PHYLOGENETIC GROUPS AND VIRULENCE GENES OF ESCHERICHIA COLI STRAINS ISOLATED FROM THE CHILDREN GUT MICROBIOTA

Escherichia coli is characterized by a wide intraspecific diversity. The species includes both commensals and pathogens that cause diarrhea and extra-intestinal diseases. Pathogenic strains differ from non-pathogenic ones by the presence of virulence factors and their genes. The phylogenetic structure of the species is represented by four main groups (A, B1, B2, D), which differ in their prevalence among residents of different geographical regions. Pathogenic members of the species have been studied in detail, while non-pathogenic strains have not received such attention. This report presents the results of a study of 511 E. coli strains isolated from the gut microbiota of children without diarrhea and urinary tract infections, aged from 1 month to 17 years, living in St. Petersburg. The main phylogenetic groups were determined by PCR, and E. coli virulence genes associated with diarrhea and extra-intestinal diseases were identified. Results: population structure of E. coli is represented by the following groups: A-33.3%, B1-6.7%, B2-34.0%, D-26%. In the studied population 2.5% of strains belonded to EPEC and 4.5% to EAggEC. EPEC virulence genes were more often detected in strains of phylogroup B1, and EAggEC virulence genes in isolates of phylogroup D. The prevalence of extra - intestinal virulence genes was as follows: pap - 29.5%; sfa - 19.8%; afa - 3.3%; hly - 20.9%; cnf - 17.4%; aer-20.0%. The pap, sfa, hly, and cnf genes were detected mostly in the B2 phylogenetic group. Obtained data shows the similarity of E. coli phylogenetic groups structure in St. Petersburg with E. coli populations isolated from residents of Paris and Sydney. Analysis of the virulence genes prevalence showed the dependence of their presence on the genetic background bacteria.

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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.

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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 ◽

Virulence factors analysis and antibiotic resistance of uropathogenic Escherichia coli isolated from patients in northeast of Iran

Iranian Journal of Microbiology ◽

10.18502/ijm.v12i3.3240 ◽

2020 ◽

Author(s):

Mahdis Ghavidel ◽

Tahere Gholamhosseini-Moghadam ◽

Kimiya Nourian ◽

Kiarash Ghazvini

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Virulence Genes ◽

High Rate ◽

Resistance Pattern ◽

Antibiotics Resistance ◽

Disk Diffusion Test ◽

E Coli ◽

Genes Encoding ◽

Tract Infections

Background and Objectives: Escherichia coli is known to be the pathogen commonly isolated from those infected with uri- nary tract infections (UTIs). The aim of this study was to investigate the presence of E. coli virulence genes and antibiotics’ resistance pattern among clinical isolates in the Northeast of Iran. Relationships between virulence genes and antimicrobial resistances were studied as well. Materials and Methods: Three hundred isolates of E. coli were isolated from patients with UTIs that referred to Ghaem and Imam Reza hospitals (Mashhad, Iran) during August 2016 to February 2017. A multiplex PCR was employed to amplify the genes encoding pyelonephritis associated pili (pap), S-family adhesions (sfa), type1fimbriae (fimH) and aerobactin (aer). Disk diffusion test was performed to test the susceptibility of isolates to β-lactams, aminoglycosides, cephalosporins, quino- lone, fluoroquinolones, carbapenems and trimethoprim-sulfamethoxazole. Results: The PCR results identified the fimH in 78.4%, aer in 70.5%, sfa in 13.6% and the pap in 8.2% of isolates. The rates of antibiotic resistance of the isolates were as follows: 64.7% resistant to cephalosporins, 34% to trimethoprim-sul- famethoxazole, 31% to fluoroquinolones, 15.3% to aminoglycosides, 13.3% to β-lactams, 7.8% to quinolones and 4.4% to carbapenems. Significant relationships existed between pap and aer, pap and sfa, aer and fluoroquinolones also pap and cephalosporins. Conclusion: fimH and aer were found in > 50% of isolates suggesting the importance of both genes in UPEC. The majority of isolates had fimH as adhesion factor for colonization. Determining antibiotic resistance patterns in specific geographical areas is necessary for appropriate treatment of urinary tract infection. The high rate of resistance to cephalosporins is most likely due to incorrect drug administration

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Presence of virulence genes and pathogenicity islands in extraintestinal pathogenic Escherichia coli isolates from Brazil

The Journal of Infection in Developing Countries ◽

10.3855/jidc.6683 ◽

2015 ◽

Vol 9 (10) ◽

pp. 1068-1075 ◽

Cited By ~ 18

Author(s):

