detection of antimicrobial resistance genes with phenotypic resistance profiles was also investigated.

RESULTS

Eleven percent of children had significant bacteriuria [male:female-1:1, > 50% were 11-18 years of age group]. E. coli was predominant (86%) followed by K. pneumoniae (11%). Susceptibility of E. coli was highest against fosfomycin (100%) followed by carbapenems (90.7%) and nitrofurantoin (88.8%). ST131 (15.8%) and ST167 (10.5%) found as high-risk clones with the presence of plasmid [IncFIB (63.1%), IncFIA (52.6%)], and composite transposon [Tn2680 (46.6%)] in many isolates. Few isolates coharboured multiple beta-lactamases including blaNDM-5 (33.3%), blaOXA-1 (53.3%), blaCTX-M-15 (60%) and blaTEM-4 (60%).

CONCLUSIONS

This study highlights horizontal transmission of resistance genes and plasmids in paediatric patients at community centers across the nation harbouring multidrug-resistant genes such as blaNDM-5 and blaCTX-M-15 associated with high-risk clones ST131 and ST167. The data is alarming and emphasizes the need for rapid identification of resistance markers to reduce the spread in community. To our knowledge, this is the first multicentric study targeting paediatric UTI patients from the community setting of India.

Laboratory diagnosis of urinary tract infections in patients with resistance genes towards antibiotics

Escherichia coli are gram-negative bacteria that cause urinary tract infections (UTIs). UTIs have affected a significant percentage of humans yearly due to bacterial infection. Our study aims to determine the prevalence of resistance genes in E. coli towards sulfamethoxazole. This study included (490) patients with UTIs, and the urine samples were cultured on media. The patients were admitted to the Medical City in Baghdad to treat UTIs. 116 E.coli isolates were isolated from urine specimens, 35 isolates of them were resistant to trimethoprim/sulfamethoxazole, and 81 isolates were sensitive to trimethoprim/sulfamethoxazole; the E. coli isolates were submitted to multiplex PCR to detection some resistance genes (Sul1, sul2) after detected the isolates by PCR depending on 16S rRNA. Our study showed that identified E. coli was (91-99%) depending on the number of the examined samples by the Vitek 2 system. The molecular study included extraction of chromosomal DNA from (53) E. coli isolates; 35 samples were taken resistant to antibiotics, while from the total of 81 sensitive isolates, only 18 sensitive samples were taken from that are the most sensitive to Timethprime/sulfamethoxazole, then identification by 16S rRNA gene. Detection of Sulfonamides resistance genes included sul1 and sul2. The results showed the 16S rRNA gene identification found in all E. coli isolates and the detection of antibiotic resistance genes. The resistant isolates with the Sul1 gene prevalence were 11(31%), while the sensitive isolates with Sul1gene were 1(6%). Moreover, the resisted isolates with Sul2 gene prevalence was 8(23%), while the sensitive isolates with the Sul1 gene were 0(0%). The numbers of the resistant isolates were (11) and (8) that carry the Sul1 gene and Sul2 gene, respectively, while the numbers of the sensitive isolates were (1) and (0), respectively. We can conclude that a high percentage of Sul1 gene and Sul2 genes in E. coil isolated from UTIs were high. Keywords. UTI, Sul1, Sul2, resistant gene, trimethoprim-sulfamethoxazole

Third generation cephalosporins and piperacillin/tazobactam have distinct impacts on the microbiota of critically ill patients

Effective implementation of antibiotic stewardship, especially in critical care, is limited by a lack of direct comparative investigations on how different antibiotics impact the microbiota and antibiotic resistance rates. We investigated the impact of two commonly used antibiotics, third-generation cephalosporins (3GC) and piperacillin/tazobactam (TZP) on the endotracheal, perineal and faecal microbiota of intensive care patients in Australia. Patients exposed to either 3GC, TZP, or no β-lactams (control group) were sampled over time and 16S rRNA amplicon sequencing was performed to examine microbiota diversity and composition. While neither treatment significantly affected diversity, numerous changes to microbiota composition were associated with each treatment. The shifts in microbiota composition associated with 3GC exposure differed from those observed with TZP, consistent with previous reports in animal models. This included a significant increase in Enterobacteriaceae and Enterococcaceae abundance in endotracheal and perineal microbiota for those administered 3GC compared to the control group. Culture-based analyses did not identify any significant changes in the prevalence of specific pathogenic or antibiotic-resistant bacteria. Exposure to clinical antibiotics has previously been linked to reduced microbiota diversity and increased antimicrobial resistance, but our results indicate that these effects may not be immediately apparent after short-term real-world exposures.

