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Lu L, Li M, Li Y, Jiang M, Jiang Y, Shi X, Zuo L, Wang L, Bian S, Qiu Y, Cai R, Liao Y, Li Q, Li L, Hu Q. A Novel Molecular Method for Simultaneous Identification of Vibrio parahaemolyticus 57 K-Serogroups Using Probe Melting Curve Analysis. Front Cell Infect Microbiol 2021; 11:594808. [PMID: 33718262 PMCID: PMC7953158 DOI: 10.3389/fcimb.2021.594808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 01/18/2021] [Indexed: 01/22/2023] Open
Abstract
The serotyping of Vibrio parahaemolyticus, which is crucial to the surveillance and detection of outbreaks of vibriosis infection, has been widely used in many countries. In this study, we developed a molecular assay, named multiplex ligation reaction based on probe melting curve analysis (MLMA), for simultaneous identification of V. parahaemolyticus 57 K-serogroups. Based on the previous genomes of 418 strains including 39 K-serogroups and the 18 K-serogroups sequences from public databases, we obtained 57 K-serogroups specific gene sequences for designing primers and probes. The developed MLMA assay for identifying the V. parahaemolyticus 57 K-serogroups showed high reproducibility, with the intra- and inter-assay standard deviations and coefficients of variation of no more than 1°C and 1%, respectively. The limit of detection for all gene targets ranged from 0.1 to 1.0 ng/µl. We validated the MLMA assay with a double-blind test identifying 595 V. parahaemolyticus isolates using conventional serotyping methods for comparison. The results showed the kappa value between the MLMA assay and the traditional serological method was 0.936 and that there was a 96.97% consistency rate with conventional serotyping methods for all detected isolates. Additionally, five rare K-serogroups were identified using the MLMA assay, as well as 18 strains that could not be identified using the traditional serotyping method. Thus, the MLMA assay provides a rapid, robust, and promising tool for the molecular serotyping of V. parahaemolyticus K-serogroups and has the potential application to the detection of outbreaks and surveillance of V. parahaemolyticus infection.
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Affiliation(s)
- Linying Lu
- School of Public Health, University of South China, Hengyang, China
| | - Minxu Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yinghui Li
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Min Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yixiang Jiang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Xiaolu Shi
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Le Zuo
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Lei Wang
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Shengzhe Bian
- School of Public Health (Shenzhen), Sun Yat-sen University, Guangzhou, China.,Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Yaqun Qiu
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Rui Cai
- Shenzhen Center for Disease Control and Prevention, Shenzhen, China
| | - Yiqun Liao
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Qingge Li
- School of Life Sciences, Xiamen University, Xiamen, China
| | - Liqiang Li
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen, China
| | - Qinghua Hu
- School of Public Health, University of South China, Hengyang, China.,Shenzhen Center for Disease Control and Prevention, Shenzhen, China
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García A, Fox JG. A One Health Perspective for Defining and Deciphering Escherichia coli Pathogenic Potential in Multiple Hosts. Comp Med 2021; 71:3-45. [PMID: 33419487 PMCID: PMC7898170 DOI: 10.30802/aalas-cm-20-000054] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/17/2020] [Accepted: 09/19/2020] [Indexed: 11/05/2022]
Abstract
E. coli is one of the most common species of bacteria colonizing humans and animals. The singularity of E. coli 's genus and species underestimates its multifaceted nature, which is represented by different strains, each with different combinations of distinct virulence factors. In fact, several E. coli pathotypes, or hybrid strains, may be associated with both subclinical infection and a range of clinical conditions, including enteric, urinary, and systemic infections. E. coli may also express DNA-damaging toxins that could impact cancer development. This review summarizes the different E. coli pathotypes in the context of their history, hosts, clinical signs, epidemiology, and control. The pathotypic characterization of E. coli in the context of disease in different animals, including humans, provides comparative and One Health perspectives that will guide future clinical and research investigations of E. coli infections.