Paula Signolfi Cyoia ◽

Gabriela Regina Rodrigues ◽

Erick Kenji Nishio ◽

Leonardo Pinto Medeiros ◽

Vanessa Lumi Koga ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

University Hospital ◽

Neonatal Meningitis ◽

Pathogenicity Islands ◽

Phylogenetic Groups ◽

Pathogenic Escherichia Coli ◽

Group A ◽

Tract Infections ◽

The University

Introduction: Extraintestinal pathogenic Escherichia coli (ExPEC) is associated with various diseases such as urinary tract infections, neonatal meningitis and septicemia. There are many virulence factors (VF) encoded by genes in ExPEC, including papC, papG, ecpA, iroN, fyuA, iutA, ompTp, tsh, hlyF, hlyA and iss. These virulence genes may be present in pathogenicity islands (PAI) or plasmids. Methodology: In this study, we analyzed the presence of VF encoding genes, PAI sequences and phylogenetic groups of 96 ExPEC strains isolated from the urine and blood of patients at the University Hospital of Londrina, and we compared them with 50 faecal commensal strains from healthy individuals. Results: The VF fyuA (65.60%) was detected in pathogenic strains and commensal strains (46%). A comparison of the distribution of ExPEC and commensal strains in the phylogenetic groups showed that more ExPEC strains belonged to group B2 whereas more of the commensal isolates belonged to group A. The distribution of the seven PAI sequences between commensal strains and ExPEC strains showed that PAI IV536 was common in both ExPEC and commensal isolates. Conclusions: These results showed that the ExPEC strains that belonged to group B2 had more PAI sequences compared to those of the other groups, especially group B1, which had virulence genes but the lowest percentage of PAI sequences, which leads us to conclude that the virulence of ExPEC strains characterized as B2 is likely attributed to PAI encoded genes, whereas the virulence of ExPEC strains belonging to phylogenetic group B1 is likely due to plasmid encoded virulence genes.

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Phylogenetic groups and antimicrobial susceptibility patterns of uropathogenic Escherichia coli clinical isolates from patients at Mulago National Referral Hospital, Kampala, Uganda

F1000Research ◽

10.12688/f1000research.20930.1 ◽

2019 ◽

Vol 8 ◽

pp. 1828 ◽

Cited By ~ 1

Author(s):

Paul Katongole ◽

Daniel Bulwadda Kisawuzi ◽

Henry Kyobe Bbosa ◽

David Patrick Kateete ◽

Christine Florence Najjuka

Keyword(s):

Escherichia Coli ◽

Antimicrobial Susceptibility ◽

Phylogenetic Group ◽

Diffusion Method ◽

Clinical Microbiology Laboratory ◽

Phylogenetic Groups ◽

E Coli ◽

Pcr Method ◽

Tract Infections ◽

Susceptibility Patterns

Introduction: Uropathogenic Escherichia coli (UPEC) remains the most common cause of urinary tract infections (UTIs). They account for over 80-90% of all community-acquired and 30-50% of all hospital-acquired UTIs. E. coli strains have been found to belong to evolutionary origins known as phylogenetic groups. In 2013, Clermont classified E. coli strains into eight phylogenetic groups using the quadruplex PCR method. The aim of this study was to identify the phylogenetic groups of UPEC strains in Uganda using Clermont’s quadruplex PCR method and to assess their antibiotic susceptibility patterns in Uganda. Methods: In this cross-sectional study, 140 stored uropathogenic E. coli isolates from the Clinical Microbiology Laboratory, Department of Medical Microbiology, College of Health Sciences Makerere University were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was performed by disk diffusion method according to Clinical & Laboratory Standards Institute (CLSI) guidelines. Phenotypic detection of extended-spectrum beta-lactamase, AmpC and carbapenemases was done according to CLSI guidelines and Laboratory SOPs. Results: Phylogenetic group B2 (40%) was the most predominant, followed by A (6.23%), clade I and II (5%), D and E (each 2.14%), B1 (1.43%) and F and C (each 0.71%). The most common resistant antibiotic was trimethoprim-sulphamethoxazole (90.71%) and the least was imipenem (1.43%). In total, 73.57% of isolates were multi-drug resistant (MDR). Antibiotic resistance was mainly detected in phylogenetic group B2 (54%). Conclusions: Our findings showed the high prevalence of MDR E. coli isolates, with the dominance of phylogenetic group B2. About 9% of E. coli isolates belonged to the newly described phylogroups C, E, F, and clade I and II.

