Bacterial Morphotypes as Important Trait for Uropathogenic E. coli Diagnostic; a Virulence-Phenotype-Phylogeny Study

Urinary tract infections (UTIs) belong to the most common pathologies in Mexico and are mainly caused by Uropathogenic Escherichia coli (UPEC). UPEC possesses a wide diversity of virulence factors that allow it to carry out its pathogenesis mechanism in the urinary tract (UT). The development of morphotypes in UT represents an important feature of UPEC because it is associated with complications in diagnosis of UTI. The aim of this study was to determine the presence of bacterial morphotypes, virulence genes, virulence phenotypes, antibiotic resistant, and phylogenetic groups in clinical isolates of UPEC obtained from women in Sonora, Mexico. Forty UPEC isolates were obtained, and urine morphotypes were observed in 65% of the urine samples from where E. coli was isolated. Phylogenetic group B2 was the most prevalent. The most frequent virulence genes were fimH (100%), fliCD (90%), and sfaD/focC (72%). Biofilm formation (100%) and motility (98%) were the most prevalent phenotypes. Clinical isolates showed high resistance to aminoglycosides and β-lactams antibiotics. These data suggest that the search for morphotypes in urine sediment must be incorporated in the urinalysis procedure and also that clinical isolates of UPEC in this study can cause upper, lower, and recurrent UTI.

Download Full-text

Enteroaggregative Escherichia coli is associated with antibiotic resistance and urinary tract infection symptomatology

PeerJ ◽

10.7717/peerj.11726 ◽

2021 ◽

Vol 9 ◽

pp. e11726

Author(s):

Verónica I. Martínez-Santos ◽

María Ruíz-Rosas ◽

Arturo Ramirez- Peralta ◽

Oscar Zaragoza García ◽

Luis Armando Resendiz-Reyes ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract Infection ◽

Antibiotic Resistance ◽

Urinary Tract ◽

Tract Infection ◽

Virulence Genes ◽

Clinical Isolates ◽

E Coli ◽

Ambulatory Patients ◽

Tract Infections

Background Uropathogenic Escherichia coli (UPEC) is the causative agent of uncomplicated urinary tract infections (UTIs) in ambulatory patients. However, enteroaggregative E. coli (EAEC), an emergent bacterial pathogen that causes persistent diarrhoea, has recently been associated with UTIs. The aim of this study was to determine the frequency of EAEC virulence genes, antibiotic resistance, as well as biofilm production of UPEC isolates obtained from ambulatory patients with non-complicated UTIs that attended to the ISSSTE clinic in Chilpancingo, Guerrero, Mexico, and correlate these with the patients’ urinary tract infection symptomatology. Methods One hundred clinical isolates were obtained. The identification of clinical isolates, antimicrobial susceptibility testing, and extended spectrum beta-lactamases (ESBLs) production were performed using the Vitek automated system. Assignment of E. coli phylogenetic groups was performed using the quadruplex phylo-group assignment PCR assay. UPEC virulence genes (hlyA, fimH, papC, iutA, and cnf1) and EAEC virulence genes (aap, aggR, and aatA) were detected by multiple PCR. Results We found that 22% of the isolates carried the aggR gene and were classified as UPEC/EAEC. The main phylogenetic group was B2 (44.1% were UPEC and 77.27% UPEC/EAEC isolates, respectively). Over half of the UPEC/EAEC isolates (63.64%) were obtained from symptomatic patients, however the aatA gene was the only one found to be associated with the risk of developing pyelonephritis (OR = 5.15, p = 0.038). A total of 77.71% of the UPEC/EAEC isolates were ESBL producers and 90.91% multidrug-resistant (MDR). In conclusion, UPEC/EAEC isolates are more frequent in symptomatic patients and the aatA gene was associated with a higher risk of developing pyelonephritis, along with UPEC genes hlyA and cfn1. UPEC/EAEC isolates obtained from UTI showed ESBL production and MDR.