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Key Words
- aa, aggregative adherence
- a/e, attaching and effacing
- aepec, atypical epec
- afa, afimbrial adhesin
- aida-i, adhesin involved in diffuse adherence
- aiec, adherent invasive e. coli
- apec, avian pathogenic e. coli
- atcc, american type culture collection
- bfp, bundle-forming pilus
- cd, crohn disease
- cdt, cytolethal distending toxin gene
- clb, colibactin
- cnf, cytotoxic necrotizing factor
- cs, coli surface (antigens)
- daec, diffusely adhering e. coli
- db, dutch belted
- eae, e. coli attaching and effacing gene
- eaec, enteroaggregative e. coli
- eaf, epec adherence factor (plasmid)
- eahec, entero-aggregative-hemorrhagic e. coli
- east-1, enteroaggregative e. coli heat-stable enterotoxin
- e. coli, escherichia coli
- ed, edema disease
- ehec, enterohemorrhagic e. coli
- eiec, enteroinvasive e. coli
- epec, enteropathogenic e. coli
- esbl, extended-spectrum β-lactamase
- esp, e. coli secreted protein
- etec, enterotoxigenic e. coli
- expec, extraintestinal pathogenic e. coli
- fyua, yersiniabactin receptor gene
- gi, gastrointestinal
- hly, hemolysin
- hus, hemolytic uremic syndrome
- ibd, inflammatory bowel disease
- la, localized adherence
- lee, locus of enterocyte effacement
- lpf, long polar fimbriae
- lt, heat-labile (enterotoxin)
- mlst, multilocus sequence typing
- ndm, new delhi metallo-β-lactamase
- nzw, new zealand white
- pap, pyelonephritis-associated pilus
- pks, polyketide synthase
- sfa, s fimbrial adhesin
- slt, shiga-like toxin
- st, heat-stable (enterotoxin)
- stec, stx-producing e. coli
- stx, shiga toxin
- tepec, typical epec
- upec, uropathogenic e. coli
- uti, urinary tract infection
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Affiliation(s)
- Alexis García
- Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts; Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts;,
| | - James G Fox
- Division of Comparative Medicine, Massachusetts Institute of Technology, Cambridge, Massachusetts
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Hou X, Perepelov AV, Guo X, Senchenkova SN, Shashkov AS, Liu B, Knirel YA, Wang L. A gene cluster at an unusual chromosomal location responsible for the novel O-antigen synthesis in Escherichia coli O62 by the ABC transporter-dependent pathway. Glycobiology 2018; 27:669-676. [PMID: 28402541 DOI: 10.1093/glycob/cwx030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 04/02/2017] [Indexed: 12/31/2022] Open
Abstract
The O-antigen is a part of the outer membrane of Gram-negative bacteria and is related to bacterial virulence. It is one of the most variable cell constituents, and its structural diversity is almost entirely due to genetic variation of the O-antigen gene cluster. In this study, the O-antigen structure of Escherichia coli O62 was elucidated by chemical analysis and nuclear magnetic resonance spectroscopy, but showing not consistent with the O-antigen gene cluster between conserved genes galF and gnd reported earlier. The complete genome of E. coli O62 was then sequenced and analyzed, and another O-antigen gene cluster was found and characterized that correlated perfectly with the established O-antigen structure. A deletion and complementation experiment confirmed the functionality of the novel gene cluster and demonstrated that the O62-antigen is synthesized by the ABC transporter-dependent system. To our knowledge, this is the first report that the O-antigen gene cluster is positioned at a novel locus in E. coli. Comparative analysis indicated that E. coli O62 likely originated from E. coli O68 via an IS event resulting in the repression of the O68-antigen synthesis, followed by the acquisition of a novel O-antigen gene cluster from Enterobacter aerogenes.
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Affiliation(s)
- Xi Hou
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, PR China
| | - Andrei V Perepelov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskii Prospekt 47, 119991 Moscow, Russia
| | - Xi Guo
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, PR China
| | - Sof'ya N Senchenkova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskii Prospekt 47, 119991 Moscow, Russia
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskii Prospekt 47, 119991 Moscow, Russia
| | - Bin Liu
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, PR China
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Leninskii Prospekt 47, 119991 Moscow, Russia
| | - Lei Wang
- TEDA Institute of Biological Sciences and Biotechnology, Nankai University, 23 Hongda Street, TEDA, Tianjin 300457, PR China.,The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, 23 Hongda Street, TEDA, Tianjin 300457, PR China
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Abstract
AbstractO-antigens present on the surface ofEscherichia coliprovide antigenic specificity for the strain and are the main components for O-serogroup designation. Serotyping using O-group-specific antisera for the identification ofE. coliO-serogroups has been traditionally the gold-standard for distinguishingE. colistrains. Knowledge of the O-group is important for determining pathogenic lineage, classifyingE. colifor epidemiological studies, for determining virulence, and for tracing outbreaks of diseases and sources of infection. However, serotyping has limitations, as the antisera generated against each specific O-group may cross-react, many strains are non-typeable, and others can autoagglutinate or be rough (lacking an O-antigen). Currently, the nucleotide sequences are available for most of the 187 designatedE. coliO-groups. Public health and other laboratories are considering whole genome sequencing to develop genotypic methods to determine O-groups. These procedures require instrumentation and analysis that may not be accessible and may be cost-prohibitive at this time. In this review, we have identified unique gene sequences within the O-antigen gene clusters and have targeted these genes for identification of O-groups using the polymerase chain reaction. This information can be used to distinguish O-groups by developing other platforms forE. colidiagnostics in the future.
