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Amábile-Cuevas CF, Lund-Zaina S. Non-Canonical Aspects of Antibiotics and Antibiotic Resistance. Antibiotics (Basel) 2024; 13:565. [PMID: 38927231 PMCID: PMC11200725 DOI: 10.3390/antibiotics13060565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
The understanding of antibiotic resistance, one of the major health threats of our time, is mostly based on dated and incomplete notions, especially in clinical contexts. The "canonical" mechanisms of action and pharmacodynamics of antibiotics, as well as the methods used to assess their activity upon bacteria, have not changed in decades; the same applies to the definition, acquisition, selective pressures, and drivers of resistance. As a consequence, the strategies to improve antibiotic usage and overcome resistance have ultimately failed. This review gathers most of the "non-canonical" notions on antibiotics and resistance: from the alternative mechanisms of action of antibiotics and the limitations of susceptibility testing to the wide variety of selective pressures, lateral gene transfer mechanisms, ubiquity, and societal factors maintaining resistance. Only by having a "big picture" view of the problem can adequate strategies to harness resistance be devised. These strategies must be global, addressing the many aspects that drive the increasing prevalence of resistant bacteria aside from the clinical use of antibiotics.
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Affiliation(s)
| | - Sofia Lund-Zaina
- Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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García-Meniño I, García V, Lumbreras-Iglesias P, Fernández J, Mora A. Fluoroquinolone resistance in complicated urinary tract infections: association with the increased occurrence and diversity of Escherichia coli of clonal complex 131, together with ST1193. Front Cell Infect Microbiol 2024; 14:1351618. [PMID: 38510968 PMCID: PMC10953827 DOI: 10.3389/fcimb.2024.1351618] [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: 12/06/2023] [Accepted: 02/02/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Urinary tract infections (UTIs) are one of the leading causes of multidrug-resistance (MDR) spread and infection-related deaths. Escherichia coli is by far the main causative agent. We conducted a prospective study on complicated urinary tract infections (cUTIs) i) to monitor the high-risk clones that could be compromising the therapeutic management and ii) to compare the cUTI etiology with uncomplicated infections (uUTIs) occurring in the same period and health area. Methods 154 non-duplicated E. coli recovered from cUTIs in 2020 at the Hospital Universitario Central de Asturias (Spain) constituted the study collection. Results Most cUTI isolates belonged to phylogroup B2 (72.1%) and met the uropathogenic (UPEC) status (69.5%) (≥3 of chuA, fyuA, vat, and yfcV genes). MDR was exhibited by 35.7% of the isolates, similarly to data observed in the uUTI collection. A significant difference observed in cUTI was the higher level of fluoroquinolone resistance (FQR) (47.4%), where the pandemic clonal groups B2-CC131 and B2-ST1193 (CH14-64) comprised 28% of the 154 E. coli, representing 52.1% of the FQR isolates. Other prevalent FQR clones were D-ST69 (CH35-27), D-ST405 (CH37-27), and B2-ST429 (CH40-20) (three isolates each). We uncovered an increased genetic and genomic diversity of the CC131: 10 different virotypes, 8 clonotypes (CH), and 2 STs. The presence of bla CTX-M-15 was determined in 12 (7.8%) isolates (all CC131), which showed 10 different core genome (cg)STs and 2 fimH types (fimH30 and fimH602) but the same set of chromosomal mutations conferring FQR (gyrA p.S83L, gyrA p.D87N, parC p.S80I, parC p.E84V, and parE p.I529L). In addition, the plasmidome analysis revealed 10 different IncF formulae in CC131 genomes. Conclusion We proved here that non-lactose fermenting screening, together with the detection of O25b (rfbO25b), H4 (fliCH4), and H5 (fliCH5) genes, and phylogroup and clonotyping assignation, is a reasonable approach that can be easily implemented for the surveillance of emerging high-risk clones associated with FQR spread in cUTIs, such as the uncommonly reported O25b:H4-B2-ST9126-CC131 (CH1267-30). Since E. coli CC131 and ST1193 are also involved in the community uUTIs of this health area, interventions to eradicate these MDR clones, along with surveillance for other emerging ones, are essential for antibiotic use optimization programs.
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Affiliation(s)
- Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
| | - Pilar Lumbreras-Iglesias
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Research and Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, Oviedo, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Departamento de Biología Funcional, Universidad de Oviedo, Oviedo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago de Compostela, Spain
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Zahoor MA, Nawaz Z, Jamil A, Yasmin A, Alagawany M, Othman SI, Allam AA, El-Shall NA. Determining the prevalence and genetic diversity of plasmid-mediated sulfonamide resistance in Escherichia coli from commercial broiler samples. Poult Sci 2024; 103:103258. [PMID: 38070402 PMCID: PMC10755487 DOI: 10.1016/j.psj.2023.103258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/22/2023] [Accepted: 11/02/2023] [Indexed: 01/01/2024] Open
Abstract
Sulfonamides are commonly used antibacterials in commercial poultry, contributing toward the development of multidrug-resistant (MDR) phenotypes among Escherichia coli and that has emerged as global concern. The current study aimed to assess the sulfonamide resistance among isolated E. coli strains among commercial broilers. The bacterial strains were identified from fecal samples (n = 100) using selective media, followed by initial identification based on biochemical profiles. The susceptibility was determined by measuring the minimum inhibitory concentration (MIC) against sulfamethoxazole. The study also evaluated mobile genetic elements (MGEs), the mediators of antibiotic resistance, by amplification of plasmid DNA using specific primer PCR. Additionally, the isolates were subjected to multilocus sequence typing (MLST) analysis to investigate the genetic diversity among E. coli carrying sulfonamide resistance genes. The results revealed that 58% (58/100) E. coli strains were resistant to sulfonamides, with 36.20% (21/58) of the strains exhibiting an MIC breakpoint ≥512 µg/mL. PCR analysis showed that 42.85% (9/21) of the strains harbored the sul-1 gene, while 38.09% (8/21) carried the sul-2 gene, and 19.04% (4/21) had both genes. No isolate showed the presence of the sul-3 gene. Furthermore, class 1 and class 2 integrons were identified among 80.95% (17/21) and 19.04% (4/21) of the strains, respectively. MLST analysis confirmed that the strains belonged to sequence types (STs) including ST1638, ST155, ST48, ST350, ST23, ST156, and ST746. These findings underscore the diversity among E. coli strains in commercial poultry, which poses a significant risk.
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Affiliation(s)
- Muhammad Asif Zahoor
- Institute of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Zeeshan Nawaz
- Institute of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Arslan Jamil
- Institute of Microbiology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Aysha Yasmin
- Department of Biochemistry, Government College University Faisalabad, Faisalabad, Pakistan
| | - Mahmoud Alagawany
- Department of Poultry, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Sarah I Othman
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Ahmed A Allam
- Department of Zoology, Faculty of Science, Beni-suef University, Beni-suef 65211, Egypt; Department of Biology, College of Science, Imam Muhammad Ibn Saud Islamic University, Riyadh 11623, Saudi Arabia
| | - Nahed A El-Shall
- Department of Poultry and Fish Diseases, Faculty of Veterinary Medicine, Alexandria University, Edfina, Egypt.
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Haley BJ, Salaheen S, Kim SW, Van Kessel JA. Virulome analysis of Escherichia coli ST117 from bovine sources identifies similarities and differences with strains isolated from other food animals. PLoS One 2024; 19:e0296514. [PMID: 38175844 PMCID: PMC10766182 DOI: 10.1371/journal.pone.0296514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 12/14/2023] [Indexed: 01/06/2024] Open
Abstract
Escherichia coli ST117 is a pandemic extraintestinal pathogenic E. coli (ExPEC) causing significant morbidity globally. Poultry are a known reservoir of this pathogen, but the characteristics of ST117 strains from other animal sources have not been adequately investigated. Here we characterize the genomes of 36 ST117 strains recovered primarily from preweaned dairy calves, but also from older postweaned calves and lactating cows, in the context of other bovine-associated strains and strains from poultry, swine, and humans. Results of this study demonstrate that bovine-associated ST117 genomes encode virulence factors (VFs) known to be involved in extraintestinal infections, but also occasionally encode the Shiga toxin, a virulence factor (VF) involved in severe gastrointestinal infections and more frequently identified in E. coli from ruminants than other animals. Bovine-associated ST117 genomes were also more likely to encode afa-VIII (adhesins), pap (P-fimbriae), cdt (cytolethal distending toxin), and stx (Shiga toxins) than were poultry and swine-associated genomes. All of the ST117 genomes were grouped into seven virulence clusters, with bovine-associated genomes grouping into Clusters 1, 2, 4, 5, but not 3, 6, or 7. Major differences in the presence of virulence factors between clusters were observed as well. Antimicrobial resistance genes were detected in 112 of 122 (91%) bovine-associated genomes, with 103 of these being multidrug-resistant (MDR). Inclusion of genomes that differed from ST117 by one multi-locus sequence type (MLST) allele identified 31 STs, four of these among the bovine-associated genomes. These non-ST117 genomes clustered with the ST117 genomes suggesting that they may cause similar disease as ST117. Results of this study identify cattle as a reservoir of ST117 strains, some of which are highly similar to those isolated from other food animals and some of which have unique bovine-specific characteristics.
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Affiliation(s)
- Bradd J. Haley
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Serajus Salaheen
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Seon Woo Kim
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
| | - Jo Ann Van Kessel
- Environmental Microbial and Food Safety Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States of America
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Nadimpalli ML, Rojas Salvatierra L, Chakraborty S, Swarthout JM, Cabrera LZ, Pickering AJ, Calderon M, Saito M, Gilman RH, Pajuelo MJ. Effects of breastfeeding on children's gut colonization with multidrug-resistant Enterobacterales in peri-urban Lima, Peru. Gut Microbes 2024; 16:2309681. [PMID: 38300753 PMCID: PMC10841006 DOI: 10.1080/19490976.2024.2309681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 01/19/2024] [Indexed: 02/03/2024] Open
Abstract
Children living in low-resource settings are frequently gut-colonized with multidrug-resistant bacteria. We explored whether breastfeeding may protect against children's incident gut colonization with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) and Klebsiella, Enterobacter, or Citrobacter spp. (ESBL-KEC). We screened 937 monthly stool samples collected from 112 children aged 1-16 months during a 2016-19 prospective cohort study of enteric infections in peri-urban Lima. We used 52,816 daily surveys to examine how exposures to breastfeeding in the 30 days prior to a stool sample were associated with children's risks of incident gut-colonization, controlling for antibiotic use and other covariates. We sequenced 78 ESBL-Ec from 47 children to explore their diversity. Gut-colonization with ESBL-Ec was increasingly prevalent as children aged, approaching 75% by 16 months, while ESBL-KEC prevalence fluctuated between 18% and 36%. Through 6 months of age, exclusively providing human milk in the 30 days prior to a stool sample did not reduce children's risk of incident gut-colonization with ESBL-Ec or ESBL-KEC. From 6 to 16 months of age, every 3 additional days of breastfeeding in the prior 30 days was associated with 6% lower risk of incident ESBL-Ec gut-colonization (95% CI: 0.90, 0.98, p = .003). No effects were observed on incident ESBL-KEC colonization. We detected highly diverse ESBL-Ec among children and few differences between children who were predominantly breastfed (mean age: 4.1 months) versus older children (10.8 months). Continued breastfeeding after 6 months conferred protection against children's incident gut colonization with ESBL-Ec in this setting. Policies supporting continued breastfeeding should be considered in efforts to combat antibiotic resistance.