DNA adenine methylation is involved in persister formation in E. coli

Uropathogenic Escherichia coli (UPEC) is a major cause of urinary tract infections (UTI). UPEC persister bacteria play crucial roles in clinical treatment failure and relapse. Although DNA methylation is known to regulate gene expression, its role in persister formation has not been investigated. Here, we show that Δdam (adenine methylase) mutant from UPEC strain UTI89 had significant defect in persister formation and complementation of the Δdam mutant restored this defect. Using PacBio sequencing of methylome and RNA sequencing of Δdam, we defined, for the first time, the role of Dam in persister formation. We found that Δdam mutation had an overwhelming effect on demethylation of the genome and the demethylation sites affected expression of genes involved in broad transcriptional and metabolic processes. Using comparative COG analysis of methylome and transcriptome, we demonstrate that Dam mediates persister formation through transcriptional control, cell motility, DNA repair and metabolite transport processes. These findings provide the first evidence and molecular basis for DNA methylation mediated persister formation and implicate Dam DNA methylation as a potential drug target for persister bacteria.

The Global Prevalence of Class 1 Integron and Associated Antibiotic Resistance in Escherichia coli from Patients with Urinary Tract Infections, a Systematic Review and Meta-Analysis

Objectives: The present systematic review and meta-analysis study aimed to investigate the prevalence of class 1 integrons and their associated antibiotic resistance in uropathogenic Escherichia coli. Materials and Methods: A systematic search was conducted to identify studies meeting our inclusion criteria in the Web of Science, PubMed, Embase, Scopus, and Google Scholar electronic databases to the end of July 2019. Finally, 35 articles were selected for data extraction, and meta-analysis was performed using the metaprop program in the STATA, version 11.0, software. Results: The pooled prevalence of class 1 integrons was 47% (95% confidence interval [CI]: 40-54), ranging from 6% to 90%. There was significant heterogeneity among the 35 studies (χ² = 840.37; p < 0.001; I² = 95.95%). The results of the subgroup analysis based on characterization of patients indicated that pooled prevalence of class 1 integrons was 52% (95% CI: 41-63; n = 14 studies) and 43% (95% CI: 34-54; n = 19 studies) in hospitalized and community patients, respectively. The lowest and highest prevalence of antibiotic resistance was observed for imipenem and ampicillin, respectively. According to the results of Begg's and Egger's tests, we did not find significant publication bias both in the included studies and in the subgroup analysis. Conclusions: The results show the high prevalence of class 1 integrons and high level of antibiotic resistance in association with those among uropathogenic E. coli. Moreover, the prevalence of class 1 integrons in Asian countries, as well as hospital-acquired urinary tract infection (UTI), was higher than in other countries and community-acquired UTI.

Recurrence of urinary tract infections with extended-spectrum β-lactamase-producing Escherichia coli caused by homologous strains among which clone ST131-O25b is dominant

OBJECTIVES

Bacterial features associated with recurrent urinary tract infections (RUTIs) due to extended-spectrum β-lactamase-producingEscherichia coli (ESBL-E. coli) are not well understood. In this study, phylogenetic groups and ST131 subclones were investigated to assess strain homology of ESBL-E. coli isolates in patients with RUTIs in inpatient and outpatient settings in western Sweden.

METHODS

Almost all isolates (319/356) from 123 patients with 2-7 episodes (median 2 episodes) of ESBL-E. coli UTI within 1 year were examined for seven E. coli phylogroups, the ST131-O25b clone and its subclone fimH30-Rx. Antimicrobial resistance and ESBL genes were determined for the index isolates. A subset of isolates was typed using pulsed-field gel electrophoresis (PFGE).

RESULTS

The same phylogroup and ST131 subclones were seen for all recurrences in 119/123 patients, and PFGE confirmed strain homology in recurrences for 43/44 patients tested. Phylogroup B2 dominated (56%), followed by D (19%) and F (10%). ST131-O25b andfimH30-Rx isolates were detected in 44% and 30%, respectively. CTX-M group 1 (71%) predominated. Elderly patients were in the majority. There were no associations between patient demographics or time to recurrence and bacterial characteristics. The fimH30-Rx subclone was associated with a higher number of recurrences (P = 0.015) compared with the remaining B2 isolates.