Download Full-text

Carbapenem Resistance Profiles of Pathogenic Escherichia coli in Uganda

European Journal of Biology and Biotechnology ◽

10.24018/ejbio.2021.2.2.171 ◽

2021 ◽

Vol 2 (2) ◽

pp. 63-73

Author(s):

Kenneth Ssekatawa ◽

Denis K. Byarugaba ◽

Jesca L. Nakavuma ◽

Charles D. Kato ◽

Francis Ejobi ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Factors ◽

Virulence Genes ◽

Carbapenem Resistance ◽

Phylogenetic Group ◽

Clinical Isolates ◽

Phylogenetic Groups ◽

Phenotypic Resistance ◽

E Coli ◽

Tract Infections

Escherichia coli has been implicated as one of the main etiological agents of diarrhea, urinary tract infections, meningitis and septicemia worldwide. The ability to cause diseases is potentiated by presence of virulence factors. The virulence factors influence the capacity of E. coli to infect and colonize different body systems. Thus, pathogenic E. coli are grouped into DEC strains that are mainly clustered in phylogenetic group B1 and A; ExPEC belonging to A, B2 and D. Coexistence of virulence and beta-lactamase encoding genes complicates treatment outcomes. Therefore, this study aimed at presenting the carbapenem resistance (CR) profiles among pathogenic E. coli. This was a retrospective cross-sectional study involving use of 421 archived E. coli clinical isolates collected in 2019 from four Uganda tertiary hospitals. The isolates were subjected to antibiotics sensitivity assays to determine phenotypic resistance. Four sets of multiplex PCR were performed to detect CR genes, DEC pathotypes virulence genes, ExPEC PAI and the E. coli phylogenetic groups. Antibiotic susceptibility revealed that all the 421 E. coli isolates used were MDR as they exhibited 100% resistance to more than one of the first-line antibiotics. The study registered phenotypic and genotypic CR prevalence of 22.8% and 33.0% respectively. The most predominant gene was blaOXA-48 with genotypic frequency of 33.0%, then blaVIM (21.0%), blaIMP (16.5%), blaKPC (14.8%) and blaNDM (14.8%). Spearman’s correlation revealed that presence of CR genes was highly associated with phenotypic resistance. Furthermore, of 421 MDR E. coli isolates, 19.7% harboured DEC virulence genes, where EPEC recorded significantly higher prevalence (10.8%) followed by S-ETEC (3.1%), STEC (2.9%), EIEC (2.0%) and L-ETEC (2.0%). Genetic analysis characterized 46.1% of the isolates as ExPEC and only PAI IV536 (33.0%) and PAI IICFT073 (13.1%) were detected. Phylogenetic group B2 was predominantly detected (41.1%), followed by A (30.2%), B1(21.6%), and D (7.1%). Furthermore, 38.6% and 23.1% of the DEC and ExPEC respectively expressed phenotypic resistance. Our results exhibited significant level of CR carriage among the MDR DEC and ExPEC clinical isolates belonging to phylogenetic groups B1 and B2 respectively. Virulence and CR genetic factors are mainly located on mobile elements. Thus, constitutes a great threat to the healthcare system as this promotes horizontal gene transfer.

Download Full-text

Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis

Microbiology ◽

10.1099/mic.0.27499-0 ◽

2005 ◽

Vol 151 (6) ◽

pp. 2097-2110 ◽

Cited By ~ 227

Author(s):

Kylie E. Rodriguez-Siek ◽

Catherine W. Giddings ◽

Curt Doetkott ◽

Timothy J. Johnson ◽

Mohamed K. Fakhr ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract Infection ◽

Urinary Tract ◽

Virulence Genes ◽

Phylogenetic Group ◽

Human Beings ◽

Phylogenetic Groups ◽

E Coli ◽

Autotransporter-Encoding Sequences Are Phylogenetically Distributed among Escherichia coli Clinical Isolates and Reference Strains

Applied and Environmental Microbiology ◽

10.1128/aem.01542-06 ◽

2007 ◽

Vol 73 (5) ◽

pp. 1553-1562 ◽

Cited By ~ 84

Author(s):

Concetta Restieri ◽

Geneviève Garriss ◽

Marie-Claude Locas ◽

Charles M. Dozois

Keyword(s):

