scholarly journals Phylogenetic Groups ofEscherichia coliStrains from Patients with Urinary Tract Infection in Iran Based on the New Clermont Phylotyping Method

2015 ◽  
Vol 2015 ◽  
pp. 1-7 ◽  
Author(s):  
Darioush Iranpour ◽  
Mojtaba Hassanpour ◽  
Hossein Ansari ◽  
Saeed Tajbakhsh ◽  
Gholamreza Khamisipour ◽  
...  

Objectives.In 2013, Clermont classifiedE. colistrains into eight phylogenetic groups using a new quadruplex PCR method. The aims of this study were to identify the phylogenetic groups ofE. colibased on this method and to assess their antibiotic resistance patterns in Bushehr, Iran.Methods. In this cross-sectional study, 140E. coliisolates were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was performed by disk diffusion method.Results. Phylogenetic group B2 was most predominant (39.3%), followed by unknown (27.1%), E (9.3%), C and clade I (each 6.4%), B1 (5%), F and D (each 2.9%), and A (0.7%). The most common antibiotic resistance was related to amoxicillin (82.1%) and the least to meropenem (0.7%). 82.14% of isolates were multiple drug resistant (MDR). Antibiotic resistance was mainly detected in group B2 (50%).Conclusions.Our findings showed the high prevalence of MDRE. coliisolates with dominance of group B2. About 25% ofE. coliisolates belong to the newly described phylogroups C, E, F, and clade I. Such studies need to be done also in other regions to provide greater understanding of the antibiotic resistance pattern and the prevalences of different phylogenetic groups.

2020 ◽  
Vol 2020 ◽  
pp. 1-6 ◽  
Author(s):  
Destaw Asfaw Ali ◽  
Belege Tadesse ◽  
Aragaw Ebabu

A cross-sectional study was conducted between December, 2013, and May, 2014, to determine the prevalence and antibiotic resistance feature of Salmonella isolated from broilers slaughtered in Debre Zeit and Modjo towns, Ethiopia. A total of 384 caecal content samples were collected for microbiological examination following the standard techniques and procedures outlined by the International Organization for Standardization to isolate Salmonella. The sensitivity of the isolates subjected to nine antimicrobials was tested by the Kirby–Bauer disk diffusion method. The overall prevalence of Salmonella was 14.6%, and its occurrence differ significantly by farm (p<0.05). The occurrence of the bacteria was not statistically different in the midland (15.2%) and lowland (13.3%) (p>0.05) and between males (13.5%) and females (15.6) (p>0.05). Of the 50 isolates, 48 were resistant to at least one drug. Multidrug resistance was recorded in 43 (86.0%) of the isolates. The study demonstrated considerable prevalence and high antimicrobial resistant Salmonella in exotic chicken and indicates the potential importance of chickens as source of foodborne salmonellosis and multiple antimicrobial resistance of Salmonella. Improving the hygienic practice of farms could help to reduce the occurrence of Salmonella in farms. Further studies are needed to describe the risk factors associated with the emergence of drug-resistant Salmonella in chicken.


2021 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Marya Shirvani ◽  
Mohammad Hossein Zamanian ◽  
Alireza Janbakhsh ◽  
Babak Sayad ◽  
Siavash Vaziri ◽  
...  

Background: Acinetobacter is a gram-negative coccobacillus, which is widespread in nature and causes several nosocomial infections, such as pneumonia, meningitis, endocarditis, skin and soft tissue infections, conjunctivitis, and bacteremia. Acinetobacter has also demonstrated resistance against multiple antimicrobial agents. Objectives: The present study aimed to investigate the antibiotic resistance pattern of the isolated Acinetobacter strains from the patients admitted to various wards of Imam Reza hospital in Kermanshah, Iran. Methods: This descriptive, cross-sectional study was performed on 726 patients with positive Acinetobacter cultures at Imam Reza hospital during 2016 - 2018. Bacterial isolates were identified using laboratory tests and based on the CLSI protocol, and the standard disc-diffusion method was used assess antibiotic susceptibility. Data analysis was performed in SPSS version 20. Results: Most of the Acinetobacter-positive cases were isolated from the intensive care units (75.88%) and sputum (73.3%) and urine samples (10.1%). In addition, the highest and lowest resistance rate of the isolates was observed against ceftriaxone (96.6%) and ampicillin-sulbactam (58.7%), respectively. Conclusions: According to the results, the bacterial isolates were multiple-drug resistant and showed resistance to ciprofloxacin, ceftazidime, cotrimoxazole, ceftriaxone, cefepime, gentamicin, imipenem, ampicillin, ampicillin-sulbactam, and amikacin. The high resistance to imipenem is rather alarming as it is considered the 'last resort' in the treatment of the infections caused by gram-negative bacteria. Therefore, monitoring programs are recommended to prevent the misuse of this drug in hospitals.