CONCLUSION

In ESBL-E. coli RUTI, most recurrences were caused by the initial infecting strain. The high frequency of the multidrug-resistant fimH30-Rx subclone and its association with multiple recurrences warrants further attention and early detection of this subclone in patients at risk of developing RUTI with ESBL-E. coli.

Molecular Characterization of Uropathogenic Escherichia coli Reveals Emergence of Drug Resistant O15, O22 and O25 Serogroups

Background and Objectives: Uropathogenic Escherichia coli (UPEC) are common pathogens causing urinary tract infections (UTIs). We aimed to investigate the relationship among clinical manifestation, serogroups, phylogenetic groups, and antimicrobial resistance among UPEC. Materials and Methods: One-hundred Escherichia coli isolates recovered from urine and ureteral scrapings were used for the study. The prevalence of antimicrobial resistance was determined by using European Committee on Antimicrobial Susceptibility Testing (EUCAST) recommendations. E. coli serogroups associated with UTI, as well as phylogenetic diversity were analyzed using multiplex PCR reactions. Results: Eighty-seven strains (87%) were isolated from females, while 13 (13%) from males. A high frequency of resistance to cephalosporins (43%) and fluoroquinolones (31%) was observed. Among UTI-associated serogroups O15 (32.8%), O22 (23.4%), and O25 (15.6%) were dominant and demonstrated elevated resistance rates. The E. coli phylogenetic group B2 was most common. These observations extended to pregnant patients with asymptomatic bacteriuria. Conclusions: Due to high rates of resistance, strategies using empirical therapy of second-generation cephalosporins and fluoroquinolones should be reconsidered in this population.

Characterization of antimicrobial resistance genes in Haemophilus parasuis isolated from pigs in China

Background

Haemophilus parasuis is a common porcine respiratory pathogen that causes high rates of morbidity and mortality in farmed swine. We performed a molecular characterization of antimicrobial resistance genes harbored by H. parasuis from pig farms in China.

Methods

We screened 143 H. parasuis isolates for antimicrobial susceptibility against six fluoroquinolone antibiotics testing by the broth microdilution method, and the presence of 64 antimicrobial resistance genes by PCR amplification and DNA sequence analysis. We determined quinolone resistance determining region mutations of DNA gyrase (gyrA and gyrB) and topoisomerase IV (parC and parE). The genetic relatedness among the strains was analyzed by pulsed-field gel electrophoresis.

Results

Susceptibility test showed that all isolates were low resistance to lomefloxacin (28.67%), levofloxacin (20.28%), norfloxacin (22.38%), ciprofloxacin (23.78%), however, high resistance levels were found to nalidixic acid (82.52%) and enrofloxacin (55.94%). In addition, we found 14 antimicrobial resistance genes were present in these isolates, including bla_TEM-1, bla_ROB-1, ermB, ermA, flor, catl, tetB, tetC, rmtB, rmtD, aadA1, aac(3′)-llc, sul1, and sul2 genes. Interestingly, one isolate carried five antibiotic resistance genes (tetB, tetC, flor, rmtB, sul1). The genes tetB, rmtB, and flor were the most prevalent resistance genes in H. parasuis in China. Alterations in the gyrA gene (S83F/Y, D87Y/N/H/G) were detected in 81% of the strains and parC mutations were often accompanied by a gyrA mutation. Pulsed-field gel electrophoresis typing revealed 51 unique patterns in the isolates carrying high-level antibiotic resistance genes, indicating considerable genetic diversity and suggesting that the genes were spread horizontally.

Discussion

The current study demonstrated that the high antibiotic resistance of H. parasuis in piglets is a combination of transferable antibiotic resistance genes and multiple target gene mutations. These data provide novel insights for the better understanding of the prevalence and epidemiology of antimicrobial resistance in H. parasuis.