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Phenotypic H-Antigen Typing by Mass Spectrometry Combined with Genetic Typing of H Antigens, O Antigens, and Toxins by Whole-Genome Sequencing Enhances Identification of Escherichia coli Isolates. J Clin Microbiol 2016; 54:2162-8. [PMID: 27307455 PMCID: PMC4963523 DOI: 10.1128/jcm.00422-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 06/06/2016] [Indexed: 11/20/2022] Open
Abstract
Mass spectrometry-based phenotypic H-antigen typing (MS-H) combined with whole-genome-sequencing-based genetic identification of H antigens, O antigens, and toxins (WGS-HOT) was used to type 60 clinical Escherichia coli isolates, 43 of which were previously identified as nonmotile, H type undetermined, or O rough by serotyping or having shown discordant MS-H and serotyping results. Whole-genome sequencing confirmed that MS-H was able to provide more accurate data regarding H antigen expression than serotyping. Further, enhanced and more confident O antigen identification resulted from gene cluster based typing in combination with conventional typing based on the gene pair comprising wzx and wzy and that comprising wzm and wzt The O antigen was identified in 94.6% of the isolates when the two genetic O typing approaches (gene pair and gene cluster) were used in conjunction, in comparison to 78.6% when the gene pair database was used alone. In addition, 98.2% of the isolates showed the existence of genes for various toxins and/or virulence factors, among which verotoxins (Shiga toxin 1 and/or Shiga toxin 2) were 100% concordant with conventional PCR based testing results. With more applications of mass spectrometry and whole-genome sequencing in clinical microbiology laboratories, this combined phenotypic and genetic typing platform (MS-H plus WGS-HOT) should be ideal for pathogenic E. coli typing.
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Fratamico PM, DebRoy C, Liu Y, Needleman DS, Baranzoni GM, Feng P. Advances in Molecular Serotyping and Subtyping of Escherichia coli. Front Microbiol 2016; 7:644. [PMID: 27199968 PMCID: PMC4853403 DOI: 10.3389/fmicb.2016.00644] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/18/2016] [Indexed: 01/25/2023] Open
Abstract
Escherichia coli plays an important role as a member of the gut microbiota; however, pathogenic strains also exist, including various diarrheagenic E. coli pathotypes and extraintestinal pathogenic E. coli that cause illness outside of the GI-tract. E. coli have traditionally been serotyped using antisera against the ca. 186 O-antigens and 53 H-flagellar antigens. Phenotypic methods, including bacteriophage typing and O- and H- serotyping for differentiating and characterizing E. coli have been used for many years; however, these methods are generally time consuming and not always accurate. Advances in next generation sequencing technologies have made it possible to develop genetic-based subtyping and molecular serotyping methods for E. coli, which are more discriminatory compared to phenotypic typing methods. Furthermore, whole genome sequencing (WGS) of E. coli is replacing established subtyping methods such as pulsed-field gel electrophoresis, providing a major advancement in the ability to investigate food-borne disease outbreaks and for trace-back to sources. A variety of sequence analysis tools and bioinformatic pipelines are being developed to analyze the vast amount of data generated by WGS and to obtain specific information such as O- and H-group determination and the presence of virulence genes and other genetic markers.
