Urinary Isolates Research Articles

Evaluation of phenotypic and genotypic methods for the identification and characterization of bacterial isolates recovered from catheter-associated urinary tract infections.

Urinary tract infections are the most common hospital-acquired infection, 80% of which are associated with catheterization. Diagnostic methods may influence the reported identities of these pathogens, and phenotypic testing under laboratory conditions may not reflect infection phenotypes. This study aimed to evaluate the efficacy of diagnostic methods and whether medium composition alters phenotypes by characterizing catheter-associated urinary tract infection isolates from a UK hospital. We compared five bacterial identification methods, including biochemical testing, matrix-assisted laser desorption/ionization biotyping, and genome sequencing, finding differences in genus- or species-level identifications. Antibiotic susceptibility comparisons between phenotypic assays and genomic predictions showed high agreement only in multidrug-resistant strains. To determine whether growth rate and biofilm formation were affected by medium composition, strains were grown in both planktonic and biofilm states. Low planktonic growth and significant biofilm formation were observed in artificial urine compared to rich laboratory media, underscoring the importance of assay design. This study highlights the risks of relying on a single diagnostic method for species identification, advocating for whole-genome sequencing for accuracy. It emphasizes the continued importance of phenotypic methods in understanding antibiotic resistance in clinical settings and the need for characterization conditions that mirror those encountered by pathogens in the body.

Optimizing antimicrobial efficacy and ammonia sensing in a novel carboxymethyl tamarind kernel gum/Fe nanocomposite

Iron nanoparticles were synthesized utilizing Carboxymethyl tamarind kernel gum (CMTKG), which acted as both a reducing and stabilizing agent. Through an in situ co-precipitation method, CMTKG/FeO nanocomposites were synthesized, employing epichlorohydrin as a cross-linking agent. Characterization of the obtained CMTKG/FeO nanocomposites was conducted through various techniques including Scanning Electron Microscopy (SEM), Dynamic light scattering (DLS), Ultraviolet spectroscopy, Fourier transform infrared (FTIR), Thermal analysis (TGA), and X-ray diffraction analysis (XRD), revealing an average size of 60–90 nm. The application of these nanocomposites was explored in the sensing of ammonia in an aqueous medium at room temperature, demonstrating a noticeable change in the intensity of the surface plasmon resonance peak with increasing ammonia concentration, resulting in a shift from 313 nm to 331 nm. Additionally, the antimicrobial efficacy of the synthesized CMTKG/FeO nanocomposites was evaluated against urinary tract isolates including Pseudomonas aeruginosa, E. coli, and Enterococcus faecalis. Interestingly, the nanocomposites exhibited significant activity specifically against Enterococcus faecalis, manifesting a zone of inhibition measuring 12.4±0.5 mm.

Pediatric urinary tract infections caused by poultry-associated Escherichia coli.

Escherichia coli is the leading cause of urinary tract infections (UTIs) in children and adults. The gastrointestinal tract is the primary reservoir of uropathogenic E. coli, which can be acquired from a variety of environmental exposures, including retail meat. In the current study, we used a novel statistical-genomic approach to estimate the proportion of pediatric UTIs caused by foodborne zoonotic E. coli strains. E. coli urine isolates were collected from DC residents aged 2 months to 17 years from the Children's National Medical Center Laboratory, 2013-2014. During the same period, E. coli isolates were collected from retail poultry products purchased from 15 sites throughout DC. A total of 52 urine and 56 poultry isolates underwent whole-genome sequencing, core genome phylogenetic analysis, and host-origin prediction by a Bayesian latent class model that incorporated data on the presence of mobile genetic elements (MGEs) among E. coli isolates from multiple vertebrate hosts. A total of 56 multilocus sequence types were identified among the isolates. Five sequence types-ST10, ST38, ST69, ST117, and ST131-were observed among both urine and poultry isolates. Using the Bayesian latent class model, we estimated that 19% (10/52) of the clinical E. coli isolates in our population were foodborne zoonotic strains. These data suggest that a substantial portion of pediatric UTIs in the Washington DC region may be caused by E. coli strains originating in food animals and likely transmitted via contaminated poultry meat.IMPORTANCEEscherichia coli UTIs are a heavy public health burden and can have long-term negative health consequences for pediatric patients. E. coli has an extremely broad host range, including humans, chickens, turkeys, pigs, and cattle. E. coli derived from food animals is a frequent contaminant of retail meat products, but little is known about the risk these strains pose to pediatric populations. Quantifying the proportion of pediatric UTIs caused by food-animal-derived E. coli, characterizing the highest-risk strains, and identifying their primary reservoir species could inform novel intervention strategies to reduce UTI burden in this vulnerable population. Our results suggest that retail poultry meat may be an important vehicle for pediatric exposure to zoonotic E. coli strains capable of causing UTIs. Vaccinating poultry against the highest-risk strains could potentially reduce poultry colonization, poultry meat contamination, and downstream pediatric infections.