Prevalence of antibiotic resistance genes in antibiotic-resistant Escherichia coli isolates in surface water of Taihu Lake Basin, China

The rapid development of antibiotic-resistant bacteria (ARB) has been of concern worldwide. In this study, antibiotic resistance genes (ARGs) were investigated in antibiotic-resistant Escherichia coli isolated from surface water samples (rivers, n = 17; Taihu Lake, n = 16) and from human, chicken, swine, and Egretta garzetta sources in the Taihu Basin. E. coli showing resistance to at least five drugs occurred in 31, 67, 58, 27, and 18% of the isolates from surface water (n = 665), chicken (n = 27), swine (n = 29), human (n = 45), and E. garzetta (n = 15) sources, respectively. The mean multi-antibiotic resistance (MAR) index of surface water samples (0.44) was lower than that of chicken (0.64) and swine (0.57) sources but higher than that of human (0.30) and E. garzetta sources (0.15). Ten tetracycline, four sulfonamide, four quinolone, five β-lactamase, and two streptomycin resistance genes were detected in the corresponding antibiotic-resistant isolates. Most antibiotic-resistant E. coli harbored at least two similar functional ARGs. Int-I was detected in at least 57% of MAR E. coli isolates. The results of multiple correspondence analysis and Spearman correlation analysis suggest that antibiotic-resistant E. coli in water samples were mainly originated from swine, chicken, and/or human sources. Most of the ARGs detected in E. garzetta sources were prevalent in other sources. These data indicated that human activities may have contributed to the spread of ARB in the aquatic environment.

Sulfonamide Resistance Genes (sul) M in Extended Spectrum Beta Lactamase (ESBL) and Non-ESBL Producing Escherichia coli Isolated From Iranian Hospitals

Background:

Extensive use of cotrimoxazole has been associated with increasing level of Escherichia coli resistance.

Objectives:

In the current study, we focused on assessing the prevalence of E. coli resistance to cotrimoxazole and frequency of its associated genes.

Materials and Methods:

One-hundred and forty-four E. coli isolates were identified during March 2007 to April 2012 at Ilam hospitals and Milad (Tehran) hospital. Antibiotic susceptibility for screening of resistance isolates was done by the Kirby-Bauer method. The sul1, sul2, sul3, dfrA1, dfrA5, int1, blaTEM, blaSHV and CTX-M genes were detected by polymerase chain reaction (PCR) amplification. Plasmid curing was done for identifying correlations between resistance genes and plasmids.

Results:

Amongst the 144 E. coli isolates, seventy-two (50%) Extended Spectrum Beta Lactamase (ESBL)-producing and seventy-two (50%) non-ESBL-producing E. coli isolates were identified; eighty-seven isolates (60.41%) were resistant to cotrimoxazole. Frequencies of sul1, sul2 and sul3, were 81% (116 isolates), 67% (96 isolates) and 2.29% (three isolates), respectively. Furthermore, 50.57% (72 isolates) had sul1 and sul2, 2.29% (3 isolates) contained sul2 and sul3, and 2.29% (three isolates) contained sul1, sul2 and sul3 genes, simultaneously. Thirty-four (39.1%) of the isolates had the dfrA1 gene. Five (5.7%) of the isolates had the dfrA5 gene. Sixty-eight (78.2%) strains contained the int1 gene. Furthermore, dfrA1 and dfrA5 were present in three (3.4%) of the isolates. The results showed that of the ESBL-producing isolates, 85.2% (n = 122), 53.2% (n = 76) and 26.1% (n = 37) were blaTEM, blaSHV and CTX-M harboring isolates, respectively.

Conclusions:

Our study indicated a high frequency of cotrimoxazole resistance gene in E. coli isolates from Ilam and Tehran (Milad) hospitals, and sul genes had a major role in cotrimoxazole resistance of these isolates.

Identification of Anti-Persister Activity against Uropathogenic Escherichia coli from a Clinical Drug Library

Uropathogenic E. coli is a major cause of urinary tract infections (UTIs), but current antibiotics do not always effectively clear the persistent infection. To identify drugs that eliminate uropathogenic E. coli persisters, we screened a clinical drug library consisting of 1524 compounds using high throughput drug exposure assay in 96-well plates. Bacterial survival was assessed by growth on LB plates. We identified 14 drug candidates (tosufloxacin, colistin, sparfloxacin, moxifloxacin and gatifloxacin, enrofloxacin and sarafloxacin, octodrine, clofoctol, dibekacin, cephalosporin C, pazufloxacin, streptomycin and neomycin), which had high anti-persister activity. Among them, tosufloxacin and colistin had the highest anti-persister activity and could completely eradicate E. coli persisters in 3 days in vitro while the current UTI antibiotics failed to do so. Our findings may have implications for the development of a more effective treatment for UTIs.

