scholarly journals Using PCR technique for diagnosis of bacterium Escherichia coli O157:H7 isolated from urine samples of humans and sheep

2014 ◽  
Vol 38 (2) ◽  
pp. 17-21
Author(s):  
Al-wgaa A. A.

     The aims of the current study were to determine the percentages of E.coli O157:H7 in the urinary tract infections (UTIs) of humans and in the urine of apparently healthy sheep, in addition to determine the genotype of the isolates by PCR assay. Two hundred and twenty eight urine samples were collected from young children and adult patients both sexes suffering from UTIs during a period December 2012 to the end of March 2013. And randomly collected 75 urine sample from apparent healthy sheep both sexes that were slaughtered in AL Shoela, AL Rahmanea Slaughterhouse and College of Veterinary Medicine field in Baghdad the end of February to half of April 2013.   All urine samples were incubated aerobically at 37°C for 24-48 hrs on blood agar, MacConkey agar as well as special media  and the isolates were identified  by  biochemical tests, then the isolates were confirmed diagnosed  by PCR assay. The  results showed that  humans urine samples ,8 samples were  E. coli O157:H7 positive  isolates(3.50%) ,young children expressed (4) isolates of E.coli O157:H7 as compare with  those   in adult (4 isolates)  and the percentage of this isolates in females were (2.6%) as compare with those  in males (0.87%). Also the current study demonstrated that all  isolates culturing positive  serotype of E.coliO 157:H7 were positive by PCR assay .The genes of  eaeA ,hly and Stx2 were recorded in 7,8 and  2 serotype of E.coliO157:H7 respectively. The result revealed that 21(28%) out 75 sheep urine samples were E.coli positive isolates, 13 out 75 samples were E.coli O157:H7 positive isolates. The percentage of isolates from rams urine samples was (14.66%) as it compare to those samples of ewes (2.66%).The result also was recorded that 10,13,12,4 and 3 of bacterial isolates of sheep urine samples  were carried eaeA, hlyA, hlyA plasmid,Stx1 and  Stx2 genes respectively. In conclusion the healthy sheep in Baghdad city,  harbor  shiga -toxin producing  E.coliO157:H7 in their  urinary tracts and these organism induced UTIs  associated with  renal failure in the humans and carried the same virulent genes that  reported in the sheep isolates.

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):  
Uju M.E. Dibua ◽  
Ifeoma S. Onyemerela ◽  
Emeka I. Nweze

Objective: This study was designed to determine the frequency and causative agent(s) of urinary tract infections (UTIs) in individuals with symptoms of urinary tract infections in Enugu State of Southeast Nigeria, and to determine the antibiotic susceptibility pattern of microbial agents isolated from urine culture. Methods: The study involved 211 individuals (149 females and 62 males) clinically suspected for UTI. Urine samples were collected by the mid-stream ‘clean catch' method and tested using standard procedures. Antibiotic susceptibility of the isolated pathogens was tested using the Kirby-Bauer technique according to the Clinical and Laboratory Standards Institute (CLSI) guidelines. Results: Microscopy of centrifuged urine samples showed 16 patients had pyuria while 54 had pus cells. Calcium oxalate crystals were found in 14 samples. Urinalysis performed with urine samples showed 17 had protein; seven were nitrite positive and three had moderate to high glucose concentration. Fifty-four urine samples (36.2%) from females and 12 (19.4%) from males showed significant growth upon culture. Gram stain and biochemical tests identified nine different organisms with Escherichia coli as the most common isolated species. Forty three randomly selected strains were further tested for their susceptibility against a panel of antibiotics. Thirty isolates (81.08%) were resistant to four or more antibiotics with the highest resistance shown by E. coli (76.67%). All the Gram- negative isolates were resistant to Ampicilox, Cefuroxime and Amoxicillin. Conclusion: Urinary tract infections were found more in females in the area under study. As found in other studies, E. coli was the most predominant isolate, although other organisms seem to be on the increase.


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.


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.


2002 ◽  
Vol 65 (1) ◽  
pp. 5-11 ◽  
Author(s):  
TAKAHISA MIYAMOTO ◽  
NATSUKO ICHIOKA ◽  
CHIE SASAKI ◽  
HIROSHI KOBAYASHI ◽  
KEN-ICHI HONJOH ◽  
...  