Co-resistance Among Escherichia coli and Klebsiella pneumoniae Urine Isolates from Female Outpatients with Presumed UTI: A Retrospective US Cohort Study.

Urinary tract infections (UTIs) caused by antimicrobial-resistant Enterobacterales are a global health threat. There are limited surveillance data available to characterize the prevalence of antimicrobial resistance among outpatients in the United States (US). This retrospective cohort (database) study investigated co-resistance among Escherichia coli and Klebsiella pneumoniae urinary isolates from US female outpatients aged ≥ 12years with presumed uncomplicated UTI (uUTI), ≥ 3months of data (2011-2019), and antimicrobial susceptibility testing results. Eligible isolates were the first urinary E.coli or K.pneumoniae isolate per patient collected within 30days; classified as not susceptible (NS) if antimicrobial susceptibility testing results were intermediate or resistant to each antibiotic tested. Four resistance phenotypes were identified: NS to fluoroquinolones (FQ), trimethoprim/sulfamethoxazole (SXT), nitrofurantoin (NTF), and extended-spectrum β-lactamase+/third-generation cephalosporin (ESBL+/3GC NS). Co-resistance phenotypes included all possible combinations of resistance to ≥ 2 drug classes. Of 1,513,882 E. coli isolates and 250,719K. pneumoniae isolates, 856,918 and 187,459 isolates with ≥ 1 resistance phenotype were included in the analysis, respectively. The most common resistance phenotypes were SXT NS for the E.coli isolates (44.8%) and NTF NS for the K. pneumoniae isolates (75.5%), while ESBL+/3GC NS comprised 11.2 and 5.9%, respectively. Among ESBL+/3GC NS E. coli isolates, 72.4, 56.7, and 46.6% were co-resistant to FQ, SXT, and FQ + SXT, respectively. For ESBL+/3GC NS K.pneumoniae isolates, 65.7 and 45.7% were co-resistant to SXT and FQ + SXT. Both species exhibited high rates of co-resistance, emphasizing the need to raise awareness of co-resistance and of the unmet need for effective treatment options for uUTI.

A STUDY ON IN VITRO ACTIVITY OF FOSFOMYCIN AGAINST ENTEROBACTERIACAE UROPATHOGEN ALONG WITH MICROBIOLOGICAL PROFILE AND ANTIBIOGRAM OF UROPATHOGENS

Background:Urinary tract infection (UTI) is one of the most common infection throughout the world that may affect both the lower and the upper urinary tracts. Aims & Objective:The present study was done to determine various organisms causing Urinary tract infections and to analyse antimicrobial sensitivity patterns of those isolates. Materials and Methods:This prospective study was conducted from April 2020 to March 2021at SIMS& RH, Tumkur. All urine samples were received in Microbiology laboratory for routine microbiology investigations were inoculated on Blood agar and MacConkey agar culture media using calibrated wire loop . Urinary isolates with significant bacteriuria were further processed by conventional biochemical tests and antimicrobial susceptibility testing was done as per standard methods. Results: A total of 697 urine samples were processed in that 324 (46.48%) samples were shown as significant growth of bacteria. Most of the cases seen in (67.28%) female and under age group of 21-30(22.22%).The predominantly Gram-negative bacteria (85.18%) were isolated followed by Gram positive bacteria(10.49%) and Candida spp(4.32%). The Gram negative bacteria showed high sensitivity to Ampicillin sulbactum (88.27%) followed by Amikacin (87.24%). All Gram-positive bacteria isolates is showed sensitivity to Vancomycin (100%).We found that 235( 92.88%) Enterobacteriaceace isolates were is susceptible for Fosfomycin. Conclusion:. Antibiotic resistance has become a major clinical problem worldwide and has increased over the years.Hence antibiotic susceptibility testing should be done to diagnose and treat the drug resistant UTI cases. Fosfomycin may be given empirically in patients with uncomplicated urinary tract infection due to Enterobacteriaceace.