Escherichia Coli ◽

Urinary Tract ◽

Clinical Isolates ◽

Phylogenetic Groups ◽

Allelic Variants ◽

E Coli ◽

Multiplex Pcr Assay ◽

Strain Collection ◽

Tract Infections ◽

Reference Strains

ABSTRACT Autotransporters are secreted bacterial proteins exhibiting diverse virulence functions. Various autotransporters have been identified among Escherichia coli associated with intestinal or extraintestinal infections; however, the specific distribution of autotransporter sequences among a diversity of E. coli strains has not been investigated. We have validated the use of a multiplex PCR assay to screen for the presence of autotransporter sequences. Herein, we determined the presence of 13 autotransporter sequences and five allelic variants of antigen 43 (Ag43) among 491 E. coli isolates from human urinary tract infections, diarrheagenic E. coli, and avian pathogenic E. coli (APEC) and E. coli reference strains belonging to the ECOR collection. Clinical isolates were also classified into established phylogenetic groups. The results indicated that Ag43 alleles were significantly associated with clinical isolates (93%) compared to commensal isolates (56%) and that agn43K12 was the most common and widely distributed allele. agn43 allelic variants were also phylogenetically distributed. Sequences encoding espC, espP, and sepA and agn43 alleles EDL933 and RS218 were significantly associated with diarrheagenic E. coli strains compared to other groups. tsh was highly associated with APEC strains, whereas sat was absent from APEC. vat, sat, and pic were associated with urinary tract isolates and were identified predominantly in isolates belonging to either group B2 or D of the phylogenetic groups based on the ECOR strain collection. Overall, the results indicate that specific autotransporter sequences are associated with the source and/or phylogenetic background of strains and suggest that, in some cases, autotransporter gene profiles may be useful for comparative analysis of E. coli strains from clinical, food, and environmental sources.

Download Full-text

Single Clinical Isolates from Acute Uncomplicated Urinary Tract Infections Are Representative of Dominant In Situ Populations

mBio ◽

10.1128/mbio.01064-13 ◽

2014 ◽

Vol 5 (2) ◽

Cited By ~ 18

Author(s):

Dana Willner ◽

Serene Low ◽

Jason A. Steen ◽

Narelle George ◽

Graeme R. Nimmo ◽

...

Keyword(s):

Escherichia Coli ◽

Urinary Tract ◽

Urinary Tract Infections ◽

Clinical Isolates ◽

Content Type ◽

E Coli ◽

Strain Diversity ◽

Amplicon Pyrosequencing ◽

Culture Independent ◽

Tract Infections

ABSTRACTUrinary tract infections (UTIs) are one of the most commonly acquired bacterial infections in humans, and uropathogenicEscherichia colistrains are responsible for over 80% of all cases. The standard method for identification of uropathogens in clinical laboratories is cultivation, primarily using solid growth media under aerobic conditions, coupled with morphological and biochemical tests of typically a single isolate colony. However, these methods detect only culturable microorganisms, and characterization is phenotypic in nature. Here, we explored the genotypic identity of communities in acute uncomplicated UTIs from 50 individuals by using culture-independent amplicon pyrosequencing and whole-genome and metagenomic shotgun sequencing. Genus-level characterization of the UTI communities was achieved using the 16S rRNA gene (V8 region). Overall UTI community richness was very low in comparison to other human microbiomes. We strain-typedEscherichia-dominated UTIs using amplicon pyrosequencing of the fimbrial adhesin gene,fimH. There were nine highly abundantfimHtypes, and each UTI sample was dominated by a single type. Molecular analysis of the corresponding clinical isolates revealed that in the majority of cases the isolate was representative of the dominant taxon in the community at both the genus and the strain level. Shotgun sequencing was performed on a subset of eightE. coliurine UTI and isolate pairs. The majority of UTI microbial metagenomic sequences mapped to isolate genomes, confirming the results obtained using phylogenetic markers. We conclude that for the majority of acute uncomplicatedE. coli-mediated UTIs, single cultured isolates are diagnostic of the infection.IMPORTANCEIn clinical practice, the diagnosis and treatment of acute uncomplicated urinary tract infection (UTI) are based on analysis of a single bacterial isolate cultured from urine, and it is assumed that this isolate represents the dominant UTI pathogen. However, these methods detect only culturable bacteria, and the existence of multiple pathogens as well as strain diversity within a single infection is not examined. Here, we explored bacteria present in acute uncomplicated UTIs using culture-independent sequence-based methods.Escherichia coliwas the most common organism identified, and analysis ofE. colidominant UTI samples and their paired clinical isolates revealed that in the majority of infections the cultured isolate was representative of the dominant taxon at both the genus and the strain level. Our data demonstrate that in most cases single cultured isolates are diagnostic of UTI and are consistent with the notion of bottlenecks that limit strain diversity during UTI pathogenesis.