2021 ◽  
Vol In Press (In Press) ◽  
Author(s):  
Mohammad Hossein Zamanian ◽  
Marya Shirvani ◽  
Alireza Janbakhsh ◽  
Babak Sayad ◽  
Siavash Vaziri ◽  
...  

Background: Staphylococcus aureus is an opportunistic pathogen, which often causes asymptomatic diseases. This bacterium could cause several disorders, ranging from skin infections to life-threatening diseases. S. aureus could also develop resistance to a wide range of antibiotics. Objectives: The present study aimed to investigate the prevalence and pattern of antibiotic resistance in isolated S. aureus in Imam Reza Hospital of Kermanshah, Iran. Methods: This descriptive cross-sectional study was conducted on 2,228 patients with a positive S. aureus culture who were admitted to Imam Reza Hospital during 2016 - 2018. In accordance with the CLSI protocol, bacterial isolates were separated using laboratory tests, and antibiotic susceptibility was assessed using the standard disk-diffusion method. Data analysis was performed in SPSS version 24. Results: Most of the S. aureus-positive cases were isolated from the emergency ward (43.7%), blood samples (40.1%), and urine samples (23.9%). The highest antibiotic resistance was observed against erythromycin, penicillin G, ofloxacin, cefoxitin, clindamycin, and piperacillin. With 93.3% and 81.8% sensitivity, vancomycin and teicoplanin were respectively the most effective antibiotics against S. aureus. Conclusions: According to the results, the prevalence of resistant S. aureus strains could be due to the long-term hospitalization of patients and the overuse of antibiotics in infection treatment. Therefore, proper monitoring and development of effective infection control methods are essential in these healthcare settings.


2020 ◽  
Author(s):  
Samane Mohebi ◽  
zahra Hashemizade ◽  
Mahtab Hadadi ◽  
Soudeh Kholdi ◽  
Kasra Javadi ◽  
...  

Abstract Background Asymptomatic bacteriuria is one of the common problems in pregnancy. Pyelonephritis, preterm labor and low birth weight infants have been associated with bacterial infection. Urinary tract infection (UTI) during pregnancy is frequently associated with complications. An observational cross-sectional study including investigated the prevalence of virulence genes, antimicrobial resistance, and its relationship with phylogenetic groups among E. coli strains isolated from pregnant women with asymptomatic bacteriuria who referred to Hafez hospital, Shiraz, Iran.Material and Methods A total of 300 urine samples were screened for Escherichia coli strains. Susceptibility testing was determined by the disk-diffusion method. The phylogenetic groups and 13 virulence genes were identified by PCR. ESBL and AmpC producing isolates were detected using phenotypic methods. PCR was used to identify the bla TEM , bla SHV and bla CTXM genes in ESBL and AmpC-positive isolates.Results Our results revealed that among 300 urine samples, 105 (35%) were positive for E. coli . The data showed that the highest and the lowest resistance rates were observed against nalidixic acid (82.1%), and imipenem (2.8%), respectively. The prevalence of ESBLs and AmpC-β-lactamase, in the E. coli isolates was 41% and 9.5% respectively. bla CTXM was the commonest genotype (93%). Phylogenetic group distribution was as follow: B1 2.8%, A 14.2%, B2 61.9%, and D 4.6%. Our result showed that most of the virulence genes belonged to group B2 and also several virulence genes such as hlyA , cnf-1 , and papGII genes were positively associated with group B2. Conclusion Among E. coli strains isolated from patients with UTIs, different features phylogroups, with special virulence factors, could cause severe infection. Awareness about the Virulence patterns distribution among Phylogenetic groups of UPEC could greatly aid in confine and prevent the development of lethal infection caused by these strains.