Molecular Detection of Virulence Genes Associated With Multi- Drug Resistant Pseudomonas Aeruginosa Isolated from Clinical and Environmental Samples within Maiduguri

Pseudomonas aeruginosa is an ubiquitous opportunistic pathogen having numerous virulence factors and the ability to acquire multidrug resistant traits. This study aimed to determine the presence of the virulence genes algD and lasB in multidrug resistant Pseudomonas aeruginosa isolated from clinical and environmental samples within Maiduguri. A total of 200 samples were collected from four sources namely; Farm soil at root region of groundnut, abattoir waste water, commercial boreholes and urine of urinary tract infected patients. All positive growths on cetrimide agar were further identified biochemically. Antibiotic profile of confirmed Pseudomonas aeruginosa was determined using Kirby-Baeur disc diffusion method. The genes algD and lasB were detected in the multidrug resistant isolates. The result also showed that 90.90%, 81.81% and 81.81% of the urine isolates were resistant to nalidixic acid, chloramphenicol and tetracycline respectively while highest sensitivity was observed against amikacin at 81.81%. Highest resistance among environmental samples was observed in abattoir wastewater with 95.24% resistance to chloramphenicol while least resistance was observed in borehole isolates with 0.00% resistance to Gentamicin, Amikaicin, Meropenem and Aztreonam. According to the findings of this study also, there is no significant difference in habouring virulence genes among the isolates of the different sources. All the multidrug resistant isolates were found to habour both algD and LasB genes. In conclusion, P. aeruginosa was found in all of the studied sources and widespread of algD and LasB genes in the multidrug resistant isolates from all the sources.

Gram Positive Cocci Associated Urinary Tract Infections, their Prevalence and Antibiotic Susceptibility Patterns

Background: Urinary tract infections (UTIs) are the third most common type of infection in humans globally. Gram-positive bacteria are said to be responsible for ten percent of urinary tract (UTI) infections. The study's goal was to profile gram-positive cocci-associated UTIs and their antibiogram, as they were observed at LASUTH. Methods: This was a retrospective assessment of the Medical Microbiology Laboratory records of the LASUTH to review the in vitro antibiotic susceptibility patterns of gram-positive urinary bacterial isolates between April 2020 and March 2021. The bacteria were isolated and identified from routine urine samples using standard bacteriological methods and the API. In vitro antibiotic susceptibility test (AST) was routinely performed by the modified Kirby-Bauer disk diffusion test and susceptibility breakpoints were determined using the Clinical and Laboratory Standards Institute (CLSI) guidelines. Results: 2,253 urine samples were processed in the medical microbiology laboratory over the one year and 662 (29.4%) samples yielded Positive cultures. Of the 662 isolates, 494 (74.6%) were gram-negative bacteria. 164 (24.8%) were gram-positive cocci while 4 (0.6%) were gram positive rod. Among the gram-positive cocci’s isolated Enterococcus faecalis had the highest frequency 58 (35.4%). Aminoglycosides (Gentamycin and Amikacin) and Linezolid antibiotics were found to be the most effective drugs against gram-positive cocci bacteria except Enterococcus spp. For empirical treatment of Enterococcus spp in our facility Fosfomycin and Tigecycline are the best options, while for Streptococcus agalactiae associated UTI, Amikacin, Cefuroxime, Linezolid, and levofloxacin can be used for empirical treatment. Conclusion: The prevalence rate of gram-positive cocci associated UTI in this study was 7.3% (164/2253). The emergence of drug resistance in these pathogens to commonly used antibiotics is a thing of concern. Therefore, efficient antimicrobial stewardship programmes must be in place.

Macrolide Resistance in the Aerococcus urinae Complex: Implications for Integrative and Conjugative Elements.

The recognition of the Aerococcus urinae complex (AUC) as an emerging uropathogen has led to growing concerns due to a limited understanding of its disease spectrum and antibiotic resistance profiles. Here, we investigated the prevalence of macrolide resistance within urinary AUC isolates, shedding light on potential genetic mechanisms. Phenotypic testing revealed a high rate of macrolide resistance: 45%, among a total of 189 urinary AUC isolates. Genomic analysis identified integrative and conjugative elements (ICEs) as carriers of the macrolide resistance gene ermA, suggesting horizontal gene transfer as a mechanism of resistance. Furthermore, comparison with publicly available genomes of related pathogens revealed high ICE sequence homogeneity, highlighting the potential for cross-species dissemination of resistance determinants. Understanding mechanisms of resistance is crucial for developing effective surveillance strategies and improving antibiotic use. Furthermore, the findings underscore the importance of considering the broader ecological context of resistance dissemination, emphasizing the need for community-level surveillance to combat the spread of antibiotic resistance within the urinary microbiome.