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Affiliation(s)
- Maya L. Nadimpalli
- Gangarosa Department of Environmental Health, Emory Rollins School of Public Health, Atlanta, GA, USA
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
| | - Luismarcelo Rojas Salvatierra
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Subhra Chakraborty
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jenna M. Swarthout
- Department of Civil and Environmental Engineering, Tufts University, Medford, MA, USA
| | - Lilia Z. Cabrera
- Asociación Benéfica Proyectos en Informática, Salud, Medicina, y Agricultura (PRISMA), Lima, Peru
| | - Amy J. Pickering
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance (Levy CIMAR), Tufts University, Boston, MA, USA
- Department of Civil and Environmental Engineering, University of California, Berkeley, CA, USA
- Blum Center for Developing Economies, University of California, Berkeley, CA, USA
| | - Maritza Calderon
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Mayuko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Robert H. Gilman
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Monica J. Pajuelo
- Laboratorio de Microbiología Molecular, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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Roy Chowdhury P, Hastak P, DeMaere M, Wyrsch E, Li D, Elankumaran P, Dolejska M, Browning GF, Marenda MS, Gottlieb T, Cheong E, Merlino J, Myers GSA, Djordjevic SP. Phylogenomic analysis of a global collection of Escherichia coli ST38: evidence of interspecies and environmental transmission? mSystems 2023; 8:e0123622. [PMID: 37675998 PMCID: PMC10654095 DOI: 10.1128/msystems.01236-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 07/11/2023] [Indexed: 09/08/2023] Open
Abstract
IMPORTANCE Extraintestinal pathogenic Escherichia coli (ExPEC) sequence type (ST) 38 is one of the top 10 human pandemic lineages. Although a major cause of urinary tract and blood stream infections, ST38 has been poorly characterized from a global phylogenomic perspective. A comprehensive genome-scale analysis of 925 ST38 isolate genomes identified two broad ancestral clades and linkage of discrete ST38 clusters with specific bla CTX-M variants. In addition, the clades and clusters carry important virulence genes, with diverse but poorly characterized plasmids. Numerous putative interhost and environment transmission events were identified here by the presence of ST38 clones (defined as isolates with ≤35 SNPs) within humans, companion animals, food sources, urban birds, wildlife, and the environment. A small cluster of international ST38 clones from diverse sources, likely representing progenitors of a hospital outbreak that occurred in Brisbane, Australia, in 2017, was also identified. Our study emphasizes the importance of characterizing isolate genomes derived from nonhuman sources and geographical locations, without any selection bias.
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Affiliation(s)
- Piklu Roy Chowdhury
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Priyanka Hastak
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Matthew DeMaere
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Ethan Wyrsch
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Dmitriy Li
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Paarthiphan Elankumaran
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Monika Dolejska
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
- Central European Institute of Technology (CEITEC), University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
- Department of Biology and Wildlife Disease, Faculty of Veterinary Hygiene and Ecology, University of Veterinary and Pharmaceutical Sciences, Brno, Czech Republic
- Biomedical Center, Charles University, Brno, Czech Republic
- Department of Clinical Microbiology and Immunology, Institute of Laboratory Medicine, The University Hospital, Brno, Czech Republic
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Mark S. Marenda
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, Parkville, Melbourne, Victoria, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Elaine Cheong
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, Concord Hospital and NSW Health Pathology, Hospital Road, Concord, New South Wales, Australia
- Faculty of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Garry S. A. Myers
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
| | - Steven P. Djordjevic
- Australian Institute for Microbiology & Infection, University of Technology Sydney, Ultimo, Sydney, New South Wales, Australia
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García V, Lestón L, Parga A, García-Meniño I, Fernández J, Otero A, Olsen JE, Herrero-Fresno A, Mora A. Genomics, biofilm formation and infection of bladder epithelial cells in potentially uropathogenic Escherichia coli (UPEC) from animal sources and human urinary tract infections (UTIs) further support food-borne transmission. One Health 2023; 16:100558. [PMID: 37363240 PMCID: PMC10288081 DOI: 10.1016/j.onehlt.2023.100558] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 04/29/2023] [Accepted: 05/01/2023] [Indexed: 06/28/2023] Open
Abstract
Escherichia coli is the main cause of urinary tract infections (UTI). While genomic comparison of specific clones recovered from animals, and human extraintestinal infections show high identity, studies demonstrating the uropathogenicity are lacking. In this study, comparative genomics combined with bladder-cell and biofilm formation assays, were performed for 31 E. coli of different origins: 7 from meat (poultry, beef, and pork); 2 from avian-farm environment; 12 from human uncomplicated UTI, uUTI; and 10 from human complicated UTI, cUTI. These isolates were selected based on their genetic uropathogenic (UPEC) status and phylogenetic background. In silico analysis revealed similar virulence-gene profiles, with flagella, type 1 and curli fimbriae, outer-membrane proteins (agn43, ompT, iha), and iron-uptake (iutA, entA, and fyuA) associated-traits as the most prevalent (>65%). In bladder-cell assays, moderate to strong values of association (83%, 60%, 77.8%) and invasion (0%, 70%, 55.5%) were exhibited by uUTI, cUTI, and animal-derived isolates, respectively. Of interest, uUTI isolates exhibited a significantly lower invasive capacity than cUTI isolates (p < 0.05). All isolates but one produced measurable biofilm. Notably, 1 turkey meat isolate O11:H6-F-ST457, and 2 cUTI isolates of the pandemic lineages O83:H42-F-ST1485-CC648 and O25b:H4-B2-ST131, showed strong association, invasion and biofilm formation. These isolates showed common carriage of type 1 fimbriae and csg operons, toxins (hlyF, tsh), iron uptake systems (iutA, entA, iroN), colicins, protectins (cvaC, iss, kpsM, traT), ompT, and malX. In summary, the similar in vitro behaviour found here for certain E. coli clones of animal origin would further reinforce the role of food-producing animals as a potential source of UPEC. Bladder-cell infection assays, combined with genomics, might be an alternative to in vivo virulence models to assess uropathogenicity.
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Affiliation(s)
- Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo 27002, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago 15706, Spain
| | - Luz Lestón
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo 27002, Spain
| | - Ana Parga
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo 27002, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago 15706, Spain
- Department for Biological Safety, German Federal Institute for Risk Assessment, Berlin 10589, Germany
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA), Oviedo 33011, Spain
- Grupo de Microbiología Traslacional, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo 33011, Spain
- Research & Innovation, Artificial Intelligence and Statistical Department, Pragmatech AI Solutions, Oviedo 33011, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Otero
- Departamento de Microbioloxía e Parasitoloxía, Facultade de Bioloxía, Edificio CIBUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - John E. Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg 1870, Denmark
| | - Ana Herrero-Fresno
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg 1870, Denmark
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Universidade de Santiago de Compostela (USC), Lugo 27002, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago 15706, Spain
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Teng L, Feng M, Liao S, Zheng Z, Jia C, Zhou X, Nambiar RB, Ma Z, Yue M. A Cross-Sectional Study of Companion Animal-Derived Multidrug-Resistant Escherichia coli in Hangzhou, China. Microbiol Spectr 2023; 11:e0211322. [PMID: 36840575 PMCID: PMC10100847 DOI: 10.1128/spectrum.02113-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/31/2023] [Indexed: 02/24/2023] Open
Abstract
Antimicrobial resistance poses a challenge to global public health, and companion animals could serve as the reservoir for antimicrobial-resistant bacteria. However, the prevalence of antimicrobial-resistant bacteria, especially multidrug-resistant (MDR) bacteria, and the associated risk factors from companion animals are partially understood. Here, we aim to investigate the prevalence of MDR Escherichia coli, as an indicator bacterium, in pet cats and dogs in Hangzhou, China, and evaluate the factors affecting the prevalence of MDR E. coli. The proportion of pets carrying MDR E. coli was 35.77% (49/137), i.e., 40.96% (34/83) for dogs and 27.28% (15/54) for cats. Isolates resistant to trimethoprim-sulfamethoxazole (49.40% and 44.44%), amoxicillin-clavulanic acid (42.17% and 38.89%), and nalidixic acid (40.96% and 35.19%) were the most prevalent in dogs and cats. Interestingly, comparable prevalence of MDR E. coli was observed in pet dogs and cats regardless of the health condition and the history of antibiotic use. Genetic diversity analysis indicates a total of 86 sequencing types (23 clonal complexes), with ST12 being the most dominant. Further genomic investigation of a carbapenem-resistant E. coli ST410 isolate reveals abundant antimicrobial-resistance genes and a plasmid-borne carbapenemase gene (NDM-5) flanked by insertion sequences of IS91 and IS31, suggesting the plasmid and insertion sequences may be involved in carbapenem-resistance dissemination. These data show that companion animal-derived MDR bacteria could threaten public health, and further regulation and supervision of antimicrobial use in pet clinics should be established in China. IMPORTANCE MDR Escherichia coli are considered a global threat because of the decreasing options for antimicrobial therapy. Companion animals could be a reservoir of MDR E. coli, and the numbers of pets and households owning pets in China are booming. However, the prevalence and risk factors of MDR E. coli carriage in Chinese pets were rarely studied. Here, we investigated the prevalence of MDR E. coli in pets in Hangzhou, one of the leading cities with the most established pet market in China, and explored the factors that affected the prevalence. Our findings showed high prevalences of MDR E. coli in pet dogs and cats regardless of their health condition and the history of antibiotic use, suggesting their potential role of public health risk. A call-to-action for improved regulation of antimicrobial use in companion animal is needed in China.
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Affiliation(s)
- Lin Teng
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Mengyao Feng
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Sihao Liao
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Zhijie Zheng
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Chenghao Jia
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Xin Zhou
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Reshma B. Nambiar
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
| | - Zhengxin Ma
- Mount Desert Island Biological Laboratory, Bar Harbor, Maine, USA
| | - Min Yue
- Department of Veterinary Medicine, Zhejiang University College of Animal Sciences, Hangzhou, China
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
- Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, Hangzhou, China
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9
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Casey JA, Tartof SY, Davis MF, Nachman KE, Price L, Liu C, Yu K, Gupta V, Innes GK, Tseng HF, Do V, Pressman AR, Rudolph KE. Impact of a Statewide Livestock Antibiotic Use Policy on Resistance in Human Urine Escherichia coli Isolates: A Synthetic Control Analysis. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:27007. [PMID: 36821707 PMCID: PMC9945560 DOI: 10.1289/ehp11221] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 01/12/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND On 1 January 2018, California implemented Senate Bill 27 (SB27), banning, for the first time in the United States, routine preventive use of antibiotics in food-animal production and any antibiotic use without a veterinarian's prescription. OBJECTIVES Our objective was to assess whether SB27 was associated with decreased antimicrobial resistance among E. coli isolated from human urine. METHODS We used U.S. nationwide monthly state-level data from BD Insights Research Database (Becton, Dickinson, and Co.) spanning 1 January 2013 to 30 June 2021 on antibiotic-resistance patterns of 30-d nonduplicate E. coli isolated from urine. Tested antibiotic classes included aminoglycosides, extended-spectrum cephalosporins (ESC), fluoroquinolones, and tetracyclines. Counts of tested and not-susceptible (resistant and intermediate, hereafter resistant) urine isolates were available by sex, age group (< 65 , 65 + year), month, and state. We applied a synthetic control approach to estimate the causal effect of SB27 on resistance patterns. Our approach created a synthetic California based on a composite of other states without the policy change and contrasted its counterfactual postpolicy trends with the observed postpolicy trends in California. FINDINGS We included 7.1 million E. coli urine isolates, 90% among women, across 33 states. From 2013 to 2017, the median (interquartile range) resistance percentages in California were 11.9% (7.4, 17.6), 13.8% (5.8, 20.0), 24.6% (9.6, 36.4), 7.9% (2.1, 13.1), for aminoglycosides, ESC, fluoroquinolones, and tetracyclines, respectively. SB27 was associated with a 7.1% reduction in ESC resistance (p-value for joint null: < 0.01 ), but no change in resistance to aminoglycosides, fluoroquinolones, or tetracyclines. DISCUSSION Further research is needed to determine the role of SB27 in the observed reduction in ESC resistance E. coli in human populations, particularly as additional states implement similar legislation. https://doi.org/10.1289/EHP11221.