Download Full-text

ANTIBIOTIC SUSCEPTIBILITY OF ESCHERICHIA COLI ISOLATE FROM URINARY TRACT INFECTION OF THALASSEMIC PATIENTS IN THI-QAR PROVINCE

Southern Brazilian Journal of Chemistry - Southern Brazilian Journal of Chemistry, Volume 28, No. 28, 2020 ◽

10.48141/sbjchem.v28.n28.2020.04_okab_pgs_22_33.pdf ◽

2020 ◽

Vol 28 (28) ◽

pp. 22-33

Author(s):

Alaa Abood Yasir OKAB ◽

Manal B SALIH

Keyword(s):

Escherichia Coli ◽

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Clavulanic Acid ◽

Rural Areas ◽

Antibiotic Resistant ◽

E Coli ◽

Amoxicillin Clavulanic Acid ◽

Tract Infections

Escherichia coli (E. coli) is the most common type of pathogen that causes Urinary tract infection disease. It can be presented as a pathogenic or non-pathogenic strain and found not only in the animal but also in the human intestine. This bacterium can cause opportunistic infection when the human host comprised of thalassemia patients or changes the healthy hemostatic flora. This study aimed to analyze the presence of bacteria in thalassemia patients with urinary tract infection. A total of 303 samples were collected during the period from August 2019 to January 2020 from thalassemia patients who suffered from urinary tract infection. The results showed that there were 6.9% of patients infected with E. coli, 2.6% of patients were infected with S. aureus, 0.7% with both Proteus and Klebsiella, while 89.1% of patients had a negative sample for bacteria. Also, the incidence of urinary tract infections in females is higher than in males. Besides, its occurrence in rural areas is higher than in city residents. Moreover, among 16 antibiotics tested to sensitize bacteria to antibiotics, Imipenem showed 100% efficacy on all isolated bacteria. In contrast, Netilmicin showed 80.1% efficacy, Gentamycin 80.1%, and Amikacin 76.2%. Ampicillin, Aztreonam, Amoxicillin-Clavulanic Acid, Tetracycline, and Ticarcillin-Clavulanic Acid, did not show any effectiveness toward the bacteria while other antibiotics showed different activities. Furthermore, the isolated microbes from thalassemia patients were the highest resistance to antibiotics in comparison with other studies, and this antibiotic-resistant may be due to the weakening of the patient's immune status and frequent blood taking and the antibodies it contains.

Download Full-text

OXA-48 Carbapenemase-Encoding Transferable Plasmids of Klebsiella pneumoniae Recovered from Egyptian Patients Suffering from Complicated Urinary Tract Infections

Biology ◽

10.3390/biology10090889 ◽

2021 ◽

Vol 10 (9) ◽

pp. 889

Author(s):

Ann A. Elshamy ◽

Sarra E. Saleh ◽

Mohammad Y. Alshahrani ◽

Khaled M. Aboshanab ◽

Mohammad M. Aboulwafa ◽

...

Keyword(s):

