scholarly journals The Direct Semi-Quantitative Detection of 18 Pathogens and Simultaneous Screening for Nine Resistance Genes in Clinical Urine Samples by a High-Throughput Multiplex Genetic Detection System

2021 ◽  
Vol 11 ◽  
Author(s):  
Zhaoyang Sun ◽  
Wenjian Liu ◽  
Jinghao Zhang ◽  
Su Wang ◽  
Feng Yang ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Resistance Genes ◽  
Sanger Sequencing ◽  
Urine Culture ◽  
Detection System ◽  
Culture Method ◽  
Urine Samples ◽  
Quantitative Detection ◽  
Genetic Detection

BackgroundUrinary tract infections (UTIs) are one the most common infections. The rapid and accurate identification of uropathogens, and the determination of antimicrobial susceptibility, are essential aspects of the management of UTIs. However, existing detection methods are associated with certain limitations. In this study, a new urinary tract infection high-throughput multiplex genetic detection system (UTI-HMGS) was developed for the semi-quantitative detection of 18 pathogens and the simultaneously screening of nine resistance genes directly from the clinical urine sample within 4 hours.MethodsWe designed and optimized a multiplex polymerase chain reaction (PCR) involving fluorescent dye-labeled specific primers to detect 18 pathogens and nine resistance genes. The specificity of the UTI-HMGS was tested using standard strains or plasmids for each gene target. The sensitivity of the UTI-HMGS assay was tested by the detection of serial tenfold dilutions of plasmids or simulated positive urine samples. We also collected clinical urine samples and used these to perform urine culture and antimicrobial susceptibility testing (AST). Finally, all urine samples were detected by UTI-HMGS and the results were compared with both urine culture and Sanger sequencing.ResultsUTI-HMGS showed high levels of sensitivity and specificity for the detection of uropathogens when compared with culture and sequencing. In addition, ten species of bacteria and three species of fungi were detected semi-quantitatively to allow accurate discrimination of significant bacteriuria and candiduria. The sensitivity of the UTI-HMGS for the all the target genes could reach 50 copies per reaction. In total, 531 urine samples were collected and analyzed by UTI-HMGS, which exhibited high levels of sensitivity and specificity for the detection of uropathogens and resistance genes when compared with Sanger sequencing. The results from UTI-HMGS showed that the detection rates of 15 pathogens were significantly higher (P<0.05) than that of the culture method. In addition, there were 41(7.72%, 41/531) urine samples were positive for difficult-to-culture pathogens, which were missed detected by routine culture method.ConclusionsUTI-HMGS proved to be an efficient method for the direct semi-quantitative detection of 18 uropathogens and the simultaneously screening of nine antibiotic resistance genes in urine samples. The UTI-HMGS could represent an alternative method for the clinical detection and monitoring of antibiotic resistance.

scholarly journals Evaluation of BacterioScan 216Dx in Comparison to Urinalysis as a Screening Tool for Diagnosis of Urinary Tract Infections in Children

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
Ferdaus Hassan ◽  
Heather Bushnell ◽  
Connie Taggart ◽  
Caitlin Gibbs ◽  
Steve Hiraki ◽  
...  
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Predictive Value ◽  
Screening Tool ◽  
Urine Culture ◽  
Antibiotic Use ◽  
Urine Samples ◽  
Maldi Tof ◽  
Tract Infections

ABSTRACTUrinalysis (UA) has routinely been used as a screening tool prior to urine culture set up. BacterioScan 216Dx is an FDA-cleared semiautomated system to detect bacterial growth in urine. The aim of this study was to evaluate 216Dx in comparison to UA for diagnosis of urinary tract infection (UTI) in children. Clean-catch, unpreserved urine samples from children aged <18 years were tested by 216Dx, and positive urine samples in media were processed for direct bacterial identification by matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry. Sensitivity and specificity of 216Dx and urinalysis (UA) were determined against urine culture. Of 287 urine samples obtained from children (median age, 108 months), 44.0% and 56.0% were UA positive and negative, respectively, while 216Dx detected 27% and 73% as positive and negative, respectively. Compared to culture, the overall sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 216Dx versus UA were 92.1% versus 97.3%, 82.7% versus 63.8%, 44.8% versus 29.1%, and 98.6% versus 99.3%, respectively. Among 216Dx true-positive (TP) samples (n= 35), 77.0% were successfully identified directly from broth by MALDI-TOF. Among urine samples that were identified as contaminated by culture (n= 127; 44%), the 216Dx detected 93 (73.0%) as negative while UA detected 69 (54.0%) as negative. Although the sensitivities of 216Dx and UA are comparable, the specificity of 216Dx was higher than that of UA. The 216Dx can be used as an alternative/adjunct screening tool to UA to rule out urinary tract infection (UTI) in children. Compared to culture, the faster turnaround time (3 hours) of 216Dx has the potential to reduce unnecessary antibiotic use and improve patient management.