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Affiliation(s)
- Joan A. Casey
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Sara Y. Tartof
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
- Department of Health Systems Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, California, USA
| | - Meghan F. Davis
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Molecular and Comparative Pathobiology, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Keeve E. Nachman
- Department of Environmental Health & Engineering, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Department of Health Policy and Management, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins Center for a Livable Future, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
- Risk Sciences and Public Policy Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lance Price
- Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Cindy Liu
- Milken Institute School of Public Health, The George Washington University, Washington, District of Columbia, USA
| | - Kalvin Yu
- Medical and Scientific Affairs, Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Vikas Gupta
- Medical and Scientific Affairs, Becton, Dickinson and Company, Franklin Lakes, New Jersey, USA
| | - Gabriel K. Innes
- Yuma Center of Excellence for Desert Agriculture (YCEDA), University of Arizona, Yuma, Arizona, USA
| | - Hung Fu Tseng
- Department of Research & Evaluation, Kaiser Permanente Southern California, Pasadena, California, USA
| | - Vivian Do
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Alice R. Pressman
- Center for Health Systems Research, Sutter Health, Walnut Creek, California, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California, USA
| | - Kara E. Rudolph
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
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10
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Holcomb DA, Quist AJL, Engel LS. Exposure to industrial hog and poultry operations and urinary tract infections in North Carolina, USA. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 853:158749. [PMID: 36108846 PMCID: PMC9613609 DOI: 10.1016/j.scitotenv.2022.158749] [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: 06/29/2022] [Revised: 09/08/2022] [Accepted: 09/09/2022] [Indexed: 06/15/2023]
Abstract
An increasing share of urinary tract infections (UTIs) are caused by extraintestinal pathogenic Escherichia coli (ExPEC) lineages that have also been identified in poultry and hogs with high genetic similarity to human clinical isolates. We investigated industrial food animal production as a source of uropathogen transmission by examining relationships of hog and poultry density with emergency department (ED) visits for UTIs in North Carolina (NC). ED visits for UTI in 2016-2019 were identified by ICD-10 code from NC's ZIP code-level syndromic surveillance system and livestock counts were obtained from permit data and aerial imagery. We calculated separate hog and poultry spatial densities (animals/km2) by Census block with a 5 km buffer on the block perimeter and weighted by block population to estimate mean ZIP code densities. Associations between livestock density and UTI incidence were estimated using a reparameterized Besag-York-Mollié (BYM2) model with ZIP code population offsets to account for spatial autocorrelation. We excluded metropolitan and offshore ZIP codes and assessed effect measure modification by calendar year, ZIP code rurality, and patient sex, age, race/ethnicity, and health insurance status. In single-animal models, hog exposure was associated with increased UTI incidence (rate ratio [RR]: 1.21, 95 % CI: 1.07-1.37 in the highest hog-density tertile), but poultry exposure was associated with reduced UTI rates (RR: 0.86, 95 % CI: 0.81-0.91). However, the reference group for single-animal poultry models included ZIP codes with only hogs, which had some of the highest UTI rates; when compared with ZIP codes without any hogs or poultry, there was no association between poultry exposure and UTI incidence. Hog exposure was associated with increased UTI incidence in areas that also had medium to high poultry density, but not in areas with low poultry density, suggesting that intense hog production may contribute to increased UTI incidence in neighboring communities.
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Affiliation(s)
- David A Holcomb
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Arbor J L Quist
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lawrence S Engel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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11
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Virulence Profile, Antibiotic Resistance, and Phylogenetic Relationships among Escherichia coli Strains Isolated from the Feces and Urine of Hospitalized Patients. Pathogens 2022; 11:pathogens11121528. [PMID: 36558862 PMCID: PMC9782660 DOI: 10.3390/pathogens11121528] [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: 11/16/2022] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Extra-intestinal pathogenic Escherichia coli (ExPEC) may inhabit the human gut microbiota without causing disease. However, if they reach extra-intestinal sites, common cystitis to bloodstream infections may occur, putting patients at risk. To examine the human gut as a source of endogenous infections, we evaluated the E. coli clonal diversity of 18 inpatients' guts and their relationship with strains isolated from urinary tract infection (UTI) in the same hospital. Random amplified polymorphic DNA evaluated the clonal diversity, and the antimicrobial susceptibility was determined by disk diffusion. One isolate of each clone detected was sequenced, and their virulome and resistome were determined. Overall, 177 isolates were screened, among which 32 clones were identified (mean of two clones per patient), with ExPEC strains found in over 75% of the inpatients' guts. Endogenous infection was confirmed in 75% of the cases. ST10, ST59, ST69, ST131, and ST1193 clones and critical mobile drug-resistance encoding genes (blaCTX-M-15, blaOXA-1, blaDHA-1, aac(6')-lb-cr, mcr-1.26, qnrB4, and qnrB19) were identified in the gut of inpatients. The genomic analysis highlighted the diversity of the fecal strains, colonization by lactose-negative E. coli, the high frequency of ExPEC in the gut of inpatients without infections, and the presence of β-lactamase producing E. coli in the gut of inpatients regardless of the previous antibiotics' usage. Considering that we found more than one ExPEC clone in the gut of several inpatients, surveillance of inpatients' fecal pathogens may prevent UTI caused by E. coli in the hospital and dissemination of risk clones.
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12
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Zhao W, Li W, Du XD, Yao H. Hybrid IncFIA/FIB/FIC(FII) plasmid co-carrying bla NDM-5 and fosA3 from an Escherichia coli ST117 strain of retail chicken. Int J Food Microbiol 2022; 382:109914. [PMID: 36088664 DOI: 10.1016/j.ijfoodmicro.2022.109914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/29/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
Carbapenems and fosfomycin are important antibiotics used to treat Enterobacteriaceae-associated infections. This study aimed to characterize the co-resistance and co-dissemination mechanism of carbapenem and fosfomycin resistance in an Escherichia coli ST117 strain isolated from retail chicken meat. Antimicrobial susceptibility testing showed that an E. coli CS18F strain had a multidrug resistance profile, including carbapenem and fosfomycin resistance. The presence of blaNDM-5 and fosA3 genes was confirmed by PCR and Sanger sequencing. The blaNDM-5 and fosA3 genes were successfully transferred to the recipient strain E. coli J53 via conjugation, and the transconjugants had elevated minimum inhibitory concentrations (MICs) for meropenem and fosfomycin. Whole genome sequencing (WGS) of E. coli CS18F revealed that blaNDM-5 and fosA3 were colocalized on an IncFIA/FIB/FIC(FII) type plasmid of 189,141 bp, which was designated as pCS18F-NDM-Fos. A novel structure with five IS26 sequences flanking the multiple drug resistance region (MDRR) was identified, and three copies of IS26 were found to be flanked blaNDM-5, fosA3, dfrA12, aadA2, and sul1. Three types of translocation units (TUs) were identified by PCR, containing either the resistance gene blaNDM-5 and an IS26 sequence, fosA3, and an IS26 sequence, or both, indicating their potential co-transfer via TUs. Thus, this is an unprecedented report of the presence of a plasmid co-carrying blaNDM-5 and fosA3 and TUs potentially mediating their simultaneous transfer.
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Affiliation(s)
- Wenbo Zhao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Wenjun Li
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China
| | - Xiang-Dang Du
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China.
| | - Hong Yao
- College of Veterinary Medicine, Henan Agricultural University, Zhengzhou 450046, PR China.
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13
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Balbuena-Alonso MG, Cortés-Cortés G, Kim JW, Lozano-Zarain P, Camps M, Del Carmen Rocha-Gracia R. Genomic analysis of plasmid content in food isolates of E. coli strongly supports its role as a reservoir for the horizontal transfer of virulence and antibiotic resistance genes. Plasmid 2022; 123-124:102650. [PMID: 36130651 PMCID: PMC10896638 DOI: 10.1016/j.plasmid.2022.102650] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
The link between E. coli strains contaminating foods and human disease is unclear, with some reports supporting a direct transmission of pathogenic strains via food and others highlighting their role as reservoirs for resistance and virulence genes. Here we take a genomics approach, analyzing a large set of fully-assembled genomic sequences from E. coli available in GenBank. Most of the strains isolated in food are more closely related to each other than to clinical strains, arguing against a frequent direct transmission of pathogenic strains from food to the clinic. We also provide strong evidence of genetic exchanges between food and clinical strains that are facilitated by plasmids. This is based on an overlapped representation of virulence and resistance genes in plasmids isolated from these two sources. We identify clusters of phylogenetically-related plasmids that are largely responsible for the observed overlap and see evidence of specialization, with some food plasmid clusters preferentially transferring virulence factors over resistance genes. Consistent with these observations, food plasmids have a high mobilization potential based on their plasmid taxonomic unit classification and on an analysis of mobilization gene content. We report antibiotic resistance genes of high clinical relevance and their specific incompatibility group associations. Finally, we also report a striking enrichment for adhesins in food plasmids and their association with specific IncF replicon subtypes. The identification of food plasmids with specific markers (Inc and PTU combinations) as mediators of horizontal transfer between food and clinical strains opens new research avenues and should assist with the design of surveillance strategies.
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Affiliation(s)
- María G Balbuena-Alonso
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Gerardo Cortés-Cortés
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico; Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Jay W Kim
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Patricia Lozano-Zarain
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico
| | - Manel Camps
- Department of Microbiology and Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.
| | - Rosa Del Carmen Rocha-Gracia
- Posgrado en Microbiología, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias de la Benemérita Universidad Autónoma de Puebla. Ciudad Universitaria, San Manuel, Puebla 72570, Mexico.
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14
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Khalifeh OM, Obaidat MM. Urinary tract virulence genes in extended-spectrum beta-lactamase E. coli from dairy cows, beef cattle, and small ruminants. Acta Trop 2022; 234:106611. [PMID: 35850234 DOI: 10.1016/j.actatropica.2022.106611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/03/2022] [Accepted: 07/14/2022] [Indexed: 11/01/2022]
Abstract
Extended-spectrum β-lactamase Escherichia coli is an important cause of urinary tract infections in humans. ESBL producers E. coli were reported in food-producing animals, but no previous study reported the virulence potential of these isolates. Thus, this study determined the virulence potential of ESBL producers E. coli isolates from 518 beef feces, 610 dairy cow feces, 305 dairy cow milk, 503 sheep milk and 445 goat milk samples. A total of 278 isolates; specifically, 130 from beef feces, 39 from the cow's feces, 42 from cow's milk, 44 from sheep milk and 23 from goats' milk were isolated and then tested for 14 virulence genes by polymerase chain reaction. After that, the correlation of virulence genes presence among the isolates was determined statistically. Overall, 97% of the isolates carried fimH, 39% carried iroN E. coli and 32% carried papC. The kpsMT K1, cnf1, papAH, papG allele II & III, papG allele II, and kpsMT II were carried by 6 to 23% of the isolates, while less than 6% of the isolates carried papG allele III, papG allele I, Univcnf, iutA and hlyA. About 68.2% of the isolates carried two or more virulence genes and 41.8% carried three or more. Moreover, the isolates had 71 different profiles of virulence genes, where the most common profiles were fimH alone (86 isolate), fimH + iroN E. coli (35 isolate), fimH + papC (20 isolate), and fimH + papC + iroN E. coli (13 isolate). The adhesion, capsule synthesis and toxins secretion genes were significantly associated (p ˂ 0.01) with each other. These results call for awareness about the risk of food animals as reservoirs of ESBL uropathogenic E. coli that would threaten public health and limits the treatment options for urinary tract infections.
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Affiliation(s)
- Omar Mohammad Khalifeh
- Faculty of Medicine, Jordan University of Science and Technology, Ar-Ramtha, Irbid, Jordan
| | - Mohammad M Obaidat
- Faculty of Veterinary Medicine, Jordan University of Science and Technology, Ar-Ramtha, Irbid 22110, Jordan.
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15
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Distribution of ESBL/AmpC-Escherichia coli on a Dairy Farm. Antibiotics (Basel) 2022; 11:antibiotics11070940. [PMID: 35884193 PMCID: PMC9311582 DOI: 10.3390/antibiotics11070940] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
The aim of the study was to determine the prevalence of ESBL/AmpC-producing Escherichia (E.) coli and to investigate their on-farm distribution on an exemplary dairy farm. For this purpose, sample sizes were calculated, and fecal samples were collected from cattle of all ages and analyzed for the presence of ESBL/AmpC-E. coli using selective media supplemented with cefotaxime. These antibiotic-resistant bacteria were detected in 22.5% of the samples tested. The prevalence was highest in the calf age group, in which 100% of the collected fecal samples were positive. With increasing age, the prevalence decreased in the other sample groups. While ESBL/AmpC E. coli could still be detected in young stock (15%) and breeding heifers (5%), no resistant pathogens could be detected in adult animals. Whole-genome sequencing of the ESBL/AmpC-E. coli isolates revealed, first, that all isolates were ESBL producers (CTX-M-1 and CTX-M-15) and, second, that ST362, which is known as a biofilm producer, was dominant in the calves (85%, n = 17). Based on these results and the evaluation of a questionnaire, possible causes for the occurrence of ESBL/AmpC-E. coli were discussed and recommendations for the reduction in transmission were formulated. Unlike most German dairy farms, no waste milk feeding was apparent; therefore, factors reducing ESBL/AmpC-E. coli are primarily related to an improvement in hygiene management to prevent biofilms, e.g., in nipple buckets, but also to question the use of antibiotics, e.g., in the treatment of diarrheic calves.
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16
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Interspecies Transmission of CMY-2-Producing Escherichia coli Sequence Type 963 Isolates between Humans and Gulls in Australia. mSphere 2022; 7:e0023822. [PMID: 35862807 PMCID: PMC9429958 DOI: 10.1128/msphere.00238-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We have provided the first comprehensive genomic study of
E. coli
ST963 by analyzing various genomic and phenotypic data sets of isolates from Australian silver gulls and comparison with genomes from geographically dispersed regions of human and animal origin. Our study suggests the emergence of a specific
bla
CMY-2
-carrying
E. coli
ST963 clone in Australia that is widely spread across the continent by humans and birds.
