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Nenninger EK, Geffert S, Charla S, Chou C, Uzun EDG, Sawyer D, Badeel R, Chargualaf T, Almaghlouth NK, Hong T. Recurrent joint infection caused by a multidrug-resistant capnophilic Escherichia coli ST131 O25H4 strain. IDCases 2024; 36:e01976. [PMID: 38690577 PMCID: PMC11059453 DOI: 10.1016/j.idcr.2024.e01976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/16/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
We report a case of a native knee septic arthritis and subsequent osteomyelitis due to a CO2-dependent (capnophilic) multidrug-resistant E. coli ST131 O25:H4 strain. Capnophilic phenotype made microbiology investigation challenging; susceptibility testing could not be performed and the organism did not grow in the urine culture using standard method. The combination of unique virotype and capnophilia may have contributed to the aggressiveness of this organism and the initial unsuccessful carbapenem course, leading to recurrent infection.
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Affiliation(s)
| | - Sara Geffert
- Brown Medicine Division of Infectious Diseases, Rhode Island Hospital, Providence, RI 02903, USA
- Microbiology Laboratory, Rhode Island Hospital, Providence, RI 02903, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI 02903, USA
- Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI 02903, USA
| | - Swapna Charla
- Microbiology Laboratory, Rhode Island Hospital, Providence, RI 02903, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI 02903, USA
| | - Charissa Chou
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI 02903, USA
| | - Ece Dilber Gamsiz Uzun
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI 02903, USA
- Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI 02903, USA
- Center for Computational Molecular Biology, Brown University, Providence, RI 02906, USA
| | - Deborah Sawyer
- Microbiology Laboratory, Rhode Island Hospital, Providence, RI 02903, USA
| | - Rozeen Badeel
- Microbiology Laboratory, Rhode Island Hospital, Providence, RI 02903, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI 02903, USA
| | - Tiffany Chargualaf
- Microbiology Laboratory, Rhode Island Hospital, Providence, RI 02903, USA
| | - Nouf K. Almaghlouth
- Brown Medicine Division of Infectious Diseases, Rhode Island Hospital, Providence, RI 02903, USA
| | - Tao Hong
- Microbiology Laboratory, Rhode Island Hospital, Providence, RI 02903, USA
- Department of Pathology and Laboratory Medicine, Rhode Island Hospital, Providence, RI 02903, USA
- Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Providence, RI 02903, USA
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2
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Yescas-Zazueta V, Rocha-Gracia RDC, González-Bonilla CR, Ayala-Zavala JF, Enciso-Martínez Y, Carreón-León EA, González Corona BA, Valencia D, Ballesteros-Monrreal MG, Barrios-Villa E. Resistance phenotype and virulence potential of Leclercia adecarboxylata strains isolated from different sources. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001457. [PMID: 38661713 PMCID: PMC11084626 DOI: 10.1099/mic.0.001457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 04/16/2024] [Indexed: 04/26/2024]
Abstract
Introduction. Leclercia adecarboxylata is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted L. adecarboxylata as an emerging pathogen harbouring virulence and resistance determinants.Gap statement. Little information exists on virulence and resistance determinants in L. adecarboxylata strains isolated from environmental, food, and clinical samples.Aim. To determine the presence of resistance and virulence determinants and plasmid features in L. adecarboxylata strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship.Results. All strains tested showed resistance to β-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of L. adecarboxylata, the resistance phenotype was only observed in 50 % of the strains; bla TEM was the most prevalent BLEE gene (70 %), while the quinolone qnrB gene was observed in 60 % of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80 % of the strains.Conclusions. L. adecarboxylata is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.