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Detection of virulence genes, phylogenetic group and antibiotic resistance of uropathogenic Escherichia coli in Mongolia

The Journal of Infection in Developing Countries ◽

10.3855/jidc.7903 ◽

2017 ◽

Vol 11 (01) ◽

pp. 51-57 ◽

Cited By ~ 17

Author(s):

Yandag Munkhdelger ◽

Nyamaa Gunregjav ◽

Altantsetseg Dorjpurev ◽

Nishi Juniichiro ◽

Jav Sarantuya

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Virulence Genes ◽

Wide Spectrum ◽

Iron Acquisition ◽

Uropathogenic Escherichia Coli ◽

Phylogenetic Group ◽

Diffusion Method ◽

Phylogenetic Groups ◽

E Coli

Introduction: The severity of urinary tract infection (UTI) produced by uropathogenic Escherichia coli (UPEC) is due to the expression of a wide spectrum of virulence genes. E. coli strains were divided into four phylogenetic groups (A, B1, B2 and D) based on their virulence genes. The present study aimed to assess the relationship between virulence genes, phylogenetic groups, and antibiotic resistance of UPEC. Methodology: A total of 148 E. coli were tested for antimicrobial resistance against 10 drugs using the disk diffusion method. The isolates were screened by polymerase chain reaction (PCR) for detection of virulence genes and categorized into the four major phylogenetic groups. Results: Phylogenetic group B2 was predominant (33.8%), followed by D (28.4%), A (19.6), and B1 (18.2%). A higher prevalence of fimH (89.9%), fyuA (70.3%), traT (66.2%), iutA (62.2%), kpsMTII (58.8%), and aer (56.1%) genes were found in UPEC, indicating a putative role of adhesins, iron acquisition systems, and protectins that are main cause of UTIs. The most common antibiotic resistance was to cephalotin (85.1%), ampicillin (78.4%) and the least to nitrofurantoin (5.4%) and imipenem (2%). In total, 93.9% of isolates were multidrug resistant (MDR). Conclusions: This study showed that group B2 and D were the predominant phylogenetic groups and virulence-associated genes were mostly distributed in these groups. The virulence genes encoding components of adhesins, iron acquisition systems, and protectins were highly prevalent among antibiotic-resistant UPEC. Although the majority of strains are MDR, nitrofurantoin is the drug of choice for treatment of UTI patients in Ulaanbaatar.

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Drug resistance, serotypes, and phylogenetic groups among uropathogenic Escherichia coli including O25-ST131 in Mexico City

The Journal of Infection in Developing Countries ◽

10.3855/jidc.1703 ◽

2011 ◽

Vol 5 (12) ◽

pp. 840-849 ◽

Cited By ~ 36

Author(s):

José Molina-López ◽

Gerardo Aparicio-Ozores ◽

Rosa María Ribas-Aparicio ◽

Sandra Gavilanes-Parra ◽

María Elena Chávez-Berrocal ◽

...

Keyword(s):

Escherichia Coli ◽

Multidrug Resistance ◽

Mexico City ◽

Uropathogenic Escherichia Coli ◽

Diffusion Method ◽

Phylogenetic Groups ◽

Disk Diffusion Method ◽

E Coli ◽

Pcr Multiplex ◽

Tract Infections

Introduction: The increasing prevalence of uropathogenic Escherichia coli (UPEC) strains resistant to multiple antibiotics complicates the treatment of urinary tract infections (UTIs). This study aimed to analyze the antimicrobial resistance, serotypes, and phylogenetic groups among strains of E. coli isolated from outpatients with UTIs in Mexico City. Methodology: A total of 119 E. coli isolates were recovered from urine samples from outpatients with clinical diagnosis of uncomplicated UTIs from 2004 to 2007. The serotype was assessed by agglutination in microtiter plates; susceptibility to antimicrobials was determined by the disk diffusion method. Clone O25-ST131 and phylogenetic groups of E. coli strains were tested by methods based on PCR multiplex. Results: The predominant serotype was O25:H4 (21.2%). Resistance to antibiotics was ampicillin (83.7%); piperacillin (53.8%); the fluoroquinolone group (55.5-60.6%), and trimethoprim/sulfamethoxazole (TMP/SMX) (56.4%). Additionally, 36 (30.2%) isolates were multidrug-resistant and 13 of these 36 strains were identified as E. coli O25-ST131 clone by an allele-specific PCR-based assay. Phylogenetic analysis showed that 15 of 17 isolates with serotype O25:H4 belonged to group B2. Conclusions: This is the first report that establishes the presence in Mexico of the O25-ST131 clonal group of E. coli, which has been associated with multidrug-resistance and with high virulence potential. The spread of this clone in Mexico should be monitored closely. We found a correlation between serotype O25:H4 and multidrug resistance in UPEC strains. Our results indicate that the use of ampicillin, fluoroquinolones, and TMP/SMX should be reviewed when selecting empirical therapy for UTIs.