scholarly journals Interaction between Antibiotic Resistance, Resistance Genes, and Treatment Response for Urinary Tract Infections in Primary Care

2019 ◽  
Vol 57 (9) ◽  
Author(s):  
Hanley J. Ho ◽  
Mei Xuan Tan ◽  
Mark I. Chen ◽  
Thean Yen Tan ◽  
Seok Hwee Koo ◽  
...  
Keyword(s):  
Primary Care ◽  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Urine Culture ◽  
Early Symptom ◽  
Content Type ◽  
Symptom Resolution ◽  
Factors Associated ◽  
The Past ◽  
Amoxicillin Clavulanate

ABSTRACTGiven increasing antimicrobial resistance, we aimed to determine antibiotic susceptibility and presence of resistance genes in uropathogens in primary care, factors associated with resistance to commonly prescribed antibiotics, and effect of treatment on early symptom resolution. We conducted a prospective study of primary care patients with urinary tract infection (UTI) symptoms and culture-confirmed UTI in Singapore from 2015 to 2016. Cohort characteristics and antimicrobial susceptibility of cultured isolates were analyzed. AmongEnterobacteriaceaeisolates, early symptom resolution (within 3 days) according to antibiotic prescribed and isolate susceptibility and factors associated with antibiotic resistance were evaluated. Of 695 symptomatic patients, 299 were urine culture positive; of these 299 patients, 259 (87%) were female.Escherichia coliwas the most common uropathogen (76%).Enterobacteriaceaeisolates (n = 283) were highly susceptible to amoxicillin-clavulanate (86%), nitrofurantoin (87%), and fosfomycin (98%), but >20% were resistant to ciprofloxacin and co-trimoxazole. Isolates resistant to appropriate indicator antibiotics were further tested to determine proportions positive forblaCTX-M(14/26, 54%), plasmid-mediatedampC(12/24, 50%),qnr(7/69, 10%), andfos(1/6, 17%) resistance genes. A total of 67% of patients given antibiotics with susceptible isolates reported early resolution versus 45% given antibiotics with nonsusceptible isolates (P = 0.001) and 27% not treated (P = 0.018). On multivariable analysis, Indian ethnicity and diabetes mellitus were associated with amoxicillin-clavulanate resistance. Genitourinary abnormalities, UTI in the past 12 months, and hospitalization in the past 6 months were associated with ciprofloxacin and co-trimoxazole resistance. Patients given active empirical antibiotics were most likely to report early symptom resolution, but correlation within vitrosusceptibility was imperfect. Factors associated with resistance may guide the decision to obtain initial urine culture.

scholarly journals Draft Genome Sequence of Corynebacterium aurimucosum UMB7769, Isolated from the Female Urinary Tract

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Samantha Eskandar ◽  
Taylor Miller-Ensminger ◽  
Adelina Voukadinova ◽  
Alan J. Wolfe ◽  
Catherine Putonti
Keyword(s):  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Genome Sequence ◽  
Resistance Genes ◽  
Draft Genome ◽  
Gc Content ◽  
Antibiotic Resistance Genes ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Female Urinary Tract

ABSTRACT Here, we present the draft genome sequence of Corynebacterium aurimucosum UMB7769, isolated from the female urinary tract. The size of the genome is 2,731,818 bp, assembled in 50 contigs, with an observed GC content of 60.9% and an N50 score of 129,518 bp. Annotation revealed 31 antibiotic resistance genes.

scholarly journals Molecular Characterization of Shiga Toxin-ProducingEscherichia coliIsolated from Ruminant and Donkey Raw Milk Samples and Traditional Dairy Products in Iran