Urinary Tract ◽

Urinary Tract Infections ◽

Antimicrobial Agents ◽

Bacterial Species ◽

Tertiary Care ◽

Carbapenem Resistance ◽

Clinical Isolates ◽

Gram Negative ◽

E Coli ◽

Tract Infections

Gram-negative bacteria are common causes of urinary tract infections (UTIs). Such pathogens can acquire genes encoding multiple mechanisms of antimicrobial resistance, including carbapenem resistance. The aim of this study was to detect the carbapenemase-producing ability of some Gram-negative bacterial isolates from urine specimens of patients suffering from complicated UTIs at two vital tertiary care hospitals in Cairo, Egypt; to determine the prevalence of carbapenemase genes among plasmid-bearing isolates; and explore the possibility of horizontal gene transfer to other bacterial species. The collected isolates were subjected to antimicrobial susceptibility testing, phenotypic analysis of carbapenemase production, and molecular detection of plasmid-borne carbapenemase genes, then the extracted plasmids were transformed into competent E. coli DH5α. A total of 256 Gram-negative bacterial clinical isolates were collected, 65 (25.4%) isolates showed carbapenem resistance of which 36 (55.4%) were carbapenemase-producers, and of these 31 (47.7%) harbored plasmids. The extracted plasmids were used as templates for PCR amplification of blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP carbapenemase genes. The blaOXA-48 gene was detected in 24 (77.4%) of the tested isolates while blaVIM gene was detected in 8 (25.8%), both blaKPC and blaNDM genes were co-present in 1 (3.2%) isolate. Plasmids carrying the blaOXA-48 gene from 4 K. pneumoniae clinical isolates were successfully transformed into competent E. coli DH5α. The transformants were carbapenemase-producers and acquired resistance to some of the tested antimicrobial agents as compared to untransformed E. coli DH5α. The study concluded that the rate of carbapenem resistance among Gram-negative bacterial uropathogens in Cairo, Egypt is relatively high and can be transferred horizontally to other bacterial host(s).

Download Full-text

Virulence genes and phylogenetic groups of uropathogenic Escherichia coli isolates from patients with urinary tract infection and uninfected control subjects: a case-control study

BMC Infectious Diseases ◽

10.1186/s12879-021-06036-4 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Seyedeh Elham Rezatofighi ◽

Mahsa Mirzarazi ◽

Mansour Salehi

Keyword(s):

Escherichia Coli ◽

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Virulence Factors ◽

Virulence Genes ◽

Strong Association ◽

Phylogenetic Groups ◽

E Coli ◽

Healthy Humans

Abstract Background Urinary Tract Infection (UTI) is one of the most common bacterial infectious diseases which causes considerable morbidity and costly health problems. Uropathogenic Escherichia coli (UPEC), the most common pathogen causing UTI, is a highly heterogeneous group of extraintestinal pathogenic E. coli (ExPEC) which may carry a variety of virulence factors and belonging to different phylogenetic backgrounds. The current study aimed to investigate the frequency and association between various virulence factors (VFs) and phylogenetic groups of UPEC and commensal isolates. Methods UPEC and commensal E. coli strains isolated from UTI and feces of healthy humans were compared for the presence of VFs and phylogenetic groups. Association between virulence genes was investigated and cluster analysis was employed. Results According to the results, among a 30 virulence markers tested, the pathogenicity-associated island (PAI), papAH, papEF, fimH, fyuA, and traT genes prevalence were statistically significant in UPEC isolates. A strong association was found between the B2 and D phylogenetic groups and clinical isolates of UPEC; while, commensal isolates were mostly associated with phylogenetic group A. The aggregated VFs scores were more than twice higher in the UPEC isolates in comparison with the commensal isolates. Interestingly, the B2 group in both UPEC and commensal isolates had the highest VF scores. A strong positive association was found between several virulence genes. The clustering results demonstrated that UPEC or commensal E. coli isolates were highly heterogeneous due to different composition of their virulence gene pool and pathogenicity islands. Conclusion Genetic structure and VFs of UPEC strains vary from region to region; therefore, to control the UTI, the epidemiological aspects and characterization of the UPEC isolates need to be investigated in different regions. Since UPEC isolates are generally originate from the commensal strains, it may be feasible to reduce the UTI burden by interfering the intestinal colonization, particularly in the highly pathogenic clonal lineages such as B2.

Download Full-text

Bacterial Profile and Antibiotic Resistance among Cancer Patients with Urinary Tract Infection in a National Tertiary Cancer Hospital of Nepal

Tropical Medicine and Infectious Disease ◽

10.3390/tropicalmed6020049 ◽

2021 ◽

Vol 6 (2) ◽

pp. 49

Author(s):

Gambhir Shrestha ◽

Xiaolin Wei ◽

Katrina Hann ◽

Kyaw Thu Soe ◽

Srinath Satyanarayana ◽

...