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Characterization of auto-agglutinating and non-typeable uropathogenic Escherichia coli strains

The Journal of Infection in Developing Countries ◽

10.3855/jidc.11098 ◽

2019 ◽

Vol 13 (06) ◽

pp. 465-472

Author(s):

Ulises Hernández-Chiñas ◽

Alejandro Pérez-Ramos ◽

Laura Belmont-Monroy ◽

María E Chávez-Berrocal ◽

Edgar González-Villalobos ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Antimicrobial Agents ◽

Multidrug Resistant ◽

Uropathogenic Escherichia Coli ◽

E Coli ◽

Resistant Strains ◽

Tract Infections ◽

Disk Method

Introduction: Uropathogenic Escherichia coli (UPEC) are the main etiological agent of urinary tract infections (UTIs). Association between different serotypes and UTIs is known, however, some strains are incapable to be serotyped. The aim of this work was to study bthe phenotypical and genotypical characteristics of 113 non-typeable (NT) and auto-agglutinating (AA) E. coli strains, isolated from UTIs in children and adults. Methodology: The 113 UPEC strains were analyzed by PCR assays using specific primers to determine their serogroups, fimH, papC, iutA, sat, hlyCA and cnf1, virulence associated genes, and chuA, yjaA and TSPE4.C2 for phylogroup determination. Additionally, the diffusion disk method was performed to evaluate the antimicrobial resistance to 18 antimicrobial agents. Results: Using the PCR assay, 63% (71) of the strains were genotyped showing O25 and O75 as the most common serogroups. The virulence genes fimH (86%) and iutA (74%) were the most prevalent, in relation to the phylogroups the commensal (A and B1) and virulent (B2 and D) showed similar frequencies (P > 0.05). The antimicrobial susceptibility test showed a high percentage (73%) of multidrug-resistant strains. Conclusions: The genotyping allowed identifying the serogroup in many of the strains that could not be typed by traditional serology. The strains carried virulence genes and were multidrug-resistant in both, commensal and virulent phylogroups. Our findings revealed that, in addition to the classical UPEC serogroups, there are pathogenic serogroups not reported yet.

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Molecular Characterization of Uropathogenic Escherichia coli Reveals Emergence of Drug Resistant O15, O22 and O25 Serogroups

Medicina ◽

10.3390/medicina55110733 ◽

2019 ◽

Vol 55 (11) ◽

pp. 733 ◽

Cited By ~ 3

Author(s):

Ruta Prakapaite ◽

Frederic Saab ◽

Rita Planciuniene ◽

Vidmantas Petraitis ◽

Thomas J. Walsh ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Asymptomatic Bacteriuria ◽

Empirical Therapy ◽

Uropathogenic Escherichia Coli ◽

Phylogenetic Groups ◽

E Coli ◽

Tract Infections ◽

Resistance Rates

Background and Objectives: Uropathogenic Escherichia coli (UPEC) are common pathogens causing urinary tract infections (UTIs). We aimed to investigate the relationship among clinical manifestation, serogroups, phylogenetic groups, and antimicrobial resistance among UPEC. Materials and Methods: One-hundred Escherichia coli isolates recovered from urine and ureteral scrapings were used for the study. The prevalence of antimicrobial resistance was determined by using European Committee on Antimicrobial Susceptibility Testing (EUCAST) recommendations. E. coli serogroups associated with UTI, as well as phylogenetic diversity were analyzed using multiplex PCR reactions. Results: Eighty-seven strains (87%) were isolated from females, while 13 (13%) from males. A high frequency of resistance to cephalosporins (43%) and fluoroquinolones (31%) was observed. Among UTI-associated serogroups O15 (32.8%), O22 (23.4%), and O25 (15.6%) were dominant and demonstrated elevated resistance rates. The E. coli phylogenetic group B2 was most common. These observations extended to pregnant patients with asymptomatic bacteriuria. Conclusions: Due to high rates of resistance, strategies using empirical therapy of second-generation cephalosporins and fluoroquinolones should be reconsidered in this population.

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Pathogenic features of urinary Escherichia coli strains causing Asymptomatic Bacteriuria during Pregnancy

10.21203/rs.2.22234/v1 ◽

2020 ◽

Author(s):

Samane Mohebi ◽

zahra Hashemizade ◽

Mahtab Hadadi ◽

Soudeh Kholdi ◽

Kasra Javadi ◽

...

Keyword(s):

Escherichia Coli ◽

Virulence Genes ◽

Asymptomatic Bacteriuria ◽

Urine Samples ◽

Diffusion Method ◽

Low Birth Weight Infants ◽

Phylogenetic Groups ◽

Disk Diffusion Method ◽

Cross Sectional ◽

E Coli

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.

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