scholarly journals 671. Same Day Identification of Enterobacteriaceae Directly from Urine Samples

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S390-S391
Author(s):  
Shelley E Kon ◽  
Sara Giddins ◽  
Irina Yushkevich ◽  
Martin Fuchs ◽  
Amy Irwin ◽  
...  

Abstract Background Urinary tract infections (UTIs) are one of the most common infections, associated with 10.5 million outpatient visits annually. Fast and accurate identification (ID) of bacteria causing a UTI would allow for immediate targeted therapy, as opposed to conventional methods which take one to three days. The Accelerate Pheno® system (ACC, Accelerate Diagnostics Inc., Tucson, AZ, USA) provides microbial ID and susceptibility (AST) from positive blood cultures. Our objective was to determine ACC’s potential to quickly ID bacterial pathogens directly from urine. Methods Remnant urine samples with >100K colony forming units (CFU)/mL of gram-negative bacteria as determined by quantitative plating were obtained from the clinical lab. 1.5ml of urine was dispensed into a capsule and loaded onto the Accelerate PhenoPrep™ module. This module automatically performs wash steps to separate bacteria from human cells and other debris. The processed sample was loaded onto ACC for analysis using a custom designed assay which detects the presence of bacteria and employs an Enterobacteriaceae family specific FISH probe. The results were compared to standard of care ID results. Results There were 10 E. coli and 1 C. koseri among the eleven samples tested. Baseline concentration of samples immediately prior to testing ranged from 2.5 x 106 to 1.08 x 1010 CFU/mL (average 4.19 x 109). After specimen processing, average concentration was 2.14 x 109 CFU/mL and average recovery was 42.83%. ACC detected bacteria and identified it as Enterobacteriaceae in 11/11 samples (100%). Average sample prep time was 55 min. Average time to Enterobacteriaceae ID was 8.6 hrs. Average total time to ID, including specimen processing, was 9.5 hrs. Table 1: Results of Direct from Urine Testing Conclusion ACC identified Enterobacteriaceae directly from remnant urine specimens in an average of 9.5 hours, approximately 24 to 48 hours faster than conventional methods. ACC was able to be adapted for use in urine samples. Future directions include improving the assay to identify bacteria to the species level and adding AST testing. This shows promise in providing fast actionable UTI diagnosis, allowing for tailored antibiotic therapy. *This information concerns a use that has not been approved or cleared by the Food and Drug Administration. Disclosures Martin Fuchs, BSEE, MSEE, Accelerate Diagnostics (Employee) Steve Metzger, BA, Accelerate Diagnostics (Employee)

2021 ◽  
Vol 11 (3) ◽  
pp. 650-658
Author(s):  
Mohammed Yahia Alasmary

Background: To explore the prevalence of urinary tract infections (UTIs) among female patients in the Najran region of Saudi Arabia and determine their antimicrobial resistance pattern. Methods: This study was conducted on 136 urine samples collected from outpatient departments (OPDs) of the different government hospitals in the Najran region of Saudi Arabia. Over one year, the results of susceptibility testing reports of outpatient midstream urine samples from three government hospitals were prospectively evaluated. Results: Of 136 urine samples, only 123 (90.45%) were found to show significant growth for UTIs, from which 23 different uropathogens were identified. Escherichia coli (58.5%) was the most commonly isolated organism, followed by Klebsiella pneumoniae (8.1%). The isolated microorganism showed increased resistance patterns from 3.3% to 62.6%, with an overall resistance of 27.19%. Meropenem was the most effective antimicrobial, followed by amikacin and ertapenem (0.47%, 0.91%, and 1.5% resistance, respectively). At the same time, ampicillin and cephazolin were the least (62.6% and 59.5% resistance, respectively) effective. Overall, eleven (8.94%) uropathogens isolates were ESBLs, among which there were eight (6.5%) Escherichia coli, one (0.81%) Klebsiella pneumoniae, one (0.81%) Klebsiella oxytoca, and one (0.81%) Citrobacter amalonaticus. Conclusions: E. coli remains the most commonly isolated causative uropathogens, followed by Klebsiella species. The prevalence of pathogenic E. coli and Klebsiella species underscores the importance of developing cost-effective, precise, and rapid identification systems to minimize public exposure to uropathogens. Antibiotic susceptibility data revealed that most of the isolates were resistant to the majority of the antibiotics. The patients with UTIs in the Najran region of Saudi Arabia are at a high risk of antibiotic resistance, leading to significant problems in outpatient department (OPD) treatment outcomes and raising the alarm for the physician to change their empiric treatment.