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Affiliation(s)
- Viviana Yescas-Zazueta
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Rosa del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
| | - Cesar R. González-Bonilla
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
| | - J. Fernando Ayala-Zavala
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C., 83304 Hermosillo, Mexico
| | - Yessica Enciso-Martínez
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
- Coordinación de Tecnología de Alimentos de Origen Vegetal, Centro de Investigación en Alimentación y Desarrollo, A.C., 83304 Hermosillo, Mexico
| | - Eder A. Carreón-León
- Laboratorio de Análisis Clínicos de la Universidad Autónoma de Chihuahua, Av. Universidad S/N, Circuito Universitario Campus 1, 31310 Chihuahua, Mexico
| | - Brigitte A. González Corona
- Laboratorio de Análisis Clínicos de la Universidad Autónoma de Chihuahua, Av. Universidad S/N, Circuito Universitario Campus 1, 31310 Chihuahua, Mexico
| | - Dora Valencia
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Manuel G. Ballesteros-Monrreal
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
| | - Edwin Barrios-Villa
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, campus Caborca, Av. Universidad e Irigoyen S/N, 83621 H. Caborca, Sonora, Mexico
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, 72570 Puebla, Mexico
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Castañeda-Meléndrez AM, Magaña-Lizárraga JA, Martínez-Valenzuela M, Clemente-Soto AF, García-Cervantes PC, Delgado-Vargas F, Bernal-Reynaga R. Genomic characterization of a multidrug-resistant uropathogenic Escherichia coli and evaluation of Echeveria plant extracts as antibacterials. AIMS Microbiol 2024; 10:41-61. [PMID: 38525046 PMCID: PMC10955171 DOI: 10.3934/microbiol.2024003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/10/2024] [Indexed: 03/26/2024] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common bacterial agent associated with urinary tract infections, threatening public health systems with elevated medical costs and high morbidity rates. The successful establishment of the infection is associated with virulence factors encoded in its genome, in addition to antibacterial resistance genes, which could limit the treatment and resolution of the infection. In this sense, plant extracts from the genus Echeveria have traditionally been used to treat diverse infectious diseases. However, little is known about the effects of these extracts on bacteria and their potential mechanisms of action. This study aims to sequence a multidrug-resistant UPEC isolate (UTI-U7) and assess the multilocus sequence typing (MLST), virulence factors, antimicrobial resistance profile, genes, serotype, and plasmid content. Antimicrobial susceptibility profiling was performed using the Kirby-Bauer disk diffusion. The antibacterial and anti-adherent effects of the methanol extracts (ME) of Echeveria (E. craigiana, E. kimnachii, and E. subrigida) against UTI-U7 were determined. The isolate was characterized as an O25:H4-B2-ST2279-CH40 subclone and had resistant determinants to aminoglycosides, β-lactams, fluoroquinolones/quinolones, amphenicols, and tetracyclines, which matched with the antimicrobial resistance profile. The virulence genes identified encode adherence factors, iron uptake, protectins/serum resistance, and toxins. Identified plasmids belonged to the IncF group (IncFIA, IncFIB, and IncFII), alongside several prophage-like elements. After an extensive genome analysis that confirmed the pathogenic status of UTI-U7 isolate, Echeveria extracts were tested to determine their antibacterial effects; as an extract, E. subrigida (MIC, 5 mg/mL) displayed the best inhibitory effect. However, the adherence between UTI-U7 and HeLa cells was unaffected by the ME of the E. subrigida extract.
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Affiliation(s)
| | | | | | | | | | | | - Rodolfo Bernal-Reynaga
- Unidad de Investigaciones en Salud Pública “Dra. Kaethe Willms”, Facultad de Ciencias Químico-Biológicas. Universidad Autónoma de Sinaloa. Ciudad Universitaria, Culiacán, Sinaloa, México
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Balbuena-Alonso MG, Camps M, Cortés-Cortés G, Carreón-León EA, Lozano-Zarain P, Rocha-Gracia RDC. Strain belonging to an emerging, virulent sublineage of ST131 Escherichia coli isolated in fresh spinach, suggesting that ST131 may be transmissible through agricultural products. Front Cell Infect Microbiol 2023; 13:1237725. [PMID: 37876872 PMCID: PMC10591226 DOI: 10.3389/fcimb.2023.1237725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/15/2023] [Indexed: 10/26/2023] Open
Abstract
Food contamination with pathogenic Escherichia coli can cause severe disease. Here, we report the isolation of a multidrug resistant strain (A23EC) from fresh spinach. A23EC belongs to subclade C2 of ST131, a virulent clone of Extraintestinal Pathogenic E. coli (ExPEC). Most A23EC virulence factors are concentrated in three pathogenicity islands. These include PapGII, a fimbrial tip adhesin linked to increased virulence, and CsgA and CsgB, two adhesins known to facilitate spinach leaf colonization. A23EC also bears TnMB1860, a chromosomally-integrated transposon with the demonstrated potential to facilitate the evolution of carbapenem resistance among non-carbapenemase-producing enterobacterales. This transposon consists of two IS26-bound modular translocatable units (TUs). The first TU carries aac(6')-lb-cr, bla OXA-1, ΔcatB3, aac(3)-lle, and tmrB, and the second one harbors bla CXT-M-15. A23EC also bears a self-transmissible plasmid that can mediate conjugation at 20°C and that has a mosaic IncF [F(31,36):A(4,20):B1] and Col156 origin of replication. Comparing A23EC to 86 additional complete ST131 sequences, A23EC forms a monophyletic cluster with 17 other strains that share the following four genomic traits: (1) virotype E (papGII+); (2) presence of a PAI II536-like pathogenicity island with an additional cnf1 gene; (3) presence of chromosomal TnMB1860; and (4) frequent presence of an F(31,36):A(4,20):B1 plasmid. Sequences belonging to this cluster (which we named "C2b sublineage") are highly enriched in septicemia samples and their associated genetic markers align with recent reports of an emerging, virulent sublineage of the C2 subclade, suggesting significant pathogenic potential. This is the first report of a ST131 strain belonging to subclade C2 contaminating green leafy vegetables. The detection of this uropathogenic clone in fresh food is alarming. This work suggests that ST131 continues to evolve, gaining selective advantages and new routes of transmission. This highlights the pressing need for rigorous epidemiological surveillance of ExPEC in vegetables with One Health perspective.