Antibiotic Resistance of Bacteria isolated in Urinary Tract Infections

Abstract Objectives: This study aimed to examine the relationships between isolated bacterial agents, age, and gender, as well as antibiotic resistance of UTI isolates, in addition to investigate the antibiotic resistance in a section of Iraqi patients with UTI. Methods: Isolates (885) from patients and outpatients with symptomatic urinary tract infections at Al-Sadder teaching hospital in Basra province, southern Iraq, from January to August 2022. Results: The results of patient specimens cultured on appropriate culture media indicate that the number of negative cultures was 528 while the number of positive cultures was 357; females are more susceptible to UTIs than males (170). The age category 60 years had the highest infection rate (31%), followed by 20-29 years (19.3%). The most prevalent etiological agent was Escherichia coli (28.3%), followed by Staphylococcus spp. (19.3%), Candida albicans (14.9%), and Klebsiella pneumonia (14.9%). Conclusion: The results demonstrate that various bacteria exhibit variable degrees of sensitivity to different antibiotics, with the significant finding that the majority of urinary isolates were highly resistant to commonly used antibiotics.

Nationwide genome surveillance of carbapenem-resistant Pseudomonas aeruginosa in Japan.

Japan is a country with an approximate 10% prevalence rate of carbapenem-resistant Pseudomonas aeruginosa (CRPA). Currently, a comprehensive overview of the genotype and phenotype patterns of CRPA in Japan is lacking. Herein, we conducted genome sequencing and quantitative antimicrobial susceptibility testing for 382 meropenem-resistant CRPA isolates that were collected from 78 hospitals across Japan from 2019 to 2020. CRPA exhibited susceptibility rates of 52.9%, 26.4%, and 88.0% against piperacillin-tazobactam, ciprofloxacin, and amikacin, respectively, whereas 27.7% of CRPA isolates was classified as difficult-to-treat resistance P. aeruginosa. Of the 148 sequence types detected, ST274 (9.7%) was predominant, followed by ST235 (7.6%). The proportion of urine isolates in ST235 was higher than that in other STs (P = 0.0056, χ2 test). Only 4.1% of CRPA isolates carried the carbapenemase genes: blaGES (2) and blaIMP (13). One ST235 isolate carried the novel blaIMP variant blaIMP-98 in the chromosome. Regarding chromosomal mutations, 87.1% of CRPA isolates possessed inactivating or other resistance mutations in oprD, and 28.8% showed mutations in the regulatory genes (mexR, nalC, and nalD) for the MexAB-OprM efflux pump. Additionally, 4.7% of CRPA isolates carried a resistance mutation in the PBP3-encoding gene ftsI. The findings from this study and other surveillance studies collectively demonstrate that CRPA exhibits marked genetic diversity and that its multidrug resistance in Japan is less prevailed than in other regions. This study contributes a valuable data set that addresses a gap in genotype/phenotype information regarding CRPA in the Asia-Pacific region, where the epidemiological background markedly differs between regions.

Molecular investigation of exoU and exoY virulence genes in Pseudomonas aeruginosa collected from hospitalized patients in North of Iran: A descriptive-analytical study

Objective: To investigate the frequency of exoU and exoY genes in patients with Pseudomonas aeruginosa infection. Methods: In this study, 100 clinical isolates of Pseudomonas aeruginosa were collected from patients hospitalized in educational- therapeutic hospitals and were identified using standard microbiological tests. Then, the antibiotic resistance pattern of the isolates was determined by the disk agar diffusion method. The bacterial DNAs were extracted by the alkaline lysis method. Finally, the presence of exoU and exoY genes was evaluated by the PCR test. Results: In this study, 47%, 72%, 29%, 39%, 40%, and 44% of the isolates were non-susceptible to piperacillin, aztreonam, ceftazidime, imipenem, tobramycin, and ciprofloxacin, respectively. In addition, 95% and 93% of the clinical isolates carried the exoU and exoY genes. Blood and fecal isolates had both virulence genes, while only one wound isolate had neither genes. Meanwhile, all urinary isolates contained the exoY gene and only one isolate lacked the exoU gene. Also, 88 isolates simultaneously had both exoU and exoY genes. Conclusions: High prevalence of exoU and exoY genes in this region indicates a significant role of type III secretion system in pathogenesis of Pseudomonas aeruginosa. The type III secretion system may be a suitable target to reduce the pathogenicity of this bacterium.