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Affiliation(s)
- Pina M. Fratamico
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Chitrita DebRoy
- Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University ParkPA, USA
| | - Yanhong Liu
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - David S. Needleman
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Gian Marco Baranzoni
- Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, WyndmoorPA, USA
| | - Peter Feng
- Division of Microbiology, U.S. Food and Drug Administration, College ParkMD, USA
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DebRoy C, Fratamico PM, Yan X, Baranzoni G, Liu Y, Needleman DS, Tebbs R, O'Connell CD, Allred A, Swimley M, Mwangi M, Kapur V, Raygoza Garay JA, Roberts EL, Katani R. Comparison of O-Antigen Gene Clusters of All O-Serogroups of Escherichia coli and Proposal for Adopting a New Nomenclature for O-Typing. PLoS One 2016; 11:e0147434. [PMID: 26824864 PMCID: PMC4732683 DOI: 10.1371/journal.pone.0147434] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 01/03/2016] [Indexed: 01/27/2023] Open
Abstract
Escherichia coli strains are classified based on O-antigens that are components of the lipopolysaccharide (LPS) in the cell envelope. O-antigens are important virulence factors, targets of both the innate and adaptive immune system, and play a role in host-pathogen interactions. Because they are highly immunogenic and display antigenic specificity unique for each strain, O-antigens are the biomarkers for designating O-types. Immunologically, 185 O-serogroups and 11 OX-groups exist for classification. Conventional serotyping for O-typing entails agglutination reactions between the O-antigen and antisera generated against each O-group. The procedure is labor intensive, not always accurate, and exhibits equivocal results. In this report, we present the sequences of 71 O-antigen gene clusters (O-AGC) and a comparison of all 196 O- and OX-groups. Many of the designated O-types, applied for classification over several decades, exhibited similar nucleotide sequences of the O-AGCs and cross-reacted serologically. Some O-AGCs carried insertion sequences and others had only a few nucleotide differences between them. Thus, based on these findings, it is proposed that several of the E. coli O-groups may be merged. Knowledge of the O-AGC sequences facilitates the development of molecular diagnostic platforms that are rapid, accurate, and reliable that can replace conventional serotyping. Additionally, with the scientific knowledge presented, new frontiers in the discovery of biomarkers, understanding the roles of O-antigens in the innate and adaptive immune system and pathogenesis, the development of glycoconjugate vaccines, and other investigations, can be explored.
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Affiliation(s)
- Chitrita DebRoy
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Pina M. Fratamico
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Xianghe Yan
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - GianMarco Baranzoni
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Yanhong Liu
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - David S. Needleman
- Eastern Regional Research Center, Agricultural Research Service, U.S. Department of Agriculture, Wyndmoor, Pennsylvania, United States of America
| | - Robert Tebbs
- Animal Health & Food Safety, Life Sciences Solutions, Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Catherine D. O'Connell
- Animal Health & Food Safety, Life Sciences Solutions, Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Adam Allred
- Animal Health & Food Safety, Life Sciences Solutions, Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Michelle Swimley
- Animal Health & Food Safety, Life Sciences Solutions, Thermo Fisher Scientific, Austin, Texas, United States of America
| | - Michael Mwangi
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Vivek Kapur
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Juan A. Raygoza Garay
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Elisabeth L. Roberts
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Robab Katani
- E. coli Reference Center, Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, University Park, Pennsylvania, United States of America
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Tajbakhsh E, Ahmadi P, Abedpour-Dehkordi E, Arbab-Soleimani N, Khamesipour F. Biofilm formation, antimicrobial susceptibility, serogroups and virulence genes of uropathogenic E. coli isolated from clinical samples in Iran. Antimicrob Resist Infect Control 2016; 5:11. [PMID: 27042294 PMCID: PMC4818419 DOI: 10.1186/s13756-016-0109-4] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 03/21/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Uropathogenic Escherichia coli O- Serogroups with their virulence factors are the most prevalent causes of UTIs. The present research performed to track common uropathogenic E.coli serogroups, antibiotic resistance pattern of strains and prevalence of virulence genes in isolations having the ability to constitute biofilm. METHODS In this research 130 E.coli isolation from patients having UTI symptoms were collected and antimicrobial resistance pattern was performed by Kirby-Bauer method. Polymerase chain reaction was done using primer pairs to identify common serogroups of uropathogenic E.coli and studying virulence genes in isolations creating biofilm. RESULTS Among 130 E.coli isolates, 80 (61.53 %) were able to make biofilm that 15 isolates (18.75 %) indicated strong reaction, 20 (25 %) of medium and 45 (56.25 %) of weak biofilm reaction. Among isolations creating biofilm, the highest resistance reported to Ampicillin (87.5 %) and the lowest to Nitrofurantoin (3.75 %). The frequency of fimH, pap, sfa and afa genes in isolations having the ability to create strong biofilm reported 93.33 %, 86.66 %, 86.66 % and 66.66 %, respectively. CONCLUSIONS The findings indicated the importance of virulence genes in serogroups producing uropathogenic E.coli biofilm. It is recommended that strains producing biofilm before antibiotic use should be studied.
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Affiliation(s)
- Elahe Tajbakhsh
- Department of Microbiology, Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | - Parvin Ahmadi
- Faculty of Basic Sciences, Shahrekord Branch, Islamic Azad University, Shahrekord, Iran
| | | | | | - Faham Khamesipour
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
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