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17
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Harrison L, Tyson GH, Strain E, Lindsey RL, Strockbine N, Ceric O, Fortenberry GZ, Harris B, Shaw S, Tillman G, Zhao S, Dessai U. Use of Large-Scale Genomics to Identify the Role of Animals and Foods as Potential Sources of Extraintestinal Pathogenic Escherichia coli That Cause Human Illness. Foods 2022; 11:foods11131975. [PMID: 35804790 PMCID: PMC9265580 DOI: 10.3390/foods11131975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 02/01/2023] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) cause urinary tract and potentially life-threatening invasive infections. Unfortunately, the origins of ExPEC are not always clear. We used genomic data of E. coli isolates from five U.S. government organizations to evaluate potential sources of ExPEC infections. Virulence gene analysis of 38,032 isolates from human, food animal, retail meat, and companion animals classified the subset of 8142 non-diarrheagenic isolates into 40 virulence groups. Groups were identified as low, medium, and high relative risk of containing ExPEC strains, based on the proportion of isolates recovered from humans. Medium and high relative risk groups showed a greater representation of sequence types associated with human disease, including ST-131. Over 90% of food source isolates belonged to low relative risk groups, while >60% of companion animal isolates belonged to medium or high relative risk groups. Additionally, 18 of the 26 most prevalent antimicrobial resistance determinants were more common in high relative risk groups. The associations between antimicrobial resistance and virulence potentially limit treatment options for human ExPEC infections. This study demonstrates the power of large-scale genomics to assess potential sources of ExPEC strains and highlights the importance of a One Health approach to identify and manage these human pathogens.
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Affiliation(s)
- Lucas Harrison
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
- Correspondence: (L.H.); (U.D.)
| | - Gregory H. Tyson
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
| | - Errol Strain
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
| | - Rebecca L. Lindsey
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.L.L.); (N.S.)
| | - Nancy Strockbine
- Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.L.L.); (N.S.)
| | - Olgica Ceric
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
| | - Gamola Z. Fortenberry
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250, USA; (G.Z.F.); (S.S.)
| | - Beth Harris
- U.S. Department of Agriculture, Animal and Plant Health Inspection Service, Ames, IA 50010, USA;
| | - Sheryl Shaw
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250, USA; (G.Z.F.); (S.S.)
| | - Glenn Tillman
- U.S. Department of Agriculture, Food Safety and Inspection Service, Athens, GA 30605, USA;
| | - Shaohua Zhao
- U.S. Food and Drug Administration, Center for Veterinary Medicine, Laurel, MD 20708, USA; (G.H.T.); (E.S.); (O.C.); (S.Z.)
| | - Uday Dessai
- U.S. Department of Agriculture, Food Safety and Inspection Service, Washington, DC 20250, USA; (G.Z.F.); (S.S.)
- Correspondence: (L.H.); (U.D.)
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18
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Tang B, Chang J, Luo Y, Jiang H, Liu C, Xiao X, Ji X, Yang H. Prevalence and characteristics of the mcr-1 gene in retail meat samples in Zhejiang Province, China. JOURNAL OF MICROBIOLOGY (SEOUL, KOREA) 2022; 60:610-619. [PMID: 35362896 DOI: 10.1007/s12275-022-1597-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/21/2022] [Accepted: 02/14/2022] [Indexed: 01/03/2023]
Abstract
Considering the serious threat to food safety and public health posed by pathogens with colistin resistance, colistin was banned as a growth promoter in 2017 in China. In recent years, the resistance rate of Escherichia coli isolated from animal intestines or feces to colistin has decreased. However, the prevalence and characteristics of the mcr-1 gene in retail meat have not been well explored. Herein, 106 mcr-1-negative and 16 mcr-1-positive E. coli isolates were randomly recovered from 120 retail meat samples and screened using colistin. The 106 E. coli isolates showed maximum resistance to sulfafurazole (73.58%) and tetracycline (62.26%) but susceptibility to colistin (0.00%). All 16 mcr-1-positive E. coli isolates showed resistance to colistin, were extended spectrum beta-lactamase (ESBL)-positive and exhibited complex multidrug resistance (MDR). For these 16 isolates, 17 plasmid replicons and 42 antibiotic resistance genes were identified, and at least 7 antibiotic resistance genes were found in each isolate. Acquired disinfectant resistance genes were identified in 75.00% (12/16) of the isolates. Furthermore, comparative genomic and phylogenetic analysis results indicated that these 16 mcr-1-positive E. coli isolates and the most prevalent mcr-1-harboring IncI2 plasmid in this study were closely related to other previously reported mcr-1-positive E. coli isolates and the IncI2 plasmid, respectively, showing their wide distribution. Taken together, our findings showed that retail meat products were a crucial reservoir of mcr-1 during the colistin ban period and should be continuously monitored.
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Affiliation(s)
- Biao Tang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310004, P. R. China.
| | - Jiang Chang
- School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai, 200240, P. R. China
| | - Yi Luo
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, Zhejiang, 310018, P. R. China
| | - Han Jiang
- Key Laboratory of Marine Food Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, Zhejiang, 310018, P. R. China
| | - Canying Liu
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong, 528225, P. R. China
| | - Xingning Xiao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310004, P. R. China
| | - Xiaofeng Ji
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310004, P. R. China
| | - Hua Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products & Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang, 310004, P. R. China.
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Xu C, Kong L, Gao H, Cheng X, Wang X. A Review of Current Bacterial Resistance to Antibiotics in Food Animals. Front Microbiol 2022; 13:822689. [PMID: 35633728 PMCID: PMC9133924 DOI: 10.3389/fmicb.2022.822689] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/04/2022] [Indexed: 12/29/2022] Open
Abstract
The overuse of antibiotics in food animals has led to the development of bacterial resistance and the widespread of resistant bacteria in the world. Antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) in food animals are currently considered emerging contaminants, which are a serious threat to public health globally. The current situation of ARB and ARGs from food animal farms, manure, and the wastewater was firstly covered in this review. Potential risks to public health were also highlighted, as well as strategies (including novel technologies, alternatives, and administration) to fight against bacterial resistance. This review can provide an avenue for further research, development, and application of novel antibacterial agents to reduce the adverse effects of antibiotic resistance in food animal farms.
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Affiliation(s)
- Chunming Xu
- School of Light Industry, Beijing Technology and Business University, Beijing, China
- Key Laboratory of Cleaner Production and Integrated Resource Utilization of China National Light Industry, Beijing Technology and Business University, Beijing, China
| | - Lingqiang Kong
- School of Light Industry, Beijing Technology and Business University, Beijing, China
| | - Hanfang Gao
- School of Light Industry, Beijing Technology and Business University, Beijing, China
| | - Xiyu Cheng
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Xiumin Wang
- Key Laboratory of Feed Biotechnology, Ministry of Agriculture and Rural Affairs, Beijing, China
- Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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20
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Li Q, Li Z, Wang Y, Chen Y, Sun J, Yang Y, Si H. Antimicrobial Resistance and Transconjugants Characteristics of sul3 Positive Escherichia coli Isolated from Animals in Nanning, Guangxi Province. Animals (Basel) 2022; 12:ani12080976. [PMID: 35454223 PMCID: PMC9025041 DOI: 10.3390/ani12080976] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 01/27/2023] Open
Abstract
Sulfonamides are the second most popular antibiotic in many countries, which leads to the widespread emergence of sulfonamides resistance. sul3 is a more recent version of the gene associated with sulfonamide resistance, whose research is relatively little. In order to comprehend the prevalence of sul3 positive E. coli from animals in Nanning, a total of 146 strains of E. coli were identified from some farms and pet hospitals from 2015 to 2017. The drug resistance and prevalence of sul3 E. coli were analyzed by polymerase chain reaction (PCR) identification, multi-site sequence typing (MLST), drug sensitivity test, and drug resistance gene detection, and then the plasmid containing sul3 was conjugated with the recipient strain (C600). The effect of sul3 plasmid on the recipient was analyzed by stability, drug resistance, and competitive test. In this study, forty-six sul3 positive E. coli strains were separated. A total of 12 ST types were observed, and 1 of those was a previously unknown type. The ST350 is the most numerous type. All isolates were multidrug-resistant E. coli, with high resistant rates to penicillin, ceftriaxone sodium, streptomycin, tetracycline, ciprofloxacin, gatifloxacin, and chloramphenicol (100%, 73.9%, 82.6%, 100%, 80.4%, 71.7%, and 97.8%, respectively). They had at least three antibiotic resistance genes (ARGs) in addition to sul3. The plasmids transferred from three sul3-positive isolates to C600, most of which brought seven antimicrobial resistance (AMR) and increased ARGs to C600. The transferred sul3 gene and the plasmid carrying sul3 could be stably inherited in the recipient bacteria for at least 20 days. These plasmids had no effect on the growth of the recipient bacteria but greatly reduced the competitiveness of the strain at least 60 times in vitro. In Nanning, these sul3-positive E. coli had such strong AMR, and the plasmid carrying sul3 had the ability to transfer multiple resistance genes that long-term monitoring was necessary. Since the transferred plasmid would greatly reduce the competitiveness of the strain in vitro, we could consider limiting the spread of drug-resistant isolates in this respect.
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21
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Extraintestinal Pathogenic Escherichia coli: Beta-Lactam Antibiotic and Heavy Metal Resistance. Antibiotics (Basel) 2022; 11:antibiotics11030328. [PMID: 35326791 PMCID: PMC8944441 DOI: 10.3390/antibiotics11030328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 02/25/2022] [Accepted: 02/26/2022] [Indexed: 12/10/2022] Open
Abstract
Multiple-antibiotic-resistant (MAR) extra-intestinal pathogenic Escherichia coli (ExPEC) represents one of the most frequent causes of human nosocomial and community-acquired infections, whose eradication is of major concern for clinicians. ExPECs may inhabit indefinitely as commensal the gut of humans and other animals; from the intestine, they may move to colonize other tissues, where they are responsible for a number of diseases, including recurrent and uncomplicated UTIs, sepsis and neonatal meningitis. In the pre-antibiotic era, heavy metals were largely used as chemotherapeutics and/or as antimicrobials in human and animal healthcare. As with antibiotics, the global incidence of heavy metal tolerance in commensal, as well as in ExPEC, has increased following the ban in several countries of antibiotics as promoters of animal growth. Furthermore, it is believed that extensive bacterial exposure to heavy metals present in soil and water might have favored the increase in heavy-metal-tolerant microorganisms. The isolation of ExPEC strains with combined resistance to both antibiotics and heavy metals has become quite common and, remarkably, it has been recently shown that heavy metal resistance genes may co-select antibiotic-resistance genes. Despite their clinical relevance, the mechanisms underlining the development and spread of heavy metal tolerance have not been fully elucidated. The aim of this review is to present data regarding the development and spread of resistance to first-line antibiotics, such as beta-lactams, as well as tolerance to heavy metals in ExPEC strains.
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22
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Hamame A, Davoust B, Rolain JM, Diene SM. Genomic characterisation of an mcr-1 and mcr-3-producing Escherichia coli strain isolated from pigs in France. J Glob Antimicrob Resist 2022; 28:174-179. [DOI: 10.1016/j.jgar.2022.01.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
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Ksiezarek M, Novais Â, Peixe L. The Darkest Place Is under the Candlestick-Healthy Urogenital Tract as a Source of Worldwide Disseminated Extraintestinal Pathogenic Escherichia coli Lineages. Microorganisms 2021; 10:27. [PMID: 35056476 PMCID: PMC8778945 DOI: 10.3390/microorganisms10010027] [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: 11/28/2021] [Revised: 12/20/2021] [Accepted: 12/21/2021] [Indexed: 11/17/2022] Open
Abstract
Since the discovery of the urinary microbiome, including the identification of Escherichia coli in healthy hosts, its involvement in UTI development has been a subject of high interest. We explored the population diversity and antimicrobial resistance of E. coli (n = 22) in the urogenital microbiome of ten asymptomatic women (representing 50% of the sample tested). We evaluated their genomic relationship with extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, including the ST131 lineage. E. coli prevalence was higher in vaginal samples than in urine samples, and occasionally different lineages were observed in the same individual. Furthermore, B2 was the most frequent phylogenetic group, with the most strains classified as ExPEC. Resistance to antibiotics of therapeutic relevance (e.g., amoxicillin-clavulanate conferred by blaTEM-30) was observed in ExPEC widespread lineages sequence types (ST) 127, ST131, and ST73 and ST95 clonal complexes. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness with strains from gastrointestinal tract and diseased host. These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including those causing UTI, e.g., ST131. Importantly, diverse E. coli lineages can be observed per individual and urogenital sample type which is relevant for future studies screening for this uropathogen.