Evaluation and management of recurrent urinary tract infections in children: state of the art

Urinary tract infections (UTIs) represent an important cause of febrile illness in young children and can lead to renal scarring and kidney failure. However, diagnosis and treatment of recurrent UTI in children is an area of some controversy. Guidelines from the American Academy of Pediatrics, National Institute for Health and Clinical Excellence and European Society of Paediatric Radiology differ from each other in terms of the diagnostic algorithm to be followed. Treatment of vesicoureteral reflux and antibiotic prophylaxis for prevention of recurrent UTI are also areas of considerable debate. In this review, we collate and appraise recently published literature in order to formulate evidence-based guidance for the diagnosis and treatment of recurrent UTI in children.

Predictive utility of prior positive urine cultures

BACKGROUND

A patient's prior urine cultures are often considered when choosing empiric antibiotic therapy for a suspected urinary tract infection. We sought to evaluate how well previous urine cultures predict the identity and susceptibility of organisms in a patient's subsequent urine cultures.

METHODS

We conducted a multinational, multicenter, retrospective cohort study, including 22 019 pairs of positive urine cultures from 4351 patients across 2 healthcare systems in Toronto, Ontario, and Chicago, Illinois. We examined the probability of the same organism being identified from the same patient's positive urine culture as a function of time elapsed from the previous positive urine specimen; in cases where the same organism was identified we also examined the likelihood of the organism exhibiting the same or better antimicrobial susceptibility profile.

RESULTS

At 4-8 weeks between cultures, the correspondence in isolate identity was 57% (95% confidence interval [CI], 55%-59%), and at >32 weeks it was 49% (95% CI, 48%-50%), still greater than expected by chance (P < .001). The susceptibility profile was the same or better in 83% (95% CI, 81%-85%) of isolate pairs at 4-8 weeks, and 75% (95% CI, 73%-77%) at >32 weeks, still greater than expected by chance (P < .001). Despite high local rates of ciprofloxacin resistance in urine isolates across all patients (40%; 95% CI, 39.5%-40.5%), ciprofloxacin resistance was <20% among patients with a prior ciprofloxacin sensitive organism and no subsequent fluoroquinolone exposure.

CONCLUSIONS

A patient's prior urine culture results are useful in predicting the identity and susceptibility of a current positive urine culture. In areas of high fluoroquinolone resistance, ciprofloxacin can be used empirically when prior urine culture results indicate a ciprofloxacin-susceptible organism and there has been no history of intervening fluoroquinolone use.

First report of the ceftazidimase CTX-M-19 in South America

We report the first detection of bla_CTX-M-19 in South America, harboured in an Escherichia coli isolate obtained from a urine sample; such an isolate belonged to phylogenetic group A, ST603, and showed a ceftazidimase profile. bla_CTX-M-19 was encoded in an approximately 100 kb IncI1/IncF conjugative plasmid, featuring pndAC and hok/sok addiction systems; the β-lactamase gene was flanked upstream by three tandem-like transposons (IS26, IS10 and ISEcp1), inserted one inside the other, and downstream by IS903.

From physiology to pharmacy: developments in the pathogenesis and treatment of recurrent urinary tract infections

Urinary tract infections (UTIs) are common, and over half of women report having had at least one in their lifetime. Nearly a third of these women experience recurrent UTI episodes, but the mechanisms of these recurrences are not fully elucidated. Frequent use of antimicrobials for treatment and prevention of UTIs and other infections has contributed to the evolution of multidrug-resistant microorganisms globally. This is a looming worldwide crisis that has created an urgent need for novel strategies for the treatment and prevention of UTIs. Furthering our understanding of the mechanisms of recurrent UTIs, from both host and bacterial perspectives, will be paramount in developing targeted management strategies. In this review, we discuss recent findings regarding recurrent UTIs in women, including progress in our understanding of the mechanisms of recurrence as well as emerging treatments.