Polarized HLA Class I Expression on Renal Tubules Hinders the Detection of Donor-Specific Urinary Extracellular Vesicles.

Kidney transplantation is the optimal treatment for patients with end-stage kidney disease. Donor-specific urinary extracellular vesicles (uEVs) hold potential as biomarkers for assessing allograft status. We aimed to develop a method for identifying donor-specific uEVs based on human leukocyte antigen (HLA) mismatching with the kidney transplant recipients (KTRs). Urine and plasma were obtained from HLA-A2+ donors and HLA-A2- KTRs pre-transplant. CD9 (tetraspanin, EV marker) and HLA-A2 double-positive (CD9+ HLA-A2+) EVs were quantified using isolation-free imaging flow cytometry (IFCM). Healthy individuals' urine was used to investigate CD9+ HLA-class-I+ uEV quantification using IFCM, time-resolved fluoroimmunoassay (TR-FIA), and immunogold staining cryo-electron microscopy (cryo-EM). Culture-derived CD9+ HLA-class-I+ EVs were spiked into the urine to investigate urine matrix effects on uEV HLA detection. Deceased donor kidneys and peritumoral kidney tissue were used for HLA class I detection with histochemistry. The concentrations of CD9+ HLA-A2+ EVs in both donor and recipient urine approached the negative (detergent-treated) control levels for IFCM and were significantly lower than those observed in donor plasma. In parallel, universal HLA class I+ uEVs were similarly undetectable in the urine and uEV isolates compared with plasma, as verified by IFCM, TR-FIA, and cryogenic electron microscopy. Culture supernatant containing HLA class I+ vesicles from B, T, and human proximal tubule cells were spiked into the urine, and these EVs remained stable at 37°C for 8 hours. Immunohistochemistry revealed that HLA class I was predominantly expressed on the basolateral side of renal tubules, with limited expression on their urine/apical side. The detection of donor-specific uEVs is hindered by the limited release of HLA class I+ EVs from the kidney into the urine, primarily due to the polarized HLA class I expression on renal tubules. Identifying donor-specific uEVs requires further advancements in recognizing transplant-specific uEVs and urine-associated markers.

Comparison of integron mediated antimicrobial resistance in clinical isolates of Escherichia coli from urinary and bacteremic sources

BackgroundAntimicrobial resistance (AMR) is a global threat driven mainly by horizontal gene transfer (HGT) mechanisms through mobile genetic elements (MGEs) including integrons. The variable region (VR) of an integron can acquire or excise gene cassettes (GCs) that confer resistance to antibiotics based on the selection pressure. Escherichia coli plays a significant role in the genetic transfer of resistance determinants to other Gram-negative bacteria. Current study is aimed to detect and compare integron-mediated resistance in clinical isolates of E. coli. Unique isolates of E. coli from urine or blood cultures were studied for their antimicrobial resistance patterns and integrons were detected using polymerase chain reaction assays followed by Sanger sequencing of GCs.ResultsDuring the study period, a total of 470 E. coli isolates were obtained, 361 (76.8%) from urinary and 109 (23.1%) from bacteremic sources. Class 1 integrons were detected in 66 (18.2%) and 26 (23.8%) isolates respectively. Urinary isolates of E. coli harbouring Class 1 integrons demonstrated significantly higher rates of resistance (p < 0.05) for most antibiotics (12/16, 75%) compared to integron negative isolates. Although not statistically significant, similar differences were observed in bacteremic isolates. Among the urinary isolates, 27 (40.9%) had a VR, in which the most common GC array detected was DfrA17-AadA5 (n = 14), followed by DfrA5 (n = 4) and DfrA12 (n = 3). Among bacteremic isolates, only 4 (15.3%) had a VR, all of which were carrying DfrA17. The detected GC array correlated with the respective isolates’ phenotypic resistance patterns.ConclusionWe found a strong correlation between integron positivity and trimethoprim resistance among E. coli from urinary sources. Although higher rates of resistance were observed in bacteremic isolates, they mostly carried empty integrons.