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Affiliation(s)
- Magdalena Ksiezarek
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.K.); (Â.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ângela Novais
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.K.); (Â.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Luísa Peixe
- UCIBIO–Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (M.K.); (Â.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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24
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Physical, Mechanical, and Water Vapor Barrier Properties of Starch/Cellulose Nanofiber/Thymol Bionanocomposite Films. Polymers (Basel) 2021; 13:polym13234060. [PMID: 34883563 PMCID: PMC8659141 DOI: 10.3390/polym13234060] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/29/2021] [Accepted: 10/30/2021] [Indexed: 12/23/2022] Open
Abstract
The application of starch films, such as food packaging materials, has been restricted due to poor mechanical and barrier properties. However, the addition of a reinforcing agent, cellulose nanofibers (CNF) and also thymol, into the films, may improve the properties of films. This work investigates the effects of incorporating different concentrations of thymol (3, 5, 7, and 10 wt.%) on physical, mechanical, water vapor barrier, and antibacterial properties of corn starch films, containing 1.5 wt.% CNF produced using the solvent casting method. The addition of thymol does not significantly affect the color and opacity of the films. It is found that the tensile strength and Young’s modulus of the films decreases from 10.6 to 6.3 MPa and from 436.9 to 209.8 MPa, respectively, and the elongation at break increased from 110.6% to 123.5% with the incorporation of 10 wt.% thymol into the films. Furthermore, the addition of thymol at higher concentrations (7 and 10 wt.%) improved the water vapor barrier of the films by approximately 60.0%, from 4.98 × 10—9 to 2.01 × 10—9 g/d.m.Pa. Starch/CNF/thymol bionanocomposite films are also found to exhibit antibacterial activity against Escherichia coli. In conclusion, the produced starch/CNF/thymol bionanocomposite films have the potential to be used as antibacterial food packaging materials.
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25
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Tate H, Li C, Nyirabahizi E, Tyson GH, Zhao S, Rice-Trujillo C, Jones SB, Ayers S, M'ikanatha NM, Hanna S, Ruesch L, Cavanaugh ME, Laksanalamai P, Mingle L, Matzinger SR, McDermott PF. A National Antimicrobial Resistance Monitoring System Survey of Antimicrobial-Resistant Foodborne Bacteria Isolated from Retail Veal in the United States. J Food Prot 2021; 84:1749-1759. [PMID: 34015113 DOI: 10.4315/jfp-21-005] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 05/16/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Little is known about the prevalence of antimicrobial-resistant (AMR) bacteria in veal meat in the United States. We estimated the prevalence of bacterial contamination and AMR in various veal meats collected during the 2018 U.S. National Antimicrobial Resistance Monitoring System (NARMS) survey of retail outlets in nine states and compared the prevalence with the frequency of AMR bacteria from other cattle sources sampled for NARMS. In addition, we identified genes associated with resistance to medically important antimicrobials and gleaned other genetic details about the resistant organisms. The prevalence of Campylobacter, Salmonella, Escherichia coli, and Enterococcus in veal meats collected from grocery stores in nine states was 0% (0 of 358), 0.6% (2 of 358), 21.1% (49 of 232), and 53.5% (121 of 226), respectively, with ground veal posing the highest risk for contamination. Both Salmonella isolates were resistant to at least one antimicrobial agent as were 65.3% (32 of 49) of E. coli and 73.6% (89 of 121) of Enterococcus isolates. Individual drug and multiple drug resistance levels were significantly higher (P < 0.05) in E. coli and Enterococcus from retail veal than in dairy cattle ceca and retail ground beef samples from 2018 NARMS data. Whole genome sequencing was conducted on select E. coli and Salmonella from veal. Cephalosporin resistance (blaCMY and blaCTX-M), macrolide resistance (mph), and plasmid-mediated quinolone resistance (qnr) genes and gyrA mutations were found. We also identified heavy metal resistance genes ter, ars, mer, fieF, and gol and disinfectant resistance genes qac and emrE. An stx1a-containing E. coli was also found. Sequence types were highly varied among the nine E. coli isolates that were sequenced. Several plasmid types were identified in E. coli and Salmonella, with the majority (9 of 11) of isolates containing IncF. This study illustrates that veal meat is a carrier of AMR bacteria. HIGHLIGHTS
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Affiliation(s)
- Heather Tate
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Cong Li
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Epiphanie Nyirabahizi
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Gregory H Tyson
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Shaohua Zhao
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Crystal Rice-Trujillo
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Sonya Bodeis Jones
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Sherry Ayers
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
| | - Nkuchia M M'ikanatha
- Division of Infectious Disease Epidemiology, Pennsylvania Department of Health, 7th and Forster Streets, Harrisburg, Pennsylvania 17120
| | - Samir Hanna
- Tennessee Department of Health, 710 James Robertson Parkway, Nashville, Tennessee 37243
| | - Laura Ruesch
- Animal Disease Research and Diagnostic Lab, South Dakota State University, Brookings, South Dakota 57007
| | | | - Pongpan Laksanalamai
- Laboratories Administration, Maryland Department of Health, 1770 Ashland Avenue, Baltimore, Maryland 21205
| | - Lisa Mingle
- Wadsworth Center Division of Infectious Diseases, New York State Department of Health, Albany, New York 12208
| | - Shannon R Matzinger
- Colorado Department of Public Health and Environment, 8100 Lowry Boulevard, Denver, Colorado 80230, USA
| | - Patrick F McDermott
- Center for Veterinary Medicine, U.S. Food and Drug Administration, 8401 Muirkirk Road, Laurel, Maryland 20708
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Sanches MS, Rodrigues da Silva C, Silva LC, Montini VH, Lopes Barboza MG, Migliorini Guidone GH, Dias de Oliva BH, Nishio EK, Faccin Galhardi LC, Vespero EC, Lelles Nogueira MC, Dejato Rocha SP. Proteus mirabilis from community-acquired urinary tract infections (UTI-CA) shares genetic similarity and virulence factors with isolates from chicken, beef and pork meat. Microb Pathog 2021; 158:105098. [PMID: 34280499 DOI: 10.1016/j.micpath.2021.105098] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/08/2021] [Accepted: 07/15/2021] [Indexed: 11/16/2022]
Abstract
Proteus mirabilis is an opportunistic pathogen associated with a variety of infections in humans, especially those in the urinary tract. The isolation of this pathogen in foods of animal origin such as meat is poorly documented and should not be neglected, in view of the zoonotic risk that this can pose to human health. Thus, the objective of this study was to evaluate the prevalence, virulence profile, and similarity between P. mirabilis strains isolated from chicken, beef, and pork meat and those causing community-acquired urinary tract infections (UTI-CA), in order to better understand the role of this bacterium as a zoonotic pathogen. P. mirabilis was isolated from the three types of meat and was found to be more prevalent in chicken. All isolates exhibited several genotypic and phenotypic virulence characteristics, such as adhesion capacity in HEp-2 cell culture, biofilm formation, cytotoxicity in Vero cells and genes that express fimbriae (mrpA, pmfA, ucaA, atfA), hemolysin (hpmA), proteases (zapA and ptA) and siderophore receptor (ireA). UTI-CA strains showed a higher prevalence of ucaA and ireA genes, whereas those from the chicken meat had a higher prevalence of the atfA gene compared with the isolates from the beef and pork meat. It was observed that chicken meat and UTI-CA strains mainly formed very strong biofilms, whereas strains isolated from beef and pork formed more weak and moderate biofilms. Several strains from meat showed close genetic similarity to those from UTI-CA and had the same virulence profiles. Thus, meats may be an important source of the dissemination of P. mirabilis responsible for causing UTIs in the community.
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Affiliation(s)
- Matheus Silva Sanches
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Caroline Rodrigues da Silva
- Microorganism Research Center, Department of Dermatological, Infectious and Parasitic Diseases, Health Sciences Center, Medical School of São José Do Rio Preto, São José Do Rio Preto, São Paulo, Brazil
| | - Luana Carvalho Silva
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Victor Hugo Montini
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Mario Gabriel Lopes Barboza
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | | | - Bruno Henrique Dias de Oliva
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Erick Kenji Nishio
- Laboratory of Basic and Applied Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Ligia Carla Faccin Galhardi
- Virology Laboratory, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil
| | - Eliana Carolina Vespero
- Department of Pathology, Clinical and Toxicological Analysis, Health Sciences Center, University Hospital of Londrina, State University of Londrina, Paraná, Brazil
| | - Mara Corrêa Lelles Nogueira
- Microorganism Research Center, Department of Dermatological, Infectious and Parasitic Diseases, Health Sciences Center, Medical School of São José Do Rio Preto, São José Do Rio Preto, São Paulo, Brazil
| | - Sergio Paulo Dejato Rocha
- Laboratory of Bacteriology, Department of Microbiology, Center of Biological Sciences, State University of Londrina, Londrina, Brazil.
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Prevalence and risk factors for faecal carriage of multidrug resistant Escherichia coli among slaughterhouse workers. Sci Rep 2021; 11:13362. [PMID: 34172803 PMCID: PMC8233315 DOI: 10.1038/s41598-021-92819-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 06/16/2021] [Indexed: 12/13/2022] Open
Abstract
The increasing occurrence of antimicrobial-resistant Escherichia coli in human and animal population has become a global public health problem that requires immediate intervention. We aimed to investigate prevalence and risk factors for faecal carriage of drug-resistant E. coli among slaughterhouse workers. We conducted this cross-sectional study among 118 apparently healthy workers in the largest slaughterhouses in Abuja and Lagos from July to December 2020. E. coli was isolated from stool samples of slaughterhouse workers and antimicrobial susceptibility testing performed using the Kirby-Bauer disk diffusion method. Multi-drug resistance (MDR) was defined as resistance to three or more classes of antibiotics. Majority were males: 88.1% (n = 104), aged > 41 years: 28.8% (n = 34), married: 70.3% (n = 83), and were butchers: 53.4% (n = 63). Prevalence of MDR E. coli was 50% (n = 59), highest among butchers compared to slaughterhouse cleaners. Of 75 E. coli isolates identified, 25.3% (n = 19) were ESBL producers; 78.7% (n = 59) were MDR. Keeping animals (p = 0.01); eating at the slaughterhouse (p = 0.03) and collecting waste (p = 0.02) remained independent risk factors for acquiring MDR E. coli. Prevalence of resistant E. coli was highest among butchers and associated with keeping animals at home, eating at work, and waste-collection. Hand-hygiene and responsible use of antibiotics among slaughterhouse workers should be encouraged.
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Diversity and Adaptations of Escherichia coli Strains: Exploring the Intestinal Community in Crohn's Disease Patients and Healthy Individuals. Microorganisms 2021; 9:microorganisms9061299. [PMID: 34203637 PMCID: PMC8232093 DOI: 10.3390/microorganisms9061299] [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: 05/18/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/17/2022] Open
Abstract
Crohn's disease (CD) is characterized by a chronic, progressive inflammation across the gastrointestinal tract with a series of exacerbations and remissions. A significant factor in the CD pathogenesis is an imbalance in gut microbiota composition, particularly the prevalence of Escherichia coli. In the present study, the genomes of sixty-three E. coli strains from the gut of patients with CD and healthy subjects were sequenced. In addition, eighteen E. coli-like metagenome-assembled genomes (MAGs) were reconstructed from the shotgun-metagenome sequencing data of fecal samples. The comparative analysis revealed the similarity of E. coli genomes regardless of the origin of the strain. The strains exhibited similar genetic patterns of virulence, antibiotic resistance, and bacteriocin-producing systems. The study showed antagonistic activity of E. coli strains and the metabolic features needed for their successful competition in the human gut environment. These observations suggest complex bacterial interactions within the gut which may affect the host and cause intestinal damage.