The DNA band patterns generated by polymerase chain reaction (PCR) using the du2 primer and template DNAs from various strains of Escherichia coli and non–E. coli bacteria were compared. Among three to five prominent bands produced, the three bands at about 1.8, 2.7, and 5.0 kb were detected in all of the E. coli O157 strains tested. Some nonpathogenic E. coli and all pathogenic E. coli except E. coli O157 showed bands at 1.8 and 5.0 kb. It seems that the band at 2.7 kb is specific to E. coli O157. Sequence analysis of the 2.7-kb PCR product revealed the presence of a DNA sequence specific to E. coli O157:H− and E. coli O157:H7. Since the DNA sequence from base 15 to base 1008 of the PCR product seems to be specific to E. coli O157, a PCR assay was carried out with various bacterial genomic DNAs and O157-FHC1 and O157-FHC2 primers that amplified the region between base 23 and base 994 of the 2.7-kb PCR product. A single band at 970 bp was clearly detected in all of the strains of E. coli O157:H− and E. coli O157:H7 tested. However, no band was amplified from template DNAs from other bacteria, including both nonpathogenic and pathogenic E. coli except E. coli O157. All raw meats inoculated with E. coli O157:H7 at 3 × 100 to 3.5 × 102 CFU/25 g were positive both for our PCR assay after cultivation in mEC-N broth at 42°C for 18 h and for the conventional cultural method.


2007 ◽  
Vol 70 (7) ◽  
pp. 1663-1669 ◽  
Author(s):  
PINA M. FRATAMICO ◽  
LORI K. BAGI

A comparison was made of the relative efficiencies of three enrichment media, RapidChek Escherichia coli O157:H7 enrichment broth (REB), R&F broth (RFB), and modified E. coli broth containing novobiocin (mEC+n), and four selective plating media for detection of cold- and freeze-stressed E. coli O157:H7 in raw ground beef. Ground beef (25 g) was inoculated with E. coli O157:H7 at ≤0.5 and ≤2 CFU/g, and samples were then enriched immediately or were stored at 4°C for 72 h or at −20°C for 2 weeks and then enriched. After 8 or 20 h of enrichment, the cultures were plated onto R&F E. coli O157: H7 chromogenic plating medium, cefixime-tellurite sorbitol MacConkey agar, CHROMagar O157, and Rainbow agar O157 and tested using the RapidChek E. coli O157 lateral flow immunoassay and a multiplex PCR assay targeting the E. coli O157: H7 eae, stx1, and stx2 genes. Recovery of E. coli O157:H7 on the four agar media was 4.0 to 7.9 log CFU/ml with the REB enrichment, 1.4 to 7.4 log CFU/ml with RFB, 1.7 to 6.7 log CFU/ml with mEC+n incubated at 42°C, and 1.3 to 3.3 log CFU/ml from mEC+n incubated at 35°C. The percentages of positive ground beef samples containing nonstressed, cold-stressed, and freeze-stressed E. coli O157:H7 as obtained by plating, the immunoassay, and the PCR assay were 97, 88, and 97%, respectively, with REB, 92, 81, and 78%, respectively, with RFB, 97, 58, and 53%, respectively, with mEC+n incubated at 42°C, and 22, 31, and 25%, respectively, with mEC+n incubated at 35°C. Logistic regression analyses of the data indicated significant main effects of treatment, type of medium, enrichment time, inoculum concentration, and detection method. In particular, a positive result was 1.1 times more likely to occur after 20 h of enrichment than after 8 h, 25 times more likely with RFB and REB than with mEC+nat35°C, 3.7 times more likely with an initial inoculum of ≤2.0 CFU/g than with ≤0.5 CFU/g, 2.5 to 3 times more likely using freeze-stressed or nonstressed bacteria than with cold-stressed bacteria, and 2.5 times more likely by plating than by the immunoassay or the PCR assay. REB had better overall performance for enrichment of cold- and freeze-stressed E. coli O157:H7 present in ground beef than did the other media examined.


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