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Affiliation(s)
- Maria G. Balbuena-Alonso
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Manel Camps
- Departament of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Gerardo Cortés-Cortés
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
- Departament of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA, United States
| | - Eder A. Carreón-León
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Chihuahua, Mexico
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Rosa del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
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Aljohani RH, ElFeky DS, Alswaji AA, Alrashidi E, Okdah L, Alalwan B, Aljohani SM, Balkhy HH, Redhwan A, Alghoribi MF. Genomic Characterization of Uropathogenic Escherichia coli Isolates from Tertiary Hospitals in Riyadh, Saudi Arabia. Int J Mol Sci 2023; 24:7582. [PMID: 37108743 PMCID: PMC10141978 DOI: 10.3390/ijms24087582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 04/29/2023] Open
Abstract
Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infections (UTIs) in hospitalised and non-hospitalised patients. Genomic analysis was used to gain further insight into the molecular characteristics of UPEC isolates from Saudi Arabia. A total of 165 isolates were collected from patients with UTIs between May 2019 and September 2020 from two tertiary hospitals in Riyadh, Saudi Arabia. Identification and antimicrobial susceptibility testing (AST) were performed using the VITEK system. Extended-spectrum β-lactamase (ESBL)-producing isolates (n = 48) were selected for whole genome sequencing (WGS) analysis. In silico analysis revealed that the most common sequence types detected were ST131 (39.6%), ST1193 (12.5%), ST73 (10.4%), and ST10 (8.3%). Our finding showed that blaCTX-M-15 gene was detected in the majority of ESBL isolates (79.2%), followed by blaCTX-M-27 (12.5%) and blaCTX-M-8 (2.1%). ST131 carried blaCTX-M-15 or blaCTX-M-27, and all ST73 and ST1193 carried blaCTX-M-15. The relatively high proportion of ST1193 in this study was notable as a newly emerged lineage in the region, which warrants further monitoring.
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Affiliation(s)
- Rawan H. Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Dalia S. ElFeky
- Department of Basic Medical Sciences, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo 12613, Egypt
| | - Abdulrahman A. Alswaji
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Eisa Alrashidi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Liliane Okdah
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
| | - Bassam Alalwan
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
| | - Sameera M. Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
| | | | - Alya Redhwan
- Department of Health, College of Health and Rehabilitation Sciences, Princess Nourah bint Abdulrahman University, Riyadh 11564, Saudi Arabia
| | - Majed F. Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh 11481, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh 11426, Saudi Arabia
- Department of Basic Science, College of Science and Health Professions, King Saud bin Abdulaziz University for Health Sciences, Riyadh 14611, Saudi Arabia
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Méndez-Moreno E, Caporal-Hernandez L, Mendez-Pfeiffer PA, Enciso-Martinez Y, De la Rosa López R, Valencia D, Arenas-Hernández MMP, Ballesteros-Monrreal MG, Barrios-Villa E. Characterization of Diarreaghenic Escherichia coli Strains Isolated from Healthy Donors, including a Triple Hybrid Strain. Antibiotics (Basel) 2022; 11:833. [PMID: 35884087 PMCID: PMC9312309 DOI: 10.3390/antibiotics11070833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/19/2022] [Accepted: 06/20/2022] [Indexed: 12/10/2022] Open
Abstract
Escherichia coli is a well-recognized inhabitant of the animal and human gut. Its presence represents an essential component of the microbiome. There are six pathogenic variants of E. coli associated with diarrheal processes, known as pathotypes. These harbor genetic determinants that allow them to be classified as such. In this work, we report the presence of diarrheagenic pathotypes of E. coli strains isolated from healthy donors. Ninety E. coli strains were analyzed, of which forty-six (51%) harbored virulence markers specifics for diarrheagenic pathotypes, including four hybrids (one of them with genetic determinants of three DEC pathotypes). We also identified phylogenetic groups with a higher prevalence of B2 (45.6%) and A (17.8%). In addition, resistance to sulfonamides (100%), and aminoglycosides (100%) was found in 100% of the strains, with a lower prevalence of resistance to cefotaxime (13.3%), ceftriaxone (12.2%), fosfomycin (10%), and meropenem (0%). All analyzed strains were classified as multidrug resistant. Virulence genes were also investigated, which led us to propose three new virotypes. Among the virulence traits observed, the ability to form biofilms stands out, which was superior to that of the E. coli and Staphylococcus aureus strains used as positive controls.