2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Hazrat Bilal ◽  
Muhammad Nadeem Khan ◽  
Tayyab Rehman ◽  
Muhammad Fazal Hameed ◽  
Xingyuan Yang

Abstract Background During the last six decades, extensive use of antibiotics has selected resistant strains, increasing the rate of fatal infectious diseases, and exerting an economic burden on society. This situation is widely accepted as a global problem, yet its degree is not well elucidated in many regions of the world. Up till now, no systemic analysis of Antimicrobial resistance (AMR) in Pakistan has been published. The current study aims to describe the antibiotic-resistance scenario of Pakistan from human samples of the last 10 y, to find the gaps in surveillances and methodology and recommendations for researchers and prescribers founded on these outcomes. Methods Original research articles analyzed the pattern of Antibiotic resistance of any World Health Organization (WHO) enlisted priority pathogens in Pakistan (published onward 2009 till March 2020), were collected from PubMed, Google scholar, and PakMedi Net search engines. These articles were selected based on predefined inclusion and exclusion criteria. Data about the study characteristics and antibiotic-resistance for a given bacterium were excluded from literature. Antibiotic resistance to a particular bacterium was calculated as a median resistance with 95% Confidence Interval (CI). Results Studies published in the last 10 y showed that Urinary Tract Infection (UTI) is the most reported clinical diagnosis (16.1%) in Pakistan. E. coli were reported in 28 (30.11%) studies showing high resistance to antibiotics’ first line. Methicillin-resistant Staphylococcus aureus (MRSA) was found in 49% of S. aureus’ total reported cases. Phenotypic resistance pattern has mostly been evaluated by Disk Diffusion Method (DDM) (82.8%), taken Clinical Laboratory Standards Institute (CLSI) as a breakpoint reference guideline (in 79.6% studies). Only 28 (30.11%) studies have made molecular identification of the resistance gene. blaTEM (78.94% in Shigella spp) and blaNDM-1 (32.75% in Klebsiella spp) are the prominent reported resistant genes followed by VanA (45.53% in Enterococcus spp), mcr-1 (1.61% in Acinetobacter spp), and blaKPC-2 (31.67% in E. coli). Most of the studies were from Sindh (40.86%), followed by Punjab (35.48%), while Baluchistan’s AMR data was not available. Conclusion Outcomes of our study emphasize that most of the pathogens show high resistance to commonly used antibiotics; also, we find gaps in surveillances and breaches in methodological data. Based on these findings, we recommend the regularization of surveillance practice and precise actions to combat the region’s AMR.


2021 ◽  
Vol 8 (4) ◽  
pp. 160-166
Author(s):  
Dominic Agbo Oche ◽  
Paul Ifeleke Oyegoke ◽  
Maryloveth Oluchukwu Akpudo ◽  
Busayo Olalekan Olayinka

Background and aims: Staphylococcus aureus, an important pathogen in bone diseases, is a highly multi-drug resistant (MDR) bacterium. This study aimed to investigate the antibiotic resistance among S. aureus isolated from patients on admission in an orthopaedic hospital. Methods: In this cross-sectional research, 140 samples comprising urine samples, wound swabs, and nasal swabs were collected from 49 patients on admission. Samples were cultured and screened for S. aureus following standard procedures. Using the agar-disk diffusion method, the isolates were subjected to antibiotics susceptibility tests. Results: S. aureus were isolated from 26 (18.6%) samples, and wound swabs were found to have the highest number of the S. aureus isolates with 12 (46.2%). Among the 26 S. aureus isolated, 25 (96.2%) isolates were resistant to at least four or more of the tested antibiotics. There were 23 (88.5%) MDR isolates, while there were only 2 (7.6%) extensively drug resistant ones. The number of methicillin-resistant S. aureus were 17 (65.4% of the isolates), while the number of methicillin-susceptible S. aureus were 9 (34.6% of the isolates). A total of 22 (84.6%) isolates had multi-antibiotic resistance (MAR) index greater than 0.2. Inducible clindamycin resistance of 2 (7.6%) was observed. Conclusion: This study showed that the S. aureus isolated from the patients were resistant to multiple antibiotics. Regular surveillance of antibiotic resistance is of utmost importance, since it facilitates the design or development of the treatment regimens that could check the spread of antimicrobial resistance.


2021 ◽  
Vol 3 (4) ◽  
pp. 25-30
Author(s):  
Md Hakimul Haque ◽  
Md. Mizanur Rahman ◽  
Md. Lovelu Miah ◽  
Soshe Ahmed ◽  
Md. Rabiul Islam Sazib ◽  
...  