Comparison of Cefazolin and Ceftriaxone Enterobacterales Susceptibilities for Inpatient Treatment of Urinary Tract Infections and Risk of Hospital-onset Clostridioides difficile Infection

Purpose: Urinary tract infection (UTI) is the second most common indication for antibiotic therapy among inpatients in the United States. Ceftriaxone, a third-generation cephalosporin, is habitually chosen to treat inpatient UTIs due to familiarity, cost and perceived safety. However, third-generation cephalosporins increase the risk of healthcare facility-onset Clostridioides difficile infection (HOCDI) more than any other antibiotic group, while no statistical risk exists for first-generation cephalosporins. Recent evidence comparing Enterobacterales susceptibility for first- and third-generation cephalosporins in urinary specimens in the United States does not exist. This analysis assesses comparative activity of cefazolin and ceftriaxone for Enterobacterales urinary isolates and incidence of HOCDI to determine the usefulness of cefazolin as an empiric agent to manage inpatient UTI and limit ceftriaxone collateral damage.Methods: This is a retrospective single center observational study. Microbiologic susceptibility data was analyzed for E. coli, K. pneumoniae, and P. mirabilis urinary specimens taken from adult inpatients admitted January 1, 2022 to December 31, 2022. Primary outcome is incidence of E. coli, K. pneumoniae, and P. mirabilis susceptibility to cefazolin in uncomplicated UTI (MIC < 16 mcg/mL). Secondary outcomes include susceptibility for complicated UTI and HOCDI risk associated with cefazolin and ceftriaxone. A larger time frame, January 1, 2016 to December 31, 2022, was used to assess HOCDI risk associated with cefazolin and ceftriaxone. HOCDI risk assessment included adults administered at least one dose of either cefazolin or ceftriaxone during a minimum of four-day hospitalization.Findings: A total of 1150 urine samples were identified as E. coli, K. pneumoniae, and P. mirabilis in 2022. Susceptibility to cefazolin was observed in 1064/1150 (92.5%) isolates using the MIC breakpoint for uncomplicated UTI, and to ceftriaxone in 1115/1150 (97.0%) isolates (p < 0.001). From 2016-2022, either cefazolin or ceftriaxone was administered in 26,462 inpatient admissions with an HOCDI diagnoses occurring in 89 admissions. HOCDI developed in 78 admissions (0.40%) with ceftriaxone exposure and 11 cases (0.15%) developed in cefazolin exposed admissions (p < 0.001, adjusted OR 2.44, 95% CI 1.25 – 4.76).Implications: Cefazolin demonstrates high susceptibility for uropathogens commonly implicated in uncomplicated UTI, the predominant UTI managed inpatient. While ceftriaxone demonstrates a higher susceptibility rate against these common uropathogens, it more than doubles the risk for HOCDI compared to cefazolin. For institutions evaluating opportunities to reduce ceftriaxone use to limit associated collateral damage like HOCDI, use of cefazolin for uncomplicated urinary tract infection may be evaluated using local susceptibility data.

Antimicrobial resistance in Enterobacterales infections among children in sub-Saharan Africa: a systematic review and meta-analysis

The burden of antimicrobial resistance (AMR) has been estimated to be the highest in sub-Saharan Africa (SSA). The current study estimated the proportion of drug-resistant Enterobacterales causing infections in SSA children. We searched MEDLINE/PubMed, Embase and the Cochrane Library to identify retrospective and prospective studies published from 01/01/2005 to 01/06/2022 reporting AMR of Enterobacterales causing infections in sub-Saharan children (0-18 years old). Studies were excluded if they had unclear documentation of antimicrobial susceptibility testing methods or fewer than ten observations per bacteria. Data extraction and quality appraisal were conducted by two authors independently. The primary outcome was the proportion of Enterobacterales resistant to antibiotics commonly used in paediatrics. Proportions were combined across studies using mixed-effects logistic regression models per bacteria and per antibiotic. Between-study heterogeneity was assessed using the I2 statistic. The protocol was registered with PROSPERO (CRD42021260157). After screening 1111 records, 122 relevant studies were included, providing data on more than 30,000 blood, urine and stool isolates. Escherichia coli and Klebsiella spp. were the predominant species, both presenting high proportions of resistance to third-generation cephalosporins, especially in blood cultures: 40.6% (95% CI: 27.7%-55%; I2: 85.7%, number of isolates (n): 1032) and 84.9% (72.8%-92.2%; I2: 94.1%, n: 2067), respectively. High proportions of resistance to other commonly used antibiotics were also observed. E.coli had high proportions of resistance, especially for ampicillin (92.5%; 95% CI: 76.4%-97.9%; I2: 89.8%, n: 888) and gentamicin (42.7%; 95% CI: 30%-56.5%; I2: 71.9%, n: 968). Gentamicin-resistant Klebsiella spp. were also frequently reported (77.6%; 95% CI: 65.5%-86.3%; I2: 91.6%, n: 1886). High proportions of resistance to antibiotics commonly used for empirical treatment of infectious syndromes were found for Enterobacterales in sub-Saharan children. There is a critical need to better identify local patterns of AMR to inform and update clinical guidelines for better treatment outcomes. No funding was received.