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Affiliation(s)
- Evelyn Méndez-Moreno
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Liliana Caporal-Hernandez
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Pablo A. Mendez-Pfeiffer
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Yessica Enciso-Martinez
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Rafael De la Rosa López
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Dora Valencia
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Margarita M. P. Arenas-Hernández
- Posgrado en Microbiología, Centro de Investigación en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Puebla CP 72570, Pue, Mexico;
| | - Manuel G. Ballesteros-Monrreal
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
| | - Edwin Barrios-Villa
- Departamento de Ciencias Químico Biológicas y Agropecuarias, Universidad de Sonora, Unidad Regional Norte, Campus Caborca. Av. Universidad e Irigoyen S/N, col. Eleazar Ortiz, H. Caborca CP 83621, Sonora, Mexico; (E.M.-M.); (L.C.-H.); (P.A.M.-P.); (Y.E.-M.); (R.D.l.R.L.); (D.V.)
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7
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Liu X, Li X, Yang AW, Tang B, Jian ZJ, Zhong YM, Li HL, Li YM, Yan Q, Liang XH, Liu WE. Community Fecal Carriage and Molecular Epidemiology of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Escherichia coli from Healthy Children in the Central South China. Infect Drug Resist 2022; 15:1601-1611. [PMID: 35418762 PMCID: PMC8995156 DOI: 10.2147/idr.s357090] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 03/26/2022] [Indexed: 12/25/2022] Open
Affiliation(s)
- Xuan Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Xin Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - A-Wen Yang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Bin Tang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Zi-Juan Jian
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yi-Ming Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Hong-Ling Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Yan-Ming Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Xiang-Hui Liang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, People's Republic of China
| | - Wen-En Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan Province, People's Republic of China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, People's Republic of China
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8
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Bacterial Morphotypes as Important Trait for Uropathogenic E. coli Diagnostic; a Virulence-Phenotype-Phylogeny Study. Microorganisms 2021; 9:microorganisms9112381. [PMID: 34835506 PMCID: PMC8621242 DOI: 10.3390/microorganisms9112381] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 11/21/2022] Open
Abstract
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.
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9
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Hernández-Chiñas U, Chávez-Berrocal ME, Ahumada-Cota RE, Navarro-Ocaña A, Rocha-Ramírez LM, Pérez-del Mazo Y, Alvarado-Cabello M, Pérez-Soto G, León-Alamilla LA, Acevedo-Monroy SE, Esquiliano D, Raya-Rivera AM, Eslava CA. Prospective Study in Children with Complicated Urinary Tract Infection Treated with Autologous Bacterial Lysates. Microorganisms 2021; 9:1811. [PMID: 34576707 PMCID: PMC8470462 DOI: 10.3390/microorganisms9091811] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/21/2021] [Accepted: 08/11/2021] [Indexed: 12/22/2022] Open
Abstract
Antimicrobial bacteria resistance is an important problem in children with recurrent urinary tract infections (rUTI), thus it is crucial to search for alternative therapies. Autologous bacterial lysates (ABL) may be a potential treatment for rUTI. Twenty-seven children with rUTI were evaluated for one year, urine and stool cultures were performed, 10 colonies of each culture were selected and those identified as Escherichia coli were characterized by serology. For patients who presented ≥105 UFC/mL, an ABL was manufactured and administered orally (1 mL/day) for a month. Twelve children were monitored for ≥1-year, 218 urine and 11 stool samples were analyzed. E. coli (80.5%) was the main bacteria isolated from urine and feces (72%). E. coli of classical urinary serotypes (UPEC), O25:H4, O75:HNM, and O9:HNM were identified in patients with persistent urinary infection (pUTI). In 54% of patients treated with ABL, the absence of bacteria was observed in urine samples after 3 months of treatment, 42% of these remained without UTI between 10-12 months. It was observed that the use of ABL controlled the infection for almost 1 year in more than 60% of the children. We consider it necessary to develop a polyvalent immunogen for the treatment and control of rUTI.