Chicken eggs are a major component of people’s diets, with an average yearly consumption of approximately 103 eggs per person in Bangladesh. Eggs act as an important carrier of food-borne pathogen worldwide. The study was conducted to identify the prevalence and antibiotic resistance pattern of E. coli, Salmonella spp., and Staphylococcus spp., in eggs isolated from farms and different markets of Rajshahi, Bangladesh. A total of 60 eggs were collected randomly between April to December 2019. The isolation and identification of bacterial pathogen was done in accordance with standard procedures. The bacterial isolates were subjected to antibiotic susceptibility testing against seven commonly used antibiotics using Kirby-Bauer disk diffusion method. An overall prevalence of E. coli, Salmonella spp., and Staphylococcus spp. were found to be 35.0%, 28.33%, and 23.33%, respectively. E. coli were found highly resistant to penicillin (100%), tetracycline (80.95%), ampicillin (100%), and erythromycin (85.71%) and were sensitive to amoxicillin (71.42%), ciprofloxacin (85.71%), and gentamicin (95.23%). Salmonella spp. was highly resistant to penicillin (100%), erythromycin (82.35%) and tetracycline (82.35%), and was sensitive to gentamicin (94.11%), amoxicillin (76.47%) and ciprofloxacin (70.58%). Staphylococcus spp. was resistant to penicillin (100%), erythromycin (78.57%), tetracycline (85.71%), amoxicillin (100%), and ampicillin (100%) but sensitive to ciprofloxacin (85.71%), and gentamicin (92.85%). The higher prevalence of multidrug-resistant (MDR) bacteria can easily enter the food chain, which poses a public health threat.


Author(s):  
Hossein Norouzian ◽  
Mohammad Katouli ◽  
Nader Shahrokhi ◽  
Sharam Sabeti ◽  
Mohammad Pooya ◽  
...  

Background and Objectives: B2 and D have been mentioned as the most common phylogenetic groups among uropatho- genic Escherichia coli. However, there is still controversy about the importance of these phylo-groups. This study was con- ducted to investigate the probable relation between these groups and antibiotic resistance patterns of E. coli isolates derived from urine and feces of the patients with acute or recurrent UTI. Materials and Methods: 10 isolates were recovered from urine and feces samples of patients with different phases of UTI in whom E. coli was causative pathogen. Biochemical fingerprinting was performed to classify the isolates and select their appropriate representatives. Phylogenetic grouping was performed using multiplex PCR, and antibiotic resistance was deter- mined by disk diffusion method. Results: Five-hundred-sixty E. coli isolates were derived from 56 UTI patients (27 acute, 29 recurrent). Among them, 261 isolates were selected using biochemical fingerprinting. All the isolates were sensitive to imipenem and nitrofurantoin. Com- pared to other phylo-groups, the isolates in group D showed considerably different frequencies in acute vs. recurrent phase of UTI, in urine vs. stool samples, in males vs. females, and in- vs. out-patients. They were more resistant to the antibiotics (except norfloxacin), and in contrast to others, this was seen more in acute UTI, especially in urine samples. Multi-drug resistance pattern was also meaningfully higher in group D. Conclusion: Although phylo-groups B2 and D of E. coli bacteria are more responsible for UTI, group D isolates seem to be more resistant and probably more virulent, even than the ones from group B2.


2020 ◽  
Author(s):  
Samane Mohebi ◽  
zahra Hashemizade ◽  
Mahtab Hadadi ◽  
Soudeh Kholdi ◽  
Kasra Javadi ◽  
...  