2021 ◽  
Vol 37 (2) ◽  
pp. 56-73
Author(s):  
F Iseghohi ◽  
J.C Igwe ◽  
M Galadima ◽  
A.F Kuta ◽  
A.M Abdullahi ◽  
...  

Globally, urinary tract infections are one of the most common infections in need of urgent clinical attention. The prevalence of extended spectrum beta-lactamases (ESBL)- producing Escherichia coli isolated from urine samples of some UTI patients and s of apparently healthy individuals in Minna, Nigeria, is investigated. Standard microbiological techniques were used to conduct this study. A total of 170 catch midstream urine samples submitted to the Medical Microbiology Laboratories of 4 different hospitals (and samples from healthy individuals) were randomly collected for 5 months and examined for microbial growths. Female patients (65.9%) submitted more urine samples for UTI test than their male counterpart (34.1%). The age ranges of 21 -30 (26.5%) and 31 - 40 (25.3%) had the highest percentages of infection rate while those within the ages 1- 10 (3.5%) and ≥ 71 (2.3%) were the least infected. This study observed a prevalence of 23.5% of E. coli in Minna metropolis and a significant number (30%) of healthy individuals (HI) was observed to harbor the E. coli in their urine. The isolates were highly susceptible to Gentamicin (65%), Ofloxacin (65%), Tetracycline (62.5%), Cotrimoxazole (62.5%), and Streptomycin (57.5%). Mildly susceptible to Pefloxacin (37.5%), Chloramphenicol (37.5%), and Ciprofloxacin (35%). There were significant resistance to most of the beta-lactames tested [Cefuroxime (80%), Amoxicillin (42.5%), Augmentin (40), Cefotaxime (20%) and Ceftaxidime (7.5%)]. Two of the isolates were resistant to all the 13 antibiotics tested; 70% (28) of the isolates had multiple antibiotics resistance index (MARI) ≥0.3. Multidrug resistance was expressed in 37.5% of the isolates tested. The study showed a vast resistant pool in the environment. Only 25% of the E. coli isolated from the urine samples produced beta-lactamases phenotypically, most of which expressed resistance to more than 5 of the antibiotics tested and had MARI of ≥ 0.5. Further evaluation showed that 25% (10/40) of the E. coli isolated from the UTI patients in Minna, Nigeria, were ESBL- producers and could harbor one or two of the genes. TEM gene was expressed in 70% (7) of the isolates that produced ESBL phenotypically, 60% 6) harbored CTXM gene, 20% (2) had the OXA gene while none of the bacteria harbored the SHV gene. The study established a 5.9% ESBL prevalence among the E. coli isolated from UTI in the environment studied. This study established that E. coli is one of the prevalent bacteri urea majorly isolated from UTI patients in Minna. The prevalent E. coli are multidrug resistant and could harbor more than one ESBL gene . keywords: Escherichia coli, Minna, UTI, ESBL, Multidrug resistance


2019 ◽  
Vol 49 ◽  
Author(s):  
Ivana Jukić ◽  
Danijel Topić ◽  
El-Jesah Đulić ◽  
Amela Dedeić- Ljubović