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Affiliation(s)
- Ulises Hernández-Chiñas
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public Health Department, Research Division, Faculty of Medicine Universidad Nacional Autónoma de México, Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico; (U.H.-C.); (M.E.C.-B.); (R.E.A.-C.); (S.E.A.-M.)
| | - María E. Chávez-Berrocal
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public Health Department, Research Division, Faculty of Medicine Universidad Nacional Autónoma de México, Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico; (U.H.-C.); (M.E.C.-B.); (R.E.A.-C.); (S.E.A.-M.)
| | - Ricardo E. Ahumada-Cota
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public Health Department, Research Division, Faculty of Medicine Universidad Nacional Autónoma de México, Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico; (U.H.-C.); (M.E.C.-B.); (R.E.A.-C.); (S.E.A.-M.)
| | - Armando Navarro-Ocaña
- Bacteriology Laboratory, Public Health Department, Faculty of Medicine, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Mexico City 04510, Mexico; (A.N.-O.); (G.P.-S.); (L.A.L.-A.)
| | - Luz M. Rocha-Ramírez
- Unidad de Investigación en Enfermedades Infeccionas, Hospital Infantil de México Federico Gómez, Secretaría de Salud, Dr. Márquez 162, Col. Doctores, Mexico City 06720, Mexico;
| | - Yolanda Pérez-del Mazo
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Faculty of Medicine Universidad Nacional Autónoma de México, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico; (Y.P.-d.M.); (M.A.-C.)
| | - Maribel Alvarado-Cabello
- Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Faculty of Medicine Universidad Nacional Autónoma de México, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico; (Y.P.-d.M.); (M.A.-C.)
| | - Gabriel Pérez-Soto
- Bacteriology Laboratory, Public Health Department, Faculty of Medicine, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Mexico City 04510, Mexico; (A.N.-O.); (G.P.-S.); (L.A.L.-A.)
| | - Luis A. León-Alamilla
- Bacteriology Laboratory, Public Health Department, Faculty of Medicine, Universidad Nacional Autónoma de México, Avenida Universidad 3000, Ciudad Universitaria, Mexico City 04510, Mexico; (A.N.-O.); (G.P.-S.); (L.A.L.-A.)
| | - Salvador E. Acevedo-Monroy
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public Health Department, Research Division, Faculty of Medicine Universidad Nacional Autónoma de México, Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico; (U.H.-C.); (M.E.C.-B.); (R.E.A.-C.); (S.E.A.-M.)
| | - Diego Esquiliano
- Tissue Engineering Laboratory, Children’s Hospital of Mexico Federico Gómez, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico;
| | - Atlántida M. Raya-Rivera
- Tissue Engineering Laboratory, Children’s Hospital of Mexico Federico Gómez, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico;
| | - Carlos A. Eslava
- Peripheral Unit of Basic and Clinical Research in Infectious Diseases, Public Health Department, Research Division, Faculty of Medicine Universidad Nacional Autónoma de México, Bacterial Pathogenicity Laboratory, Hemato-Oncology and Research Unit, Children’s Hospital of Mexico Federico Gómez, Dr. Márquez 162, Col. De los Doctores, Mexico City 06720, Mexico; (U.H.-C.); (M.E.C.-B.); (R.E.A.-C.); (S.E.A.-M.)