Detection of intracellular bacterial communities in a child with Escherichia coli recurrent urinary tract infections

The formation of intracellular bacterial communities (IBC) has been proposed as a new pathogenic model for urinary tract infections. Scarce reports describe this phenomenon in humans. We describe the presence of IBC in uroepithelial cells of a child with recurrent urinary infections. Urine specimen was collected from a child with Escherichia coli UTI and analyzed by light and confocal laser scanning microscopy (CLSM). The capability of this strain to produce intracellular infection in bladder tissue was confirmed in mice models. Escherichia coli phylogenetic group, presence of virulence factors genes, and its multiple locus sequence type were determined. CLSM showed large collections of morphologically coccoid and rod bacteria in eukaryotic cells cytoplasm, even seemingly protruding from the cells. Escherichia coli EC7U, ST3626, harbored type 1, P, and S/F1C fimbriae and K1 capsule genes. In this report, we confirm the presence of IBC in children with UTI, as it has been described before in women.

Similarity and divergence of phylogenies, antimicrobial susceptibilities, and virulence factor profiles of Escherichia coli isolates causing recurrent urinary tract infections that persist or result from reinfection

In order to obtain a better molecular understanding of recurrent urinary tract infection (RUTI), we collected 75 cases with repeatedly occurring uncomplicated UTI. The genetic relationships among uropathogenic Escherichia coli (UPEC) isolates were analyzed by pulsed-field gel electrophoresis. While 39 (52%) of the RUTI cases were defined as "persistence" of the same strain as the primary infecting strain, 36 (48%) were characterized by "reinfection" with a new strain that is different from the primary strain. We then examined the antimicrobial susceptibilities and phylogenetic backgrounds of 39 persistence and 86 reinfection UPEC isolates, and screened 44 virulence factor (VF) genes. We found that isolates had significant differences in the following: placement in phylogenetic group B2 (41% versus 21%; P = 0.0193) and the presence of adhesin genes iha (49% versus 28%; P = 0.0233) and papG allele I' (51% versus 24%; P = 0.003), iron uptake genes fyuA (85% versus 58%; P = 0.0037), irp-2 (87% versus 65%; P = 0.0109), and iutA (87% versus 58%; P = 0.0014), and an aggregate VF score (median, 11 versus 9; P = 0.0030). In addition, 41% of persistence strains harbored three adhesin genes simultaneously, whereas 22% of reinfection isolates did (P = 0.0289). Moreover, 59% versus 29% (P = 0.0014) of persistence and reinfection isolates contained seven types of iron uptake genes. Taken together, the antimicrobial susceptibilities of UPEC isolates had little effect on the RUTI. Compared with reinfection strains, persistence UPEC isolates exhibited higher VF scores and carried more VF genes than may be involved in the development and progression of RUTI.

Effect of long-term trimethoprim/sulfamethoxazole treatment on resistance and integron prevalence in the intestinal flora: a randomized, double-blind, placebo-controlled trial in children

OBJECTIVES

The aim of this study was to test the hypothesis that trimethoprim/sulfamethoxazole selects for integron-positive and multidrug-resistant Enterobacteriaceae in the intestinal flora.

METHODS

During 1 year of follow-up, antibiotic susceptibility and the presence of integrons were determined in faecal Enterobacteriaceae isolated from 99 children with chronic active otitis media, randomly assigned to treatment with trimethoprim/sulfamethoxazole or placebo (http://www.clinicaltrials.gov/; trial registration number NCT00189098).

RESULTS

At 6 and 12 weeks of follow-up, 32 (91%) and 24 (67%) children in the trimethoprim/sulfamethoxazole group carried trimethoprim/sulfamethoxazole-resistant Enterobacteriaceae versus 10 (21%) and 8 (17%) children in the placebo group [rate differences (RDs): 70 (95% CI: 55; 85) and 50 (95% CI: 31; 69)], respectively. Multiresistance also increased during trimethoprim/sulfamethoxazole treatment. At 6 weeks of follow-up, the integron prevalence was 26 (79%) in the trimethoprim/sulfamethoxazole group and 10 (22%) in the placebo group [RD: 57 (95% CI: 39; 75)]. After 12 weeks the integron prevalence, and after 1 year the susceptibility levels, had returned to baseline values.

CONCLUSIONS

Initially, trimethoprim/sulfamethoxazole usage was strongly associated with the appearance of integron-positive (multi)drug-resistant Enterobacteriaceae in the intestinal flora. After prolonged exposure to trimethoprim/sulfamethoxazole, however, this population of Enterobacteriaceae was substituted by a population with non-integron-associated resistance mechanisms. After trimethoprim/sulfamethoxazole was discontinued, susceptibility rates to all antibiotics returned to baseline levels.