Objectives/Aim: Urinary tract infections (UTI) are a serious public health problem and caused by many pathogens, most often by Escherichia coli and Klebsiella pneumoniae.Aim of this study was to show the frequency and antimicrobial susceptibility pattern of E. coli and K. pneumoniae in hospital isolates, following the GLASS methodology.Methods: This is a retrospective study that was conducted in the Laboratory for Urinary Infections OU Clinical Microbiology CCUS in the period from January till December 2018.A total of 13760 urine samples were processed, using standard laboratory methods, in which significant bacteriuria was detected in 3218 (23.4%) of specimens.Results: Out of the total number of positive samples, E. coli was isolated in 1166 (36.2%) and K. pneumoniae at 341 (10.6%) patients. The presence of E. coli and K. pneumoniae isolates is dominant in females (1103/73.2%) and age group 60 and older (812/54.7%). Out of the total E. coli isolates, the ESBL strain was presented with 79 (6.8%) and K. pneumoniae with 145 (42.5%). The proportion of carbapenemase (CPE) produced by K. pneumoniae isolates was 8 (2.4%). The ESBL strain distribution analysis on clinics showed the highest prevalence of both isolates at the Clinic for Nephrology: K. pneumoniae 26/17,9%; E. coli: 12/15.4%. Isolated E. coli showed the highest resistance to ampicillin 673/1166 (57,7%), trimethoprim-sulfamethoxazole 454/1166 (38.9%) and ciprofloxacin 253/970 (26.1%), while K. pneumoniae to ciprofloxacin and trimethoprim-sulfamethoxazole with 151/285 (53.0%) and 164/341 (48.1%), respectively.Conclusions: Our study has shown that the most common cause of urinary infections in hospital settings are E. coli and K. pneumoniae. Data analysis showed that the presence of ESBL isolates was significantly higher in K. pneumoniae than E. coli. CPE isolates of K. pneumoniae were also detected.


Author(s):  
Rachana Kanaujia ◽  
Amit Kumar ◽  
Malay Bajpai

Background: Urinary tract infections (UTIs) are one of the most common infections. For treatment of UTIs, there are limited antibiotics due to increased resistance among uropathogens. Two older antibiotics; Nitrofurantoin and Fosfomycin have become novel oral therapeutic options against uropathogens. Aim of the study was to identify UTI causing micro-organisms and evaluate in-vitro activity of nitrofurantoin and fosfomycin against most common isolated organism (E. coli).Methods: Results of urine samples culture and susceptibility testing over a period of 1 year were analysed and included in this study.Results: Micro-organisms were isolated from 568 urine samples. Most commonly isolated organism was Escherichia coli (40.50%), followed by Klebsiella spp. (20.07%) and Staphylococcus spp. (17.07%). Susceptibility of E. coli to nitrofurantoin and fosfomycin was 91.74% and 65.65% respectively. Conclusion: Good activity of nitrofurantoin and fosfomycin against E. coli indicates that these two drugs are potential therapeutic alternatives for urinary tract infections.


2018 ◽  
Vol 31 (2) ◽  
pp. 61-64
Author(s):  
Mana Baziboroun ◽  
Masomeh Bayani ◽  
Zahra Poormontaseri ◽  
Mehran Shokri ◽  
Tahmineh Biazar

AbstractReceived 08 November 2017 Accepted 15 February 2018 The incidence of community-acquired UTIs due to extended-spectrum beta-lactamase (ESBL) producing E. coli isolates, has increased worldwide and is considered a great problem in the treatment of infections. The aim of this study was to determine the prevalence of ESBL producing E. coli isolates in urine samples of outpatients in Babol, North of Iran. A total of 3 699 urine samples from outpatients referred to Yahyanejad Hospital, Babol, Iran, were collected during 15 months, from March 2016 to June 2017. The samples were processed for bacterial culture using conventional methods, while antimicrobial susceptibility testing for E. coli isolates was performed by the disc diffusion method. The prevalence of ESBL producing E. coli isolates were assessed by Double-Disc tests. Of 3699 tested sample, 201 samples showed the growth of pathogens and among them, 106 isolates (52/7%) were E. coli. The rate of ESBL producing E. coli isolates was 25/4%.The majority (81/5%) of the isolates were from females. High percent resistance was found against ceftazidime, cefotaxime, ceftriaxone, cefixime and ciprofloxacin, ranging from 61-100%, while the highest percent susceptibility was seen to meropenem, piperacillin- tazobactam (100%), followed by nitrofurantoin and amikacin (91%). The high prevalence of ESBL producing E. coli isolates from outpatients calls for the need to aware of this increasing resistance between uropathogens and update bacterial susceptibility data and to set up our empirical therapy accordingly.