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10
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Findlay J, Gould VC, North P, Bowker KE, Williams MO, MacGowan AP, Avison MB. Characterization of cefotaxime-resistant urinary Escherichia coli from primary care in South-West England 2017-18. J Antimicrob Chemother 2021; 75:65-71. [PMID: 31538190 DOI: 10.1093/jac/dkz397] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 08/06/2019] [Accepted: 08/22/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Third-generation cephalosporin-resistant Escherichia coli from community-acquired urinary tract infections are increasingly reported worldwide. We sought to determine and characterize the mechanisms of cefotaxime resistance employed by urinary E. coli obtained from primary care, over 12 months, in Bristol and surrounding counties in South-West England. METHODS Cefalexin-resistant E. coli isolates were identified from GP-referred urine samples using disc susceptibility testing. Cefotaxime resistance was determined by subsequent plating onto MIC breakpoint plates. β-Lactamase genes were detected by PCR. WGS was performed on 225 isolates and analyses were performed using the Center for Genomic Epidemiology platform. Patient information provided by the referring general practices was reviewed. RESULTS Cefalexin-resistant E. coli (n=900) isolates were obtained from urines from 146 general practices. Following deduplication by patient approximately 69% (576/836) of isolates were cefotaxime resistant. WGS of 225 isolates identified that the most common cefotaxime-resistance mechanism was blaCTX-M carriage (185/225), followed by plasmid-mediated AmpCs (pAmpCs) (17/225), AmpC hyperproduction (13/225), ESBL blaSHV variants (6/225) or a combination of both blaCTX-M and pAmpC (4/225). Forty-four STs were identified, with ST131 representing 101/225 isolates, within which clade C2 was dominant (54/101). Ciprofloxacin resistance was observed in 128/225 (56.9%) of sequenced isolates, predominantly associated with fluoroquinolone-resistant clones ST131 and ST1193. CONCLUSIONS Most cefalexin-resistant E. coli isolates were cefotaxime resistant, predominantly caused by blaCTX-M carriage. The correlation between cefotaxime resistance and ciprofloxacin resistance was largely attributable to the high-risk pandemic clones ST131 and ST1193. Localized epidemiological data provide greater resolution than regional data and can be valuable for informing treatment choices in the primary care setting.
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Affiliation(s)
- Jacqueline Findlay
- School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
| | - Virginia C Gould
- School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
| | - Paul North
- Department of Infection Sciences, Severn Infection Partnership, Southmead Hospital, Bristol, UK
| | - Karen E Bowker
- Department of Infection Sciences, Severn Infection Partnership, Southmead Hospital, Bristol, UK
| | - Martin O Williams
- Department of Infection Sciences, Severn Infection Partnership, Southmead Hospital, Bristol, UK
| | - Alasdair P MacGowan
- Department of Infection Sciences, Severn Infection Partnership, Southmead Hospital, Bristol, UK
| | - Matthew B Avison
- School of Cellular & Molecular Medicine, Biomedical Sciences Building, University of Bristol, University Walk, Bristol, UK
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11
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Braz VS, Melchior K, Moreira CG. Escherichia coli as a Multifaceted Pathogenic and Versatile Bacterium. Front Cell Infect Microbiol 2020; 10:548492. [PMID: 33409157 PMCID: PMC7779793 DOI: 10.3389/fcimb.2020.548492] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 11/17/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic plasticity promotes evolution and a vast diversity in Escherichia coli varying from avirulent to highly pathogenic strains, including the emergence of virulent hybrid microorganism. This ability also contributes to the emergence of antimicrobial resistance. These hybrid pathogenic E. coli (HyPEC) are emergent threats, such as O104:H4 from the European outbreak in 2011, aggregative adherent bacteria with the potent Shiga-toxin. Here, we briefly revisited the details of these E. coli classic and hybrid pathogens, the increase in antimicrobial resistance in the context of a genetically empowered multifaceted and versatile bug and the growing need to advance alternative therapies to fight these infections.