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Hu Y, Rubin J, Mussio K, Riley LW. Risk factors for faecal carriage of multidrug-resistant Escherichia coli in a college community: a penalised regression model. J Glob Antimicrob Resist 2021; 26:166-173. [PMID: 34051401 DOI: 10.1016/j.jgar.2021.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 04/02/2021] [Accepted: 05/16/2021] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Bacterial antimicrobial resistance is a serious global public-health threat. Intestinal commensal drug-resistant bacteria have been suggested as an important reservoir of antimicrobial resistance genes (ARGs), which may be acquired via food. We aimed to identify risk factors associated with faecal carriage of drug-resistant commensal Escherichia coli among healthy adults focused on their dietary habits. METHODS We conducted a cross-sectional study targeting healthy adult volunteers in a college community. Faecal samples and questionnaires were obtained from 113 volunteers. We conducted backward elimination logistic regression and least absolute shrinkage and selection operator (LASSO) methods to identify risk factors. RESULTS We analysed responses from 81 of 113 volunteers who completed the questionnaire. The logistic regression and LASSO methods identified red meat consumption to be associated with an increased risk [OR = 6.13 (95% CI 1.83-24.2) and 1.82, respectively] and fish consumption with a reduced risk [OR = 0.27 (95% CI 0.08-0.85) and 0.81] for carriage of multidrug-resistant (MDR) E. coli, adjusted for biological sex, employment status, frequently used supermarket and previous travel. CONCLUSION Dietary habits are associated with risk of faecal carriage of MDR E. coli. This study supports the growing evidence that food may be an important source of ARGs present in human commensal E. coli.
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Affiliation(s)
- Yuan Hu
- Division of Epidemiology, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Julia Rubin
- Division of Environmental Health Science, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Kaitlyn Mussio
- Division of Environmental Health Science, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
| | - Lee W Riley
- Division of Infectious Diseases and Immunology, School of Public Health, University of California Berkeley, Berkeley, CA 94720, USA
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30
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Graham JP, Amato H, Mendizabal-Cabrera R, Alvarez D, Ramay B. Waterborne Urinary Tract Infections: Have We Overlooked an Important Source of Exposure? Am J Trop Med Hyg 2021; 105:12-17. [PMID: 33939640 DOI: 10.4269/ajtmh.20-1271] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/16/2021] [Indexed: 11/07/2022] Open
Abstract
The presence of intestinal pathogenic Escherichia coli in drinking water is well recognized as a risk for diarrhea. The role of drinking water in extraintestinal infections caused by E. coli-such as urinary tract infections (UTIs)-remains poorly understood. Urinary tract infections are a leading cause of outpatient infections globally, with a lifetime incidence of 50-60% in adult women. We reviewed the scientific literature on the occurrence of uropathogenic E. coli (UPEC) in water supplies to determine whether the waterborne route may be an important, overlooked, source of UPEC. A limited number of studies have assessed whether UPEC isolates are present in drinking water supplies, but no studies have measured whether their presence in water may increase UPEC colonization or the risk of UTIs in humans. Given the prevalence of drinking water supplies contaminated with E. coli across the globe, efforts should be made to characterize UTI-related risks associated with drinking water, as well as other pathways of exposure.
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Affiliation(s)
- Jay P Graham
- 1Berkeley School of Public Health, University of California Berkeley, Berkeley, California
| | - Heather Amato
- 2Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | | | - Danilo Alvarez
- 2Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala
| | - Brooke Ramay
- 2Center for Health Studies, Universidad del Valle de Guatemala, Guatemala City, Guatemala.,3Paul G. Allen School for Global Animal Health, Washington State University Pullman, Guatemala City, Guatemala
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Díaz-Jiménez D, García-Meniño I, Herrera A, Lestón L, Mora A. Microbiological risk assessment of Turkey and chicken meat for consumer: Significant differences regarding multidrug resistance, mcr or presence of hybrid aEPEC/ExPEC pathotypes of E. coli. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Murray M, Salvatierra G, Dávila-Barclay A, Ayzanoa B, Castillo-Vilcahuaman C, Huang M, Pajuelo MJ, Lescano AG, Cabrera L, Calderón M, Berg DE, Gilman RH, Tsukayama P. Market Chickens as a Source of Antibiotic-Resistant Escherichia coli in a Peri-Urban Community in Lima, Peru. Front Microbiol 2021; 12:635871. [PMID: 33737922 PMCID: PMC7961087 DOI: 10.3389/fmicb.2021.635871] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/02/2021] [Indexed: 12/17/2022] Open
Abstract
The widespread and poorly regulated use of antibiotics in animal production in low- and middle-income countries (LMICs) is increasingly associated with the emergence and dissemination of antibiotic resistance genes (ARGs) in retail animal products. Here, we compared Escherichia coli from chickens and humans with varying levels of exposure to chicken meat in a low-income community in the southern outskirts of Lima, Peru. We hypothesize that current practices in local poultry production result in highly resistant commensal bacteria in chickens that can potentially colonize the human gut. E. coli was isolated from cloacal swabs of non-organic (n = 41) and organic chickens (n = 20), as well as from stools of market chicken vendors (n = 23), non-vendors (n = 48), and babies (n = 60). 315 E. coli isolates from humans (n = 150) and chickens (n = 165) were identified, with chickens showing higher rates of multidrug-resistant and extended-spectrum beta-lactamase phenotypes. Non-organic chicken isolates were more resistant to most antibiotics tested than human isolates, while organic chicken isolates were susceptible to most antibiotics. Whole-genome sequencing of 118 isolates identified shared phylogroups between human and animal populations and 604 ARG hits across genomes. Resistance to florfenicol (an antibiotic commonly used as a growth promoter in poultry but not approved for human use) was higher in chicken vendors compared to other human groups. Isolates from non-organic chickens contained genes conferring resistance to clinically relevant antibiotics, including mcr-1 for colistin resistance, blaCTX-M ESBLs, and blaKPC-3 carbapenemase. Our findings suggest that E. coli strains from market chickens are a potential source of ARGs that can be transmitted to human commensals.
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Affiliation(s)
- Matthew Murray
- Johns Hopkins School of Medicine, Baltimore, MD, United States
| | - Guillermo Salvatierra
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.,Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandra Dávila-Barclay
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Brenda Ayzanoa
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Camila Castillo-Vilcahuaman
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Michelle Huang
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Mónica J Pajuelo
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Laboratorio de Microbiología Molecular, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Andrés G Lescano
- Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Maritza Calderón
- Laboratorios de Enfermedades Infecciosas, Laboratorios de Investigación y Desarrollo, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Douglas E Berg
- Department of Medicine, University of California, San Diego, San Diego, CA, United States
| | - Robert H Gilman
- Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Peru.,Emerge, Emerging Diseases and Climate Change Research Unit, School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru.,Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.,Wellcome Sanger Institute, Hinxton, United Kingdom
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Szmolka A, Wami H, Dobrindt U. Comparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli. Front Microbiol 2021; 12:642125. [PMID: 33717039 PMCID: PMC7947892 DOI: 10.3389/fmicb.2021.642125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/03/2021] [Indexed: 01/06/2023] Open
Abstract
Introduction Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants. Objectives In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources. Results The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis. Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers. Conclusion This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.
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Affiliation(s)
- Ama Szmolka
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Budapest, Hungary
| | - Haleluya Wami
- Institute of Hygiene, University of Münster, Münster, Germany
| | - Ulrich Dobrindt
- Institute of Hygiene, University of Münster, Münster, Germany
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Effect of Hydrolysable Tannins and Anthocyanins on Recurrent Urinary Tract Infections in Nephropathic Patients: Preliminary Data. Nutrients 2021; 13:nu13020591. [PMID: 33670236 PMCID: PMC7916964 DOI: 10.3390/nu13020591] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/11/2022] Open
Abstract
Urinary tract infections (UTIs) are caused by uropathogenic microorganism colonization. UTIs often require an antibiotic therapy that can cause the selection of antibiotic-resistant bacterial strains. A natural bioactive compound may represent a valid therapeutic adjuvant approach, in combination with drug therapy. In this paper, we present a pilot study, based on the administration of an oral food supplement (OFS), containing chestnut tannins and anthocyanins, to nephropathic patients suffering from recurrent UTIs (16 treated patients with 1 cp/day and 10 untreated patients). We performed laboratory tests and quality of life and body composition assessments, at T0 (baseline) and T1 (after 6 weeks OFS assumption). The analysis of OFS was performed by HPLC-DAD-MS for its content in polyphenols and by in vitro tests for its antioxidative and anti-free radical activities. In each capsule, polyphenol content was 6.21 mg (4.57 mg hydrolysable tannins, 0.94 mg anthocyanosides, 0.51 mg proanthocyanidins, 0.18 mg quercetin derivatives). A significant reduction of erythrocyte sedimentation rate was observed only in male patients. Urinalysis showed a significant reduction of leukocytes in both genders, whereas urinary bacterial flora at T1 significantly decreased only in male subjects. Tannins seem to exert an antimicrobial action according to gender, useful to counteract the recurrence of UTIs.
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Kurittu P, Khakipoor B, Aarnio M, Nykäsenoja S, Brouwer M, Myllyniemi AL, Vatunen E, Heikinheimo A. Plasmid-Borne and Chromosomal ESBL/AmpC Genes in Escherichia coli and Klebsiella pneumoniae in Global Food Products. Front Microbiol 2021; 12:592291. [PMID: 33613476 PMCID: PMC7886708 DOI: 10.3389/fmicb.2021.592291] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/14/2021] [Indexed: 01/09/2023] Open
Abstract
Plasmid-mediated extended-spectrum beta-lactamase (ESBL), AmpC, and carbapenemase producing Enterobacteriaceae, in particular Escherichia coli and Klebsiella pneumoniae, with potential zoonotic transmission routes, are one of the greatest threats to global health. The aim of this study was to investigate global food products as potential vehicles for ESBL/AmpC-producing bacteria and identify plasmids harboring resistance genes. We sampled 200 food products purchased from Finland capital region during fall 2018. Products originated from 35 countries from six continents and represented four food categories: vegetables (n = 60), fruits and berries (n = 50), meat (n = 60), and seafood (n = 30). Additionally, subsamples (n = 40) were taken from broiler meat. Samples were screened for ESBL/AmpC-producing Enterobacteriaceae and whole genome sequenced to identify resistance and virulence genes and sequence types (STs). To accurately identify plasmids harboring resistance and virulence genes, a hybrid sequence analysis combining long- and short-read sequencing was employed. Sequences were compared to previously published plasmids to identify potential epidemic plasmid types. Altogether, 14 out of 200 samples were positive for ESBL/AmpC-producing E. coli and/or K. pneumoniae. Positive samples were recovered from meat (18%; 11/60) and vegetables (5%; 3/60) but were not found from seafood or fruit. ESBL/AmpC-producing E. coli and/or K. pneumoniae was found in 90% (36/40) of broiler meat subsamples. Whole genome sequencing of selected isolates (n = 21) revealed a wide collection of STs, plasmid replicons, and genes conferring multidrug resistance. blaCTX–M–15-producing K. pneumoniae ST307 was identified in vegetable (n = 1) and meat (n = 1) samples. Successful IncFII plasmid type was recovered from vegetable and both IncFII and IncI1-Iγ types from meat samples. Hybrid sequence analysis also revealed chromosomally located beta-lactamase genes in two of the isolates and indicated similarity of food-derived plasmids to other livestock-associated sources and also to plasmids obtained from human clinical samples from various countries, such as IncI type plasmid harboring blaTEM–52C from a human urine sample obtained in the Netherlands which was highly similar to a plasmid obtained from broiler meat in this study. Results indicate certain foods contain bacteria with multidrug resistance and pose a possible risk to public health, emphasizing the importance of surveillance and the need for further studies on epidemiology of epidemic plasmids.
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Affiliation(s)
- Paula Kurittu
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Banafsheh Khakipoor
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.,Finnish Food Authority, Seinäjoki, Finland
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Chuang S, Sheen S, Sommers CH, Sheen LY. Modeling the effect of simultaneous use of allyl isothiocyanate and cinnamaldehyde on high hydrostatic pressure inactivation of Uropathogenic and Shiga toxin-producing Escherichia coli in ground chicken. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:1193-1201. [PMID: 32785931 DOI: 10.1002/jsfa.10731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/07/2020] [Accepted: 08/12/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND A combination of high-pressure processing (HPP) and antimicrobials is a well-known approach for enhancing the microbiological safety of foods. However, few studies have applied multiple antimicrobials simultaneously with HPP, which could be an additional hurdle for microbial inactivation. The present study applied a full factorial design to investigate the impact of HPP (225-325 MPa; 10-20 min), allyl isothiocyanate (AITC) (0.3-0.9 g kg-1 ) and trans-cinnamaldehyde (tCinn) (1.0-2.0 g kg-1 ) on the inactivation of Shiga toxin-producing Escherichia coli (STEC) O157:H7 and uropathogenic E. coli (UPEC) in ground chicken meat. RESULTS The regulatory requirement of 5-log reduction was achieved at 305 MPa, 18 min, 0.8 g kg-1 AITC and 1.7 g kg-1 tCinn for STEC O157:H7 and at 293 MPa, 16 min, 0.6 g kg-1 AITC and 1.6 g kg-1 tCinn for UPEC, as specified by response surface analysis and verified via experiments. The surviving population was eliminated by post-treatment storage of 9 days at 10 °C. The developed linear regression models showed r2 > 0.9 for the E. coli inactivation. The developed dimensionless non-linear regression models covered a factorial range slightly wider than the original experimental limit, with probability Pr > F (< 0.0001). CONCLUSION Simultaneous use of AITC and tCinn reduced not only the necessary concentration of each compound, but also the intensity of high-pressure treatments, at the same time achieving a similar level of microbial inactivation. STEC O157:H7 was found to be more resistant than UPEC to the HPP-AITC-tCinn stress. The developed models may be applied in commercial application to enhance the microbiological safety of ground chicken meat. Published 2020. This article is a U.S. Government work and is in the public domain in the USA.