2020 ◽  
Author(s):  
Mohammad Hasan Namaei ◽  
Hengameh Hamzei ◽  
Marzie Moghanni ◽  
Azadeh Ebrahimzadeh

Abstract Background: Urinary Tract Infection (UTI) is the most common bacterial infection in the world. E. coli is the predominant Pathogen. This study evaluates the prevalence of ESBL in E. colis isolated from patients with urinary tract infections with phenotypic and genotypic methods.Methods: This descriptive-analytical study was done on 155 isolates of E. coli isolated from patients with urinary tract infection who had received the study consent. After accurate identification of E. coli strains. ESBL production for Escherichia coli isolates which are resistant to ceftriaxone or ceftazidime was evaluated by CDT method. TEM, SHV and CTX-M genes were identified by PCR.Results: The results showed that 30 strains from 155 strains of E. coli had ESBL. Strains of ESBL producer were more in males was lower in educated persons. 38.9% of ESBL producer had antibiotic use, 29.9% -producing Escherichia hospitalization and 31.6% uti history. The highest level of drug allergy in the ESBL was related to nitrofurantoin, and the highest resistance was related to cefazolin, co-trimoxazole. The CTX-M and the CTX-M15 gene were found in 92.7% and 57.1% of cases, respectively; also the SHV and TEM genes were not found in any of ESBL-producing Escherichia coli strains. Most therapeutic response in patients was related to cefexime, ciprofloxacin and nitrofurantoin 27.4%, 26% 21.9%, respectively.Conclusion: This study showed that the history of antibiotic use, hospitalization, uti related to increase of ESBL-producing in E. coli isolates., the CTMX-M gene is the most common gene in ESBL-producing E. coli strains.


2018 ◽  
Vol 12 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Yacoub R. Nairoukh ◽  
Azmi M. Mahafzah ◽  
Amal Irshaid ◽  
Asem A. Shehabi

Background: Emergence of multi-drug resistant uropathogenic E. coli strains is an increasing problem to empirical treatment of urinary tract infections in many countries. This study investigated the magnitude of this problem in Jordan. Methods: A total of 262 E. coli isolates were recovered from urine samples of Jordanian patients which were suspected to have urinary tract infections (UTIs). All isolates were primarily identified by routine biochemical tests and tested for antimicrobial susceptibility by disc diffusion method. Fifty representative Multidrug Resistance (MDR) E. coli isolates to 3 or more antibiotic classes were tested for the presence of resistance genes of blaCTX-M- 1, 9 and 15, carbapenemase (blaIMP, blaVIM, blaNDM-1, blaOXA-48), fluoroquinolones mutated genes (parC and gyrA) and clone of ST131 type using PCR methods. Results: A total of 150/262 (57.3%) of E. coli isolates were MDR. Urine samples of hospitalized patients showed significantly more MDR isolates than outpatients. Fifty representative MDR E. coli isolates indicated the following molecular characteristics: All were positive for mutated parC gene and gyrA and for ST131 clone, and 78% were positive for genes of CTX-M-15, 76% for CTX-M-I and for 8% CTX-M-9, respectively. Additionally, all 50 MDR E. coli isolates were negative for carbapenemase genes (blaIMP, blaVIM, blaNDM-1, blaOXA-48), except of one isolate was positive for blaKPC-2 . Conclusion: This study indicates alarming high rates recovery of MDR uropathogenic E. coli from Jordanian patients associated with high rates of positive ST131 clone, fluoroquinolone resistant and important types of blaCTX-M.


Author(s):  
Stéphanie Larramendy ◽  
Aurélie Gaultier ◽  
Jean-Pascal Fournier ◽  
Jocelyne Caillon ◽  
Leïla Moret ◽  
...  