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Affiliation(s)
- Vânia Santos Braz
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Karine Melchior
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
| | - Cristiano Gallina Moreira
- Department of Biological Sciences, School of Pharmaceutical Sciences, São Paulo State University (UNESP), Araraquara, Brazil
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12
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Tavares RDS, Tacão M, Figueiredo AS, Duarte AS, Esposito F, Lincopan N, Manaia CM, Henriques I. Genotypic and phenotypic traits of bla CTX-M-carrying Escherichia coli strains from an UV-C-treated wastewater effluent. WATER RESEARCH 2020; 184:116079. [PMID: 32717492 DOI: 10.1016/j.watres.2020.116079] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 06/11/2023]
Abstract
Wastewater treatment plants (WWTPs) are relevant sources of antibiotic resistance into aquatic environments. Disinfection of WWTPs' effluents (e.g. by UV-C irradiation) may attenuate this problem, though some clinically relevant bacteria have been shown to survive disinfection. In this study we characterized 25 CTX-M-producing Escherichia coli strains isolated from a WWTP's UV-C-irradiated effluent, aiming to identify putative human health hazards associated with such effluents. Molecular typing indicated that the strains belong to the phylogroups A, B2 and C and clustered into 9 multilocus sequence types (STs), namely B2:ST131 (n = 7), A:ST58 (n = 1), A:ST155 (n = 4), C:ST410 (n = 2), A:ST453 (n = 2), A:ST617 (n = 2), A:ST744 (n = 1), A:ST1284 (n = 3) and a putative novel ST (n = 3). PCR-screening identified 9 of the 20 antibiotic resistance genes investigated [i.e. sul1, sul2, sul3, tet(A), tet(B), blaOXA-1-like, aacA4, aacA4-cr and qnrS1]. The more prevalent were sul1, sul2 (n = 15 isolates) and tet(A) (n = 14 isolates). Plasmid restriction analysis indicated diverse plasmid content among strains (14 distinct profiles) and mating assays yielded cefotaxime-resistant transconjugants for 8 strains. Two of the transconjugants displayed a multi-drug resistance (MDR) phenotype. All strains were classified as cytotoxic to Vero cells (9 significantly more cytotoxic than the positive control) and 10 of 21 strains were invasive towards this cell line (including all B2:ST131 strains). The 10 strains tested against G. mellonella larvae exhibited a virulent behaviour. Twenty-four and 7 of the 25 strains produced siderophores and haemolysins, respectively. Approximately 66% of the strains formed biofilms. Genome analysis of 6 selected strains identified several virulence genes encoding toxins, siderophores, and colonizing, adhesion and invasion factors. Freshwater microcosms assays showed that after 28 days of incubation 3 out of 6 strains were still detected by cultivation and 4 strains by qPCR. Resistance phenotypes of these strains remained unaltered. Overall, we confirmed WWTP's UV-C-treated outflow as a source of MDR and/or virulent E. coli strains, some probably capable of persisting in freshwater, and that carry conjugative antibiotic resistance plasmids. Hence, disinfected wastewater may still represent a risk for human health. More detailed evaluation of strains isolated from wastewater effluents is urgent, to design treatments that can mitigate the release of such bacteria.
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Affiliation(s)
- Rafael D S Tavares
- Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal; Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Marta Tacão
- Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal; Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal.
| | - Ana S Figueiredo
- Department of Biology, University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal
| | - Ana S Duarte
- Universidade Católica Portuguesa, Faculdade de Medicina Dentária, Centro de Investigação Interdisciplinar Em Saúde (CIIS), Estrada da Circunvalação, 3504-505, Viseu, Portugal
| | - Fernanda Esposito
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil; Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina, Laboratório Associado, Escola Superior de Biotecnologia, Rua de Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Isabel Henriques
- Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Campus Universitário Santiago, 3810-193, Aveiro, Portugal; University of Coimbra, Department of Life Sciences, Faculty of Sciences and Technology, Calçada Martins de Freitas, 3000-456, Coimbra, Portugal
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13
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Martinez-Medina M, Strozzi F, Ruiz Del Castillo B, Serrano-Morillas N, Ferrer Bustins N, Martínez-Martínez L. Antimicrobial Resistance Profiles of Adherent Invasive Escherichia coli Show Increased Resistance to β-Lactams. Antibiotics (Basel) 2020; 9:antibiotics9050251. [PMID: 32414140 PMCID: PMC7277491 DOI: 10.3390/antibiotics9050251] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
The adherent invasive Escherichia coli (AIEC) pathotype has been associated with the aetiology of Crohn’s disease (CD). Scarce reports have shown the antimicrobial resistance (AMR) profiles of AIEC. Despite antibiotics not being recommended to treat CD, antimicrobial therapy could be useful in stratified patients, such as AIEC carriers. We examined the antimicrobial resistance profiles of AIEC strains to identify which therapies could be effective or confer a risk for such patients. Phenotypic resistance to 30 antimicrobials was tested according to CLSI standards. AIEC (n = 22) and non-pathogenic E. coli (non-AIEC) strains (n = 37) isolated from the gut mucosa of 31 CD patients and 18 controls were studied. De novo genome sequencing was carried out for 39 of the 59 strains, and AMR genes were searched using the DeepARG database in these genomes and 33 additional AIEC publicly available genomes. The strains isolated from CD and controls showed similar phenotypic AMR profiles. The genomic analysis did not reveal an increased prevalence of AMR genes. However, AIEC strains were more frequently resistant to β-lactams than non-AIEC strains (11 AIEC (50%) and 5 non-AIEC (22%) strains were resistant to at least one β-lactam; p < 0.042). Two AIEC strains were resistant to expanded-spectrum cephalosporins. One strain carried a plasmid-mediated AmpC β-lactamase (CMY-69), and the other presented mutations in the promotor of the intrinsic chromosomal AmpC related to the hyperproduction of this enzyme. The rest of the strains were resistant to β-lactams not including expanded-spectrum cephalosporins. The majority carried TEM-related β-lactamases. Genomic analysis including external AIEC revealed that the gene sul1 encoding for sulphonamide resistance was more frequent in AIEC strains than non-AIEC strains (34.6% vs. 9.5%, p = 0.030). AMR in AIEC is a matter of concern regarding the putative implication of the pathotype in CD. The high proportion of AIEC resistant to β-lactams warrants caution about the risk there may be in the use of these antimicrobials in AIEC-colonized CD patients.