Keyword(s):

Antibiotic Resistance ◽

Urinary Tract ◽

Cancer Patients ◽

Positive Culture ◽

Cross Sectional Study ◽

Cross Sectional ◽

Antibiotic Resistant ◽

E Coli ◽

Cancer Hospital ◽

Tract Infections

Cancer patients are at high risk of antibiotic resistant bacterial urinary tract infections (UTIs). In this study, we assessed the bacterial profile and antibiotic resistance among cancer patients suspected of UTI in B.P. Koirala Memorial Cancer Hospital in Nepal through a cross-sectional study with routinely collected data. All cancer patients who had a recorded urine culture between July 2018–June 2019 were included in the study. Out of 308 patients who had undergone culture, 73 (24%) of samples had bacterial growth. The most common organisms isolated were E. coli (58%), Staphylococcus (11%) and Klebsiella (10%). These bacteria had undergone susceptibility testing to 27 different antibiotics in various proportions. Of the limited antibiotic testing levels, nitrofurantoin (54/66, 82%) and amikacin (30/51, 59%) were the most common. Among those tested, there were high levels of resistance to antibiotics in the “Access” and “Watch” groups of antibiotics (2019 WHO classification). In the “Reserve” group, both antibiotics showed resistance (polymyxin 15%, tigecycline 8%). Multidrug resistance was seen among 89% of the positive culture samples. This calls for urgent measures to optimize the use of antibiotics in UTI care at policy and health facility levels through stewardship to prevent further augmentation of antibiotic resistance among cancer patients.

Download Full-text

Detection of Phylogenetic Groups and Drug Resistance Genes of Escherichia coli Causing Urinary Tract Infection in Southwest Iran

Jundishapur Journal of Microbiology ◽

10.5812/jjm.112547 ◽

2021 ◽

Vol 14 (2) ◽

Author(s):

Mostafa Boroumand Boroumand ◽

Mohsen Naghmachi ◽

Mohammad Amin Ghatee

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Urinary Tract ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Phylogenetic Group ◽

Phylogenetic Groups ◽

E Coli ◽

Pcr Method ◽

Tract Infections

Background: Many bacteria can cause urinary tract infections (UTIs), among which Escherichia coli is the most common causative agent. E. coli strains are divided into eight phylogenetic groups based on the new Quadroplex-PCR method, which are different in terms of patterns of resistance to antibiotics, virulence, and environmental characteristics. Objectives: This study aimed to determine the phylogenetic groups and the prevalence of drug resistance genes in E. coli strains causing UTIs. Methods: In this descriptive cross-sectional study, 129 E. coli isolates obtained from the culture of patients with UTIs were evaluated for phylogenetic groups using the new method of Clermont et al. The identification of phylogenetic groups and antibiotic resistance genes was performed using the multiplex polymerase chain reaction (PCR) method. Results: In this study, concerning the distribution of phylogenetic groups among E. coli isolates, the phylogenetic group B2 (36.4%) was the most common phylogenetic group, followed by phylogroups C (13.2%), clade I (10.1%), D (9.3%), and A (3.1%) while groups B1 and F were not observed in any of the isolates, and 20.2% had an unknown state. Also, out of 129 E. coli isolates, the total frequency of tetA, tetB, sul1, sul2, CITM, DfrA, and qnr resistance genes was 59.7%, 66.7, 69, 62, 30.2, 23.3, and 20.2%, respectively. In this study, there was a significant relationship between antibiotics (P = 0.026), cefotaxime (P = 0.003), and nalidixic acid (P = 0.044) and E. coli phylogenetic groups. No significant relationship was observed between E. coli phylogenetic groups and antibiotic resistance genes. Conclusions: The results of this study showed that strains belonging to group B2 had the highest prevalence among other phylogroups, and also, the frequency of antibiotic resistance genes and drug-resistant isolates had a higher prevalence in this phylogroup. These results show that phylogroup B2 has a more effective role in causing urinary tract infections compared to other phylogroups, and this phylogroup can be considered a genetic reservoir of antibiotic resistance.

Download Full-text