Abstract Objectives The prevalence of ESBL-producing Escherichia coli (ESBL-E. coli) in community-acquired urinary tract infections (UTI) has been increasing worldwide since 2000, but with large geographical variations. The aim of this study was to determine whether the ESBL-E. coli rate in urine samples from individuals with community-acquired UTI was associated with the local socio-economic, environmental, agricultural and healthcare characteristics. Methods This was a cross-sectional study in western France using data on antibiotic susceptibility of E. coli isolated from urine samples of individuals with community-acquired UTI analysed in non-hospital laboratories from 2015 to 2017. The ESBL-E. coli rate was calculated for each laboratory. Data on socio-economic characteristics, human antibiotic consumption, hospital bed density, animal farming density and percentage of agricultural land and surface water were retrieved at the municipality level and aggregated by study area. Their association with ESBL-E. coli prevalence was quantified using multivariate linear regression models with a backward selection. Results From 358 291 E. coli isolates from urine samples tested in 92 laboratories, the mean ESBL-E. coli prevalence for the study period was 3.30%. In an adjusted model, the ESBL-E. coli rate was significantly (P < 0.05) and positively associated with the local percentage of people >65 years old, third-generation cephalosporin use (DDD/1000 inhabitants), number of hospital beds/km2, poultry density, pig density and percentage of agricultural land. Lower deprivation was associated with a higher ESBL-E. coli rate. Conclusions Several anthropogenic factors (primary care, hospitals and animal farming) are associated with the local ESBL-E. coli rate in community-acquired UTI. These results could contribute to improve risk management, including identification of at-risk patient groups.


2021 ◽  
Vol 20 (2) ◽  
pp. 128-139
Author(s):  
Ladan Fatahi ◽  
Mohammad Soleymani Zar ◽  

Background and Objectives: Urinary Tract Infection (UTI) is one of the most common infections in the community and hospitalized patients. The aim of the present study was to investigate bacteria isolated from urinary tract infections and their antibiotic resistance in hospitalized patients. Subjects and Methods In the this descriptive-cross-sectional study, the results of about 5,000 urine samples sent for culture from the hospitalized patients of Golestan Hospital in Ahvaz in 2019 were examined. Relevant information was extracted from patients’ medical records. Results Out of 5000 samples studied (39.7% female and 60.3% male), about 468 samples (9.36%) showed positive urine culture. Of the patients with UTI, 205 patients were women (43.8%). The risk of UTI increased with age. The most common bacteria caused urinary tract infections were E. coli with 51.5%, followed by Klebsiella with 29.3%. It was also observed that bacteria isolated from urine samples of people with UTI had antibiotic resistance, and for each bacteria special groups of antibiotics were more effective. Conclusion The prevalence of UTI in the studied patients was 9.36%. In females and with increasing age, the prevalence of UTI was higher. The most common bacteria that caused UTI were E. coli and then Klebsiella. Due to the fact that the resistance and sensitivity of bacteria to antibiotic used, it is recommended that the most common bacterial agents of UTI must be diagnosed and then the most appropriate antibiotic must be prescribed


2019 ◽  
Vol 21 (6) ◽  
pp. 280-283
Author(s):  
Farshad Kakian ◽  
Behnam Zamanzad ◽  
Abolfazle Gholipour ◽  
Kiarash Zamanzad

Background and aims: Carbapenems are the final-line treatments for multidrug-resistant, gram-negative infections. The patterns of resistance to carbapenems among hospital bacterial pathogens vary widely across different hospitals in a country. Considering that Escherichia coli is one of the most important causes of nosocomial infections, it is essential to study its drug resistance. Methods: In this descriptive-analytical study, a total of 80 samples of E. coli isolated from inpatients with urinary tract infections (UTIs) were collected in different wards (i.e., women, urology, infectious, and ICU) of Shahrekord hospitals. After the diagnosis and confirmation of bacteria by standard bacteriological methods, their sensitivity to imipenem and meropenem was investigated by the antibiogram (diskdiffusion) method. Then, the minimum inhibitory concentration (MIC) was determined by the E-test strip according to the Clinical and Laboratory Standards Institute (CLSI) standard. Results: In this study, resistance to meropenem and imipenem by antibiogram (disc diffusion) was observed in 21 (25.26%) and 20 (25%) of the isolates, respectively. Twenty isolates had MIC ≥4 μg/mL for meropenem, 13 isolates demonstrated MIC≥4 μg/mL for imipenem, and 14 isolates had 1≤MIC<4 μg/mL and were semi-sensitive. Conclusion: In general, E. coli had significant resistance to carbapenems. Therefore, rapid and accurate identification of these strains can be a major step to the treatment and control of these strains and prevention of the spread of the resistance.


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