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Affiliation(s)
- Shihyu Chuang
- Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Shiowshuh Sheen
- Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - Christopher H Sommers
- Eastern Regional Research Center, Agricultural Research Service, US Department of Agriculture, Wyndmoor, PA, USA
| | - Lee-Yan Sheen
- Institute of Food Science and Technology, National Taiwan University, Taipei, Taiwan
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Genomic Investigation into the Virulome, Pathogenicity, Stress Response Factors, Clonal Lineages, and Phylogenetic Relationship of Escherichia coli Strains Isolated from Meat Sources in Ghana. Genes (Basel) 2020; 11:genes11121504. [PMID: 33327465 PMCID: PMC7764966 DOI: 10.3390/genes11121504] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/26/2022] Open
Abstract
Escherichia coli are among the most common foodborne pathogens associated with infections reported from meat sources. This study investigated the virulome, pathogenicity, stress response factors, clonal lineages, and the phylogenomic relationship of E. coli isolated from different meat sources in Ghana using whole-genome sequencing. Isolates were screened from five meat sources (beef, chevon, guinea fowl, local chicken, and mutton) and five areas (Aboabo, Central market, Nyorni, Victory cinema, and Tishegu) based in the Tamale Metropolis, Ghana. Following microbial identification, the E. coli strains were subjected to whole-genome sequencing. Comparative visualisation analyses showed different DNA synteny of the strains. The isolates consisted of diverse sequence types (STs) with the most common being ST155 (n = 3/14). Based Upon Related Sequence Types (eBURST) analyses of the study sequence types identified four similar clones, five single-locus variants, and two satellite clones (more distantly) with global curated E. coli STs. All the isolates possessed at least one restriction-modification (R-M) and CRISPR defence system. Further analysis revealed conserved stress response mechanisms (detoxification, osmotic, oxidative, and periplasmic stress) in the strains. Estimation of pathogenicity predicted a higher average probability score (Pscore ≈ 0.937), supporting their pathogenic potential to humans. Diverse virulence genes that were clonal-specific were identified. Phylogenomic tree analyses coupled with metadata insights depicted the high genetic diversity of the E. coli isolates with no correlation with their meat sources and areas. The findings of this bioinformatic analyses further our understanding of E. coli in meat sources and are broadly relevant to the design of contamination control strategies in meat retail settings in Ghana.
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Extended spectrum β lactamase-producing Enterobacteriaceae shedding by race horses in Ontario, Canada. BMC Vet Res 2020; 16:479. [PMID: 33298039 PMCID: PMC7726890 DOI: 10.1186/s12917-020-02701-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 12/02/2020] [Indexed: 11/29/2022] Open
Abstract
Background We aimed to investigate the prevalence, molecular epidemiology and prevalence factors for Extended Spectrum β-Lactamase-producing Enterobacteriaceae (ESBL-E) shedding by race horses. A cross-sectional study was performed involving fecal samples collected from 169 Thoroughbred horses that were housed at a large racing facility in Ontario, Canada. Samples were enriched, plated on selective plates, sub-cultured to obtain pure cultures and ESBL production was confirmed. Bacterial species were identified and antibiotic susceptibility profiles were assessed. E. coli sequence types (ST) and ESBL genes were determined using multilocus sequence type (MLST) and sequencing. Whole genome sequencing was performed to isolates harboring CTX-M-1 gene. Medical records were reviewed and associations were investigated. Results Adult horses (n = 169), originating from 16 different barns, were sampled. ESBL-E shedding rate was 12% (n = 21/169, 95% CI 8–18%); 22 ESBL-E isolates were molecularly studied (one horse had two isolates). The main species was E. coli (91%) and the major ESBL gene was CTX-M-1 (54.5%). Ten different E. coli STs were identified. Sixty-four percent of total isolates were defined as multi-drug resistant. ESBL-E shedding horses originated from 8/16 different barns; whereas 48% (10/21) of them originated from one specific barn. Overall, antibiotic treatment in the previous month was found as a prevalence factor for ESBL-E shedding (p = 0.016, prevalence OR = 27.72, 95% CI 1.845–416.555). Conclusions Our findings demonstrate the potential diverse reservoir of ESBL-E in Thoroughbred race horses. Multi-drug resistant bacteria should be further investigated to improve antibiotic treatment regimens and equine welfare. Supplementary Information The online version contains supplementary material available at 10.1186/s12917-020-02701-z.
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Liao N, Borges CA, Rubin J, Hu Y, Ramirez HA, Chen J, Zhou B, Zhang Y, Zhang R, Jiang J, Riley LW. Prevalence of β-Lactam Drug-Resistance Genes in Escherichia coli Contaminating Ready-to-Eat Lettuce. Foodborne Pathog Dis 2020; 17:739-742. [PMID: 33112663 DOI: 10.1089/fpd.2020.2792] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Thirty-four Escherichia coli isolates from 91 ready-to-eat lettuce packages, obtained from local supermarkets in Northern California, were genotyped by multilocus sequence typing, tested for susceptibility to antimicrobial agents, and screened for β-lactamase genes. We found 15 distinct sequence types (STs). Six of these genotypes (ST1198, ST2625, ST2432, ST2819, ST4600, and ST5143) have been reported as pathogens found in human samples. Twenty-six (76%) E. coli isolates were resistant to ampicillin, 17 (50%) to ampicillin/sulbactam, 8 (23%) to cefoxitin, and 7 (20%) to cefuroxime. blaCTX-M was the most prevalent β-lactamase gene, identified in eight (23%) isolates. We identified a class A broad-spectrum β-lactamase SED-1 gene, blaSED, reported by others in Citrobacter sedlakii isolated from bile of a patient. This study found that fresh lettuce carries β-lactam drug-resistant E. coli, which might serve as a reservoir for drug-resistance genes that could potentially be transmitted to pathogens that cause human infections.
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Affiliation(s)
- Ningbo Liao
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, China
| | - Clarissa A Borges
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Julia Rubin
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Yuan Hu
- Division of Epidemiology, School of Public Health, University of California, Berkeley, California, USA
| | - Hector A Ramirez
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
| | - Jiang Chen
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Biao Zhou
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yanjun Zhang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Ronghua Zhang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Jianmin Jiang
- Department of Nutrition and Food Safety, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, California, USA
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Riley LW. Distinguishing Pathovars from Nonpathovars: Escherichia coli. Microbiol Spectr 2020; 8:10.1128/microbiolspec.ame-0014-2020. [PMID: 33385193 PMCID: PMC10773148 DOI: 10.1128/microbiolspec.ame-0014-2020] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.
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Affiliation(s)
- Lee W Riley
- Division of Infectious Diseases and Vaccinology, School of Public Health, University of California, Berkeley, CA 94720
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41
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Meena PR, Yadav P, Hemlata H, Tejavath KK, Singh AP. Poultry-origin extraintestinal Escherichia coli strains carrying the traits associated with urinary tract infection, sepsis, meningitis and avian colibacillosis in India. J Appl Microbiol 2020; 130:2087-2101. [PMID: 33095966 DOI: 10.1111/jam.14905] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 10/03/2020] [Accepted: 10/12/2020] [Indexed: 12/29/2022]
Abstract
AIM In-depth 'One Health' risk assessment of extraintestinal pathogenic Escherichia coli (ExPEC) strains carrying the traits of urinary tract infection, sepsis, meningitis and avian colibacillosis in poultry of India. METHODS AND RESULTS A total of 230 E. coli isolates were recovered from chicken samples representing the different sources (faeces vs caeca), stages (poultry farms vs retails butcher shop) or environments (rural vs urban) of poultry in India. Among all poultry-origin E. coli isolates, 49 (21·1%) strains were identified as ExPEC possessing multiple virulence determinants regardless of their association with any specific phylogenetic lineages. Of particular, potentially virulent ExPEC pathotypes, that is, uropathogenic E.coli (UPEC, 20·4%), avian pathogenic E. coli (APEC, 34·6%), septicaemia-associated E. coli (SEPEC, 47·0%) and neonatal meningitis-causing E.39 coli (NMEC, 2·0%) were also detected among all ExPEC strains. CONCLUSIONS Our study is the first to assess ExPEC strains circulating in the different settings of poultry in India and significantly demonstrates their potential ability to cause multiple extraintestinal infections both in humans and animals. SIGNIFICANCE AND IMPACT OF THE STUDY The data of our study are in favour of the possibility that poultry-origin putative virulent ExPEC pathotypes consequently constitute a threat risk to 'One Health' or for food safety and a great concern for poultry production of India.
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Affiliation(s)
- P R Meena
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - P Yadav
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - H Hemlata
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - K K Tejavath
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
| | - A P Singh
- Department of Microbiology, School of Life Sciences, Central University of Rajasthan, Rajasthan, India
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Valiatti TB, Santos FF, Santos ACM, Nascimento JAS, Silva RM, Carvalho E, Sinigaglia R, Gomes TAT. Genetic and Virulence Characteristics of a Hybrid Atypical Enteropathogenic and Uropathogenic Escherichia coli (aEPEC/UPEC) Strain. Front Cell Infect Microbiol 2020; 10:492. [PMID: 33134184 PMCID: PMC7550682 DOI: 10.3389/fcimb.2020.00492] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/08/2020] [Indexed: 12/23/2022] Open
Abstract
Hybrid strains of Escherichia coli combine virulence traits of diarrheagenic (DEC) and extraintestinal pathogenic E. coli (ExPEC), but it is poorly understood whether these combined features improve the virulence potential of such strains. We have previously identified a uropathogenic E. coli (UPEC) strain (UPEC 252) harboring the eae gene that encodes the adhesin intimin and is located in the locus of enterocyte effacement (LEE) pathogenicity island. The LEE-encoded proteins allow enteropathogenic E. coli (EPEC) and enterohemorrhagic E. coli (EHEC) to form attaching and effacing (A/E) lesions in enterocytes. We sought to characterize UPEC 252 through whole-genome sequencing and phenotypic virulence assays. Genome analysis unveiled that this strain harbors a complete LEE region, with more than 97% of identity comparing to E2348/69 (EPEC) and O157:H7 Sakai (EHEC) prototype strains, which was functional, since UPEC 252 expressed the LEE-encoded proteins EspB and intimin and induced actin accumulation foci in HeLa cells. Phylogenetic analysis performed comparing 1,000 single-copy shared genes clustered UPEC 252 with atypical EPEC strains that belong to the sequence type 10, phylogroup A. Additionally, UPEC 252 was resistant to the bactericidal power of human serum and colonized cells of the urinary (T24 and HEK293-T) and intestinal (Caco-2 and LS174T) tracts. Our findings suggest that UPEC 252 is an atypical EPEC strain that emerges as a hybrid strain (aEPEC/UPEC), which could colonize new niches and potentially cause intestinal and extraintestinal infections.