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Affiliation(s)
- Margarita Martinez-Medina
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
- Correspondence: ; Tel.: +34-972-418261
| | - Francesco Strozzi
- Data Science Departement, Enterome Biosciences S.A., 75011 Paris, France;
| | - Belén Ruiz Del Castillo
- Service of Microbiology, Hospital Universitario Marqués de Valdecilla, Instituto de Investigación Marqués de Valdecilla (IDIVAL), 39008 Santander, Spain;
| | - Natalia Serrano-Morillas
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
| | - Nuria Ferrer Bustins
- Microbiology of Intestinal Disease Group, Biology Department, University of Girona, 17003 Girona, Spain; (N.S.-M.); (N.F.B.)
| | - Luis Martínez-Martínez
- Unit of Microbiology, University Hospital Reina Sofia, 14004 Córdoba, Spain;
- Maimonides Biomedical Research Institute, 14004 Córdoba, Spain
- Department of Agricultural Chemistry and Microbiology, University of Córdoba, 14004 Córdoba, Spain
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Barrios-Villa E, Martínez de la Peña CF, Lozano-Zaraín P, Cevallos MA, Torres C, Torres AG, Rocha-Gracia RDC. Comparative genomics of a subset of Adherent/Invasive Escherichia coli strains isolated from individuals without inflammatory bowel disease. Genomics 2019; 112:1813-1820. [PMID: 31689478 DOI: 10.1016/j.ygeno.2019.10.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 09/05/2019] [Accepted: 10/22/2019] [Indexed: 02/07/2023]
Abstract
There is increased evidence demonstrating the association between Crohn's Disease (CD), a type of Inflammatory Bowel Disease (IBD), and non-diarrheagenic Adherent/Invasive Escherichia coli (AIEC) isolates. AIEC strains are phenotypically characterized by their adhesion, invasion and intra-macrophage survival capabilities. In the present study, the genomes of five AIEC strains isolated from individuals without IBD (four from healthy donors and one from peritoneal liquid) were sequenced and compared with AIEC prototype strains (LF82 and NRG857c), and with extra-intestinal uropathogenic strain (UPEC CFT073). Non-IBD-AIEC strains showed an Average Nucleotide Identity up to 98% compared with control strains. Blast identities of the five non-IBD-AIEC strains were higher when compared to AIEC and UPEC reference strains than with another E. coli pathotypes, suggesting a relationship between them. The SNPs phylogeny grouped the five non-IBD-AIEC strains in one separated cluster, which indicates the emergence of these strains apart from the AIEC group. Additionally, four genomic islands not previously reported in AIEC strains were identified. An incomplete Type VI secretion system was found in non-IBD-AIEC strains; however, the Type II secretion system was complete. Several groups of genes reported in AIEC strains were searched in the five non-IBD-AIEC strains, and the presence of fimA, fliC, fuhD, chuA, irp2 and cvaC were confirmed. Other virulence factors were detected in non-IBD-AIEC strains, which were absent in AIEC reference strains, including EhaG, non-fimbrial adhesin 1, PapG, F17D-G, YehA/D, FeuC, IucD, CbtA, VgrG-1, Cnf1 and HlyE. Based on the differences in virulence determinants and SNPs, it is plausible to suggest that non-IBD AIEC strains belong to a different pathotype.
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Affiliation(s)
- Edwin Barrios-Villa
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Claudia Fabiola Martínez de la Peña
- Posgrado en Microbiología, Laboratorio de Biología Molecular de Enteropatógenos, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Patricia Lozano-Zaraín
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel A Cevallos
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carmen Torres
- Área de Bioquímica y Biología Molecular, Universidad de La Rioja, Logroño, Spain
| | - Alfredo G Torres
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Laboratorio de Microbiología Hospitalaria y de la Comunidad, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico.
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