Phenotypic characterization of ESBL-producing urinary isolates of E. coli and Klebsiella spp. in a tertiary care children's hospital in Nepal

BackgroundThe production of extended-spectrum beta-lactamases (ESBLs) among uropathogens, particularly E. coli and Klebsiella spp., poses a severe public health concern. This study explored the epidemiology of ESBL-producing E. coli and Klebsiella spp. isolated from urine samples obtained at a tertiary care children's hospital in Nepal.MethodsA cross-sectional study was conducted from August 2016 to February 2017. A total of 745 clean catch urine samples were obtained from pediatric patients under the age of 13 and subjected to semiquantitative culture. E. coli and Klebsiella spp. were identified using standard laboratory protocols. Antibiotic susceptibility testing was performed using the Kirby-Bauer disc diffusion method, and ESBL producers were phenotypically identified using the combined disk method.ResultsAmong the bacterial isolates, E. coli predominated, accounting for 139 (81.8%) positive cases. Notably, E. coli showed high susceptibility to nitrofurantoin, with 117 (84.2%) isolates being susceptible. Meanwhile, K. pneumoniae showed high susceptibility to gentamicin, with 21 (91.3%) isolates being susceptible. Of the 163 isolates of E. coli and Klebsiella spp., 62 (38.0%) were identified as multidrug-resistant (MDR), with 42 (25.8%) confirmed as phenotypic ESBL producers. Remarkably, all 41 (100%) ESBL-producing E. coli isolates were susceptible to imipenem.ConclusionsThe prevalence of ESBL producers among E. coli and K. pneumoniae isolates from pediatric patients underscores the importance of antimicrobial stewardship. Nitrofurantoin and gentamicin emerge as effective empirical treatment choices against these pathogens in children. However, the high rates of multidrug resistance and ESBL production highlight the necessity for routine surveillance, and early detection strategies to manage such infections effectively.

Molecular characterization of ESBL-producing uropathogenic Escherichia coli isolates among kidney transplant patients: Emergence and spread of B2-ST131 clone type

This study was conducted to identify the distribution of virulence determinants in uropathogenic Escherichia coli (UPEC) isolates obtained from kidney transplant (KTP) and non-transplant patients (non-KTP) with urinary tract infections (UTI). Additionally, the (GTG)5 fingerprinting technique was used to investigate the genetic diversity of Extended-Spectrum B-Lactamase (ESBL)-positive isolates.In this case-control study, 111 urine isolates were obtained from non-KTPs and KTPs, respectively. The presence of genetic markers encoding adhesion proteins, toxins and major E. coli phylogroups was assessed through PCR amplification. Molecular typing of ESBL-positive UPEC strains was performed using (GTG)5 fingerprinting and Multilocus sequence typing (MLST) techniques.Overall, 65 and 46 UPEC isolates were obtained from non-KTPs and KTPs, respectively. Among the studied isolates, traT (85.6%) gene was the most frequently observed virulence gene, followed by kpsMT (49.5%). Using the 80% cut-off point, all the 35 UPEC isolates were classified into four major clusters, namely A, B, C, and D. The majority of the Sequence Type (ST) 131 isolates belonged to cluster A. Additionally, three ST1193 isolates belonged to cluster A and phylogroup B2. Moreover, ST38, ST131 and ST10 were in different cluster.In general, we observed significant differences in the papA, ompT, sat, and vat genes between KTPs and non-KTPs. Furthermore, since all the isolates carried one or more virulence factors (VFs), these findings are concerning in the context of managing UTIs caused by the UPEC strain. Additionally, the distribution of ST and Clonal Complex (CC) among isolates in the main clusters revealed significant differences between MLST and (GTG)5 fingerprinting analysis.