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
Hassan Momtaz ◽  
Rahil Farzan ◽  
Ebrahim Rahimi ◽  
Farhad Safarpoor Dehkordi ◽  
Negar Souod
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Shiga Toxin ◽  
Dairy Products ◽  
Antibiotic Resistance Genes ◽  
Culture Method ◽  
Raw Milk ◽  
Antibiotics Resistance ◽  
E Coli ◽  
Pathogenic Genes

The aims of the current study were to detect the virulence factors and antibiotic resistance of Shiga toxin-producingE. coli, in animal milk and dairy products in Iran. AfterE. colidentification with culture method, PCR assay were developed for detection of pathogenic genes, serotypes and antibiotic resistance genes ofE. coli. Results showed that out of 719 samples, 102 (14.18%) were confirmed to be positive forE. coliand out of 102 positive samples, 17.64% were O26 and 13.72% were O157 and 1.96% were O91 and 1.96% were O145 serotypes. Totally, the prevalence ofstx1 andpapAgenes were the highest while the prevalence ofsfaSandfyuAwere the lowest in the positive samples. PCR results showed thattetA, tetBwere the highest (64.70%) andaac(3)-IVwere the lowest (27.45%) antibiotic resistant genes inE. colipositive samples. Our study indicated that the isolatedE. colitrains in these regions had a highest antibiotic resistance to tetracycline (58.82%) and the lowest to nitrofurantoin (3.92%).tetAgene andE. coliO157 serotype had highest andaac(3)-IVgene, andE. coliO145 serotype had a lowest frequency rates of antibiotics resistance genes, in the region.

scholarly journals Evaluation of Urine Isolated Bacteria and Their Antimicrobial Resistance in Hospitalized Patients in Ahvaz Golestan Hospital in 2019

2021 ◽  
Vol 20 (2) ◽  
pp. 128-139
Author(s):  
Ladan Fatahi ◽  
Mohammad Soleymani Zar ◽  
Keyword(s):  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Urinary Tract Infections ◽  
Relevant Information ◽  
Cross Sectional Study ◽  
Hospitalized Patients ◽  
Urine Samples ◽  
Cross Sectional ◽  
E Coli ◽  
Tract Infections

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

scholarly journals Antibiotic Resistance Pattern of Extended Spectrum Beta Lactamase Producing Escherichia coli Isolated From Patients With Urinary Tract Infection in Morocco

2021 ◽  
Vol 11 ◽  
Author(s):  
Mohamed Kettani Halabi ◽  
Fatima Azzahra Lahlou ◽  
Idrissa Diawara ◽  
Younes El Adouzi ◽  
Rabiaa Marnaoui ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Urinary Tract Infection ◽  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Tract Infection ◽  
Urine Samples ◽  
Resistance Pattern ◽  
E Coli ◽  
Antibiotic Resistance Pattern ◽  
Extended Spectrum

Extended-spectrum β-lactamases producing Escherichia coli (ESBL-EC) lend resistance to most β-lactam antibiotics. Because of limited treatment options, ESBL-EC infections are generally more difficult to treat, leading to higher hospital costs, reduced rates of microbiological and clinical responses, and a threat to the patient’s life. This study aimed to determine the antibiotic resistance pattern of ESBL-EC isolated from patients with urinary tract infection in Morocco. This retrospective laboratory-based study was conducted at Cheikh Khalifa International University Hospital, Casablanca, from January 2016 to June 2019. A total of 670 urine samples were collected from urinary tract infection patients and processed by standard microbiological methods. In vitro susceptibility testing to different antibiotics of all identified isolates of Escherichia coli (E. coli) was performed following Kirby–Bauer’s disc diffusion method on Mueller–Hinton Agar according to the EUCAST standards. The reviewing of ESBL-EC was confirmed by the appearance of a characteristically shaped zone referred to as a “champagne cork” using the Combined Disk Test. Among a total of 438 E. coli isolated from nonrepetitive urine samples, two hundred fifty-nine (59%) were ESBL-EC, of which 200 (77%) were isolated from adult patients (over the age of 50) and the majority were female. All ESBL-EC isolates were resistant to third-generation cephalosporin and quinolones and sensitive to carbapenem and fosfomycin. Knowledge of antimicrobial resistance patterns in ESBL-EC, the major pathogen associated with urinary tract infection, is indispensable as a guide in choosing empirical antimicrobial treatment.