Abstract Background Asymptomatic bacteriuria is one of the common problems in pregnancy. Pyelonephritis, preterm labor and low birth weight infants have been associated with bacterial infection. Urinary tract infection (UTI) during pregnancy is frequently associated with complications. An observational cross-sectional study including investigated the prevalence of virulence genes, antimicrobial resistance, and its relationship with phylogenetic groups among E. coli strains isolated from pregnant women with asymptomatic bacteriuria who referred to Hafez hospital, Shiraz, Iran. Material and Methods A total of 300 urine samples were screened for Escherichia coli strains. Susceptibility testing was determined by the disk-diffusion method. The phylogenetic groups and 13 virulence genes were identified by PCR. ESBL and AmpC producing isolates were detected using phenotypic methods. PCR was used to identify the bla TEM , bla SHV and bla CTXM genes in ESBL and AmpC-positive isolates. Results Our results revealed that among 300 urine samples, 105 (35%) were positive for E. coli . The data showed that the highest and the lowest resistance rates were observed against nalidixic acid (82.1%), and imipenem (2.8%), respectively. The prevalence of ESBLs and AmpC-β-lactamase, in the E. coli isolates was 41% and 9.5% respectively. bla CTXM was the commonest genotype (93%). Phylogenetic group distribution was as follow: B1 2.8%, A 14.2%, B2 61.9%, and D 4.6%. Our result showed that most of the virulence genes belonged to group B2 and also several virulence genes such as hlyA , cnf-1 , and papGII genes were positively associated with group B2. Conclusion Among E. coli strains isolated from patients with UTIs, different features phylogroups, with special virulence factors, could cause severe infection. Awareness about the Virulence patterns distribution among Phylogenetic groups of UPEC could greatly aid in confine and prevent the development of lethal infection caused by these strains.


2020 ◽  
Vol 18 ◽  
Author(s):  
Elhassan Benyagoub ◽  
Miaad K. Alkhudhairy ◽  
S. Mohamed Benchaib ◽  
Abdelmadjid Zaalan ◽  
Youcef Mekhfi ◽  
...  

Background: Emergence of multidrug-resistant uropathogenic strains mainly the global spread of extended-spectrum betalactamase (ESBL) genes accompanied both by uncontrolled use of antibacterial agents and a considerable decrease in their activities makes the monitoring of the resistance pattern one of necessary means that could help the medical practitioners to choose the best treatment. For this purpose and during four months from March 1 to June 30 (2019), an experimental study has been carried out on urine specimens of 123 inpatients (IP) and outpatients (OP) at infectious disease service Boudjemaa TOURABI Public Hospital of Bechar (Algeria), aiming the detection of ESBL-producing Enterobacteriaceae uropathogenic strains. Methods: Firstly, the antibiotic susceptibility testing has been carried out by using the disk diffusion method to determine not only the multidrug resistance patterns, but also the multiple antibiotic resistance indexes of uropathogenic strains isolated from clinical IP and OP samples. Secondly, the ESBL detection was done by using the following methods: synergy tests based on the synergy between a thirdgeneration cephalosporin and clavulanate, double-disc synergy test (DDST) and phenotypic tests on a cloxacillin-containing agar. Results: As a result, 56 patients had a urinary tract infection (UTI) in overall 123 patients; a frequency of 45,52%. Through a UTI’s frequency of 64,7%, the female gender was the most affected. All age groups were affected by UTI, with a mean age of 38,47±19,97 years old. Knowing that UTIs’ patients having ages ranged from 16 to 49 years old were most affected compared to other ages’ groups, with a frequency of 66,6 and 50% for female and male gender, respectively. The microbial strains represented by the bacteria group were predominant, ie (98,22%) followed by yeasts (1,78%), where Gram-negative bacilli showed (96,36%) of the uropathogenic agents, so (3,64%) were Gram-positive bacteria. The antibiotic resistance profile of isolated Enterobacteriaceae showed very high resistance rates for the species of Escherichia coli, Klebsiella spp, and Proteus spp to aminopenicillins, cephalosporins, and less against carbapenems and other drug groups. E. coli had presented the highest multidrug resistance followed by Klebsiella spp with a MAR index ranged from 0,53 to 0,82. Within this range, a total of 28 isolate (25 E. coli, 2 Klebsiella spp, and 1 Proteus mirabilis) had shown resistance against 9 to 14 out of the 17 tested antibiotics. The rate of ESBL-producing Enterobacteriaceae strains was 23,07 and 55,26% for inpatients and outpatients respectively, where E.coli was the most important ESBL producers out of all isolated strains. Conclusion: An alarming ESBLs rate for outpatients which is usually higher among inpatients with UTI, who receive several classes of antibiotics. Such condition should be considered as a major public health concern, and measures must be taken to establish the sources and drivers of this issue. Thus, the findings of this research pushes health sector stakeholders as well as scientific communities to act on reducing the transmission of the multidrug-resistant strains that threatens several classes of life-saving antibiotics.


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