Prevalence, regional distribution, and trends of antimicrobial resistance among female outpatients with urine Klebsiella spp. isolates: a multicenter evaluation in the United States between 2011 and 2019

BackgroundAntimicrobial resistance research in uncomplicated urinary tract infection typically focuses on the main causative pathogen, Escherichia coli; however, little is known about the antimicrobial resistance burden of Klebsiella species, which can also cause uncomplicated urinary tract infections. This retrospective cohort study assessed the prevalence and geographic distribution of antimicrobial resistance among Klebsiella species and antimicrobial resistance trends for K. pneumoniae in the United States (2011–2019).MethodsK. pneumoniae and K. oxytoca urine isolates (30-day, non-duplicate) among female outpatients (aged ≥ 12 years) with presumed uUTI at 304 centers in the United States were classified by resistance phenotype(s): not susceptible to nitrofurantoin, trimethoprim/sulfamethoxazole, or fluoroquinolone, extended-spectrum β-lactamase-positive/not susceptible; and multidrug-resistant based on ≥ 2 and ≥ 3 resistance phenotypes. Antimicrobial resistance prevalence by census division and age, as well as antimicrobial resistance trends over time for Klebsiella species, were assessed using generalized estimating equations.Results270,552 Klebsiella species isolates were evaluated (250,719 K. pneumoniae; 19,833 K. oxytoca). The most frequent resistance phenotypes in 2019 were nitrofurantoin not susceptible (Klebsiella species: 54.0%; K. pneumoniae: 57.3%; K. oxytoca: 15.1%) and trimethoprim/sulfamethoxazole not susceptible (Klebsiella species: 10.4%; K. pneumoniae: 10.6%; K. oxytoca: 8.6%). Extended-spectrum β-lactamase-positive/not susceptible prevalence was 5.4%, 5.3%, and 6.8%, respectively. K. pneumoniae resistance phenotype prevalence varied (p < 0.0001) geographically and by age, and increased over time (except for the nitrofurantoin not susceptible phenotype, which was stable and > 50% throughout).ConclusionsThere is a high antimicrobial resistance prevalence and increasing antimicrobial resistance trends among K. pneumoniae isolates from female outpatients in the United States with presumed uncomplicated urinary tract infection. Awareness of K. pneumoniae antimicrobial resistance helps to optimize empiric uncomplicated urinary tract infection treatment.

Genotypic characterization of bacterial isolates causing urinary tract infections among adults at Kiambu Level 5 Hospital, Kenya: selected extended-spectrum β-lactamase genes and biofilm formation.

The menace of antimicrobial resistance affecting public health is rising globally. Many pathogenic bacteria use mechanisms such as mutations and biofilm formation, significantly reducing the efficacy of antimicrobial agents. In this cross-sectional study, we aimed to determine the prevalence of selected extended-spectrum β-lactamase (ESβL) genes and analyse the biofilm formation abilities of the isolated bacteria causing urinary tract infection among adult patients seeking Medicare at Kiambu Level 5 Hospital, Kenya. The double-disc synergy test was used for phenotypic identification of ESβL-producing isolates, while microtitre plate assays with some modifications were used for the biofilm formation test. Ten isolates were bioassayed for ESβL genes out of 57 bacterial isolates obtained from urine samples. This study found the bla TEM genes to be the most prevalent ESβL type [10/10 (100 %)], followed by blaOXA and blaSHV genes at 4/10 (40 %) and 3/10 (30 %), respectively. In addition, co-carriage of blaTEM and blaSHV was 50 % lower than that of blaTEM+bla OXA genes at 66.7 % among Escherichia coli isolates studied. Biofilm formation was positive in 36/57 (63.2 %) of the isolates tested, with most being Gram-negative [25/36 (69.4 %)]. Escherichia coli [15/36 (41.7 %)], Klebsiella species [7/36 (19.4 %)] and Staphylococcus aureus [7/36 (19.4 %)] were the dominant biofilm formers. However, there was no significant difference in biofilm formation among all tested isolates, with all isolates recording P-values >0.05. In light of these findings, biofilm formation potential coupled with antimicrobial resistance genes in urinary tract infection isolates may lead to difficult-to-treat infections.

Artificial intelligence in UTI – can machine learning models accurately predict antimicrobial susceptibility in urinary culture isolates?

Artificial intelligence in UTI – can machine learning models accurately predict antimicrobial susceptibility in urinary culture isolates?