scholarly journals Antibiotic sensitivity pattern of bacterial isolates from urine samples of admitted patients with urinary tract infection in a tertiary care teaching hospital of Tripura, India: a hospital record based study

2018 ◽  
Vol 7 (4) ◽  
pp. 585
Author(s):  
Uttam K. Das ◽  
Prithul Bhattacharjee ◽  
Shubhaleena Debnath ◽  
Maitrayee Chakraborty ◽  
Ranjib Ghosh ◽  
...  
Keyword(s):  
Urinary Tract Infection ◽  
Antibiotic Resistance ◽  
Urinary Tract ◽  
Tract Infection ◽  
Teaching Hospital ◽  
Antibiotic Sensitivity ◽  
Urine Samples ◽  
Hospital Record ◽  
E Coli ◽  
Sensitivity Pattern

Background: Urinary tract infection (UTI) being one of the most common and a serious health problem both in the community and hospital settings each year worldwide, the emergence of antibiotic resistance in the management of UTI is a serious public health issue. The present study will analyse the antimicrobial sensitivity pattern of pathogens isolated from the urine samples of admitted patients suffering from UTI in Tripura Medical College and Dr. B.R. Ambedkar Memorial Teaching Hospital (TMC).Methods: This was a hospital record-based study. The urine samples of clinically diagnosed UTI patients admitted in various departments of the hospital during the study period were included. The reports of culture and sensitivity testing of the samples were collected. The results were interpreted according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI).Results: During the 12-month study period, a total of 752 urine samples were analysed. Enterococcus (43.75%) was the most frequently isolated bacteria, followed by E. coli (28.45%) and Klebsiella (14.89%). Enterococcus was highly sensitive (p<0.001) to vancomycin (95.33%), E. coli was mostly sensitive to nitrofurantoin (83.65%) and Klebsiella mainly sensitive to imipenem (75.49%).Conclusions: The study showed that positive urine culture with the antibiotic sensitivity of the isolates is very important for antimicrobial therapy, as antibiotic resistance is a worldwide problem which causes ineffectiveness of treatment.

scholarly journals Assessment of Rapid Dipstick Test for Diagnosis of Urinary Tract Infection in Asymptomatic Pregnant Female

2016 ◽  
Vol 5 (1) ◽  
pp. 965
Author(s):  
Ashish Khanna ◽  
Menka Khanna
Keyword(s):  
Urinary Tract Infection ◽  
Urinary Tract ◽  
Tract Infection ◽  
Gold Standard ◽  
Urine Culture ◽  
Asymptomatic Bacteriuria ◽  
Culture Method ◽  
Premature Delivery ◽  
Dipstick Test ◽  
In Pregnancy

<strong>Background:</strong>Bacteriuria during pregnancy has been known to cause many complications like low birth weight and premature delivery.<p><strong>Objective</strong>: This study was done to evaluate the diagnostic accuracy of rapid dipstick test to predict urinary tract infection in pregnancy against the gold standard urine culture.</p><p><strong>Material&amp;Methods:</strong> A total of 200 mid stream urine samples were collected from asymptomatic pregnant females. These specimens were cultured in blood agar and MacConkey's agar by using the standard loop technique and incubated aerobically at 37°C overnight. The criterion for clinically significant bacteriuria was either a pure or predominant culture of &gt;10<sup>5</sup> colony forming units (CFU)/ml. All the specimens were also examined microscopically for pyuria and bacteriuria.</p><p><strong>Results:</strong> The prevalence of asymptomatic bacteriuria in pregnancy was 15 % in our study. The sensitivity and the specificity for leucocyte esterase were 85.7% and 74.4% and for nitrites, they were 64.2% and 72%.</p><p><strong>Conclusion:</strong> The study revealed that use of either leukocyte esterase or nitrite for screening of asymptomatic bacteriuria in pregnancy was associated with many false positive and negative results when compared with the gold standard urine culture method. By using their combination maximum negative predictive value of .98 was achieved.</p>

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