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Affiliation(s)
- Tiago B Valiatti
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda F Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana C M Santos
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Júllia A S Nascimento
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rosa M Silva
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Eneas Carvalho
- Laboratório de Bacteriologia, Instituto Butantan, São Paulo, Brazil
| | - Rita Sinigaglia
- Centro de Microscopia Eletrônica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tânia A T Gomes
- Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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Zhi S, Stothard P, Banting G, Scott C, Huntley K, Ryu K, Otto S, Ashbolt N, Checkley S, Dong T, Ruecker NJ, Neumann NF. Characterization of water treatment-resistant and multidrug-resistant urinary pathogenic Escherichia coli in treated wastewater. WATER RESEARCH 2020; 182:115827. [PMID: 32580076 DOI: 10.1016/j.watres.2020.115827] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 04/06/2020] [Accepted: 04/11/2020] [Indexed: 05/29/2023]
Abstract
A growing body of evidence has demonstrated that extraintestinal pathogenic E. coli (ExPEC), such as the urinary pathogenic E. coli (UPEC), are common constituents of treated wastewater, and therefore represent a potential public health risk. However, no single virulence gene, or set of virulence genes, can be used to conclusively identify this genetically diverse pathotype. As such we sought to identify and characterize the public health relevance of potential UPEC found in treated sewage/wastewater using a comparative genomics approach. Presumptive wastewater UPEC (W-UPEC) were initially identified by virulence gene screening against 5 virulence genes, and for which isolates containing ≥3 virulence genes were whole genome sequenced (n = 24). Single nucleotide polymorphic (SNP) spanning tree analysis demonstrated that many of these wastewater UPEC (WUPEC) were virtually identical at the core genome (0.4 Mbp) when compared to clinical UPEC (C-UPEC) sequences obtained from NCBI, varying by as little as 1 SNP. Remarkably, at the whole genome level, W-UPEC isolates displayed >96% whole genome similarity to C-UPEC counterparts in NCBI, with one strain demonstrating 99.5% genome similarity to a particular C-UPEC strain. The W-UPEC populations were represented by sequence types (ST) known to be clinically important, including ST131, ST95, ST127 and ST640. Many of the W-UPEC carried the exact same complement of virulence genes as their most closely related C-UPEC strains. For example, O25b-ST131 W-UPEC strains possessed the same 80 virulence genes as their most closely related C-UPEC counterparts. Concerningly, W-UPEC strains also carried a plethora of antibiotic resistance genes, and O25b-ST131strains were designated as extended spectrum beta-lactamase (ESBL) producing E. coli by both genome profiling and phenotypic resistance testing. W-UPEC ST131 strains were found in the effluents of a single treatment plant at different times, as well as different wastewater treatment plants, suggesting a differentially ability to survive wastewater treatment. Indeed, in sewage samples treated with chlorine doses sufficient for inducing a ∼99.99% reduction in total E. coli levels, UPEC represented a significant proportion of the chlorine-resistant population. By contrast, no Shiga toxin-producing E. coli were observed in these chlorinated sewage libraries. Our results suggest that clinically-relevant UPEC exist in treated wastewater effluents and that they appear to be specifically adapted to survive wastewater treatment processes.
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Affiliation(s)
- Shuai Zhi
- School of Medicine, Ningbo University, Ningbo, China
| | - Paul Stothard
- Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Graham Banting
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Candis Scott
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Kristin Huntley
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Kanghee Ryu
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Simon Otto
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Nicholas Ashbolt
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada
| | - Sylvia Checkley
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Tao Dong
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Norma J Ruecker
- City of Calgary, Water Quality Services, Calgary, Alberta, Canada
| | - Norman F Neumann
- School of Public Health, University of Alberta, Edmonton, Alberta, Canada.
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Santos ACDM, Santos FF, Silva RM, Gomes TAT. Diversity of Hybrid- and Hetero-Pathogenic Escherichia coli and Their Potential Implication in More Severe Diseases. Front Cell Infect Microbiol 2020; 10:339. [PMID: 32766163 PMCID: PMC7381148 DOI: 10.3389/fcimb.2020.00339] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Accepted: 06/04/2020] [Indexed: 12/17/2022] Open
Abstract
Although extraintestinal pathogenic Escherichia coli (ExPEC) are designated by their isolation site and grouped based on the type of host and the disease they cause, most diarrheagenic E. coli (DEC) are subdivided into several pathotypes based on the presence of specific virulence traits directly related to disease development. This scenario of a well-categorized E. coli collapsed after the German outbreak of 2011, caused by one strain bearing the virulence factors of two different DEC pathotypes (enteroaggregative E. coli and Shiga toxin-producing E. coli). Since the outbreak, many studies have shown that this phenomenon is more frequent than previously realized. Therefore, the terms hybrid- and hetero-pathogenic E. coli have been coined to describe new combinations of virulence factors among the classic E. coli pathotypes. In this review, we provide an overview of these classifications and highlight the E. coli genomic plasticity that results in some mixed E. coli pathotypes displaying novel pathogenic strategies, which lead to a new symptomatology related to E. coli diseases. In addition, as the capacity for genome interrogation has grown in the last few years, it is clear that genes encoding some virulence factors, such as Shiga toxin, are found among different E. coli pathotypes to which they have not traditionally been associated, perhaps foreshowing their emergence in new and severe outbreaks caused by such hybrid strains. Therefore, further studies regarding hetero-pathogenic and hybrid-pathogenic E. coli isolates are necessary to better understand and control the spread of these pathogens.
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Affiliation(s)
- Ana Carolina de Mello Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Rosa Maria Silva
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Tânia Aparecida Tardelli Gomes
- Disciplina de Microbiologia, Departamento de Microbiologia, Imunologia e Parasitologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
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Phillips LE, Verma S, Surapaneni BK, Dutta SK. Potential clinical application of an automated fluorescent microbial cell counter in the detection of urinary tract infection. J Clin Lab Anal 2020; 34:e23334. [PMID: 32621559 PMCID: PMC7439331 DOI: 10.1002/jcla.23334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 02/21/2020] [Accepted: 03/16/2020] [Indexed: 11/17/2022] Open
Abstract
Background Urinary tract infections (UTI) account for millions of office visits and approximately 400 000 hospital admissions every year in the United States; as a result, the cost burden of UTI in the USA is estimated at approximately $2.8 billion. There is a great deal of interest in finding newer, faster, and more reliable methods for diagnosing UTI as compared to the standard urine culture. Methods An automated fluorescent microbial cell counter was used to compare urine samples found to be positive for Escherichia coli UTI via cell culturing (n = 11) with UTI‐negative samples (n = 10). Results Patients with a positive urine culture had significantly higher cell count results using the microbial cell counter (1.01 × 108 cells/mL) as compared to the negative samples (2.35 × 106 cells/mL; P = .0022). Conclusions These observations suggest that automated microbial cell counters may serve as a rapid, objective method for the detection of bacteriuria in urine samples submitted for evaluation of suspected UTI.
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Affiliation(s)
- Laila E Phillips
- Division of Gastroenterology Research, Sinai Hospital, Baltimore, MD, USA
| | - Sandeep Verma
- Division of Gastroenterology Research, Sinai Hospital, Baltimore, MD, USA
| | - Balarama K Surapaneni
- Department of Internal Medicine, Aventura Hospital and Medical Center, Aventura, FL, USA
| | - Sudhir K Dutta
- Division of Gastroenterology Research, Sinai Hospital, Baltimore, MD, USA.,University of Maryland School of Medicine, Baltimore, MD, USA
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Díaz-Jiménez D, García-Meniño I, Fernández J, García V, Mora A. Chicken and turkey meat: Consumer exposure to multidrug-resistant Enterobacteriaceae including mcr-carriers, uropathogenic E. coli and high-risk lineages such as ST131. Int J Food Microbiol 2020; 331:108750. [PMID: 32559710 DOI: 10.1016/j.ijfoodmicro.2020.108750] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Revised: 04/10/2020] [Accepted: 06/06/2020] [Indexed: 12/13/2022]
Abstract
For the first time, this study evaluates consumer exposure via poultry meat to Enterobacteriaceae with capacity to develop severe extraintestinal infections by either bacterial virulence and/or antibiotic resistance traits. The characterization of 256 isolates and the assessment of five parameters, showed that 96 of 100 poultry meat samples from supermarkets of northwest Spain posed ≥ one potential risk: i) 96% carried Enterobacteriaceae resistant to antimicrobials of categories A (64% to monobactams) or B (95% to cephalosporins 3rd and 4rd- generation, quinolones and/or polymixins) of the new categorization of EMA. ii) More than one extended-spectrum-β-lactamase (ESBL)-producing Enterobacteriaceae species were recovered from 28% of poultry meat. iii) High-risk lineages of E. coli, including multidrug-resistant ST131-H22, were present in 62% of samples. iv) E. coli recovered from 25% of samples conformed the ExPEC status. v) E. coli from 17% of samples satisfied the UPEC status. Of note, the recovery from different samples of two E. coli CC10-A (CH11-54) carrying mcr-1.1-bearing IncX4 plasmids, and four E. coli CC10-A (eae-beta1) of the hybrid pathotype aEPEC/ExPEC. (ESBL)-producing K. pneumoniae were isolated from 27% of samples. In summary, poultry meat microbiota is a source of genetically diverse Enterobacteriaceae, resistant to relevant antimicrobials and potentially pathogenic for consumers.
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Affiliation(s)
- Dafne Díaz-Jiménez
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Isidro García-Meniño
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Javier Fernández
- Servicio de Microbiología, Hospital Universitario Central de Asturias (HUCA). Instituto de Investigación del Principado de Asturias (ISPA), Oviedo, Spain
| | - Vanesa García
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain.; Department of Veterinary and Animal Sciences, Section of Veterinary Clinical Microbiology, University of Copenhagen, København, Denmark
| | - Azucena Mora
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbiología y Parasitología, Facultad de Veterinaria, Universidad de Santiago de Compostela (USC), Lugo, Spain.; Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain..
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Draft Genome Sequence of an Escherichia coli Sequence Type 420 Isolate from a Patient with Urinary Tract Infection in Northern California. Microbiol Resour Announc 2020; 9:9/23/e00251-20. [PMID: 32499367 PMCID: PMC7272548 DOI: 10.1128/mra.00251-20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The genome sequence of a uropathogenic Escherichia coli sequence type 420 strain isolated from a patient with urinary tract infection in northern California is described here. The draft genome sequence includes a 4.8-Mb chromosome, accompanied by a 114-kb plasmid containing IncFIB/IncFII/Col156 and a 35-kb plasmid containing IncN3. The genome sequence of a uropathogenic Escherichia coli sequence type 420 strain isolated from a patient with urinary tract infection in northern California is described here. The draft genome sequence includes a 4.8-Mb chromosome, accompanied by a 114-kb plasmid containing IncFIB/IncFII/Col156 and a 35-kb plasmid containing IncN3.
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Virulence Potential of a Multidrug-Resistant Escherichia coli Strain Belonging to the Emerging Clonal Group ST101-B1 Isolated from Bloodstream Infection. Microorganisms 2020; 8:microorganisms8060827. [PMID: 32486334 PMCID: PMC7355805 DOI: 10.3390/microorganisms8060827] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 02/07/2023] Open
Abstract
Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from a bloodstream infection of an inpatient with persistent gastroenteritis and T-zone lymphoma that died due to septic shock. Despite causing an extraintestinal infection, previous studies showed that it did not have the usual characteristics of an extraintestinal pathogenic E. coli. Instead, it belonged to phylogenetic group B1 and harbored few known virulence genes. To evaluate the pathogenic potential of strain EC121, an extensive genome sequencing and in vitro characterization of various pathogenicity-associated properties were performed. The genomic analysis showed that strain EC121 harbors more than 50 complete virulence genetic clusters. It also displays the capacity to adhere to a variety of epithelial cell lineages and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, EC121 was shown to be virulent in the Galleria mellonella model. Furthermore, EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2. Completing the scenario, it belongs to serotype O154:H25 and to sequence type 101-B1, which has been epidemiologically linked to extraintestinal infections as well as to antimicrobial resistance spread. This study with E. coli strain EC121 shows that clinical isolates considered opportunistic might be true pathogens that go underestimated.
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Antimicrobial Resistance, Genetic Diversity and Multilocus Sequence Typing of Escherichia coli from Humans, Retail Chicken and Ground Beef in Egypt. Pathogens 2020; 9:pathogens9050357. [PMID: 32397188 PMCID: PMC7281645 DOI: 10.3390/pathogens9050357] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/28/2020] [Accepted: 05/06/2020] [Indexed: 01/02/2023] Open
Abstract
Contamination of retail foods with foodborne pathogens, particularly the antimicrobial resistant ones, poses a persistent threat to human health. There is a dearth of information about the overlapping Escherichia coli (E. coli) lineages circulating among retail foods and humans in Egypt. This study aimed to determine the clonal diversity of 120 E. coli isolates from diarrheic patients (n = 32), retail chicken carcasses (n = 61) and ground beef (n = 27) from Mansoura, Egypt using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Simpson’s index of diversity was calculated to compare the results of both typing methods. Antimicrobial resistance phenotypes, genotypes and phylogrouping of the isolates were also determined. Higher frequencies of antimicrobial resistance were found among chicken isolates compared to beef and human isolates; regardless of isolate source, the predominant antimicrobial resistances were found against ampicillin (87/120, 72.5%), tetracycline and sulfisoxazole (82/120, 68.3%, each), and streptomycin (79/120, 65.8%). None of the isolates displayed resistance to meropenem. The prevalent genes detected were tetA (64.2%), blaTEM (62.5%), sul1 (56.7%), floR (53.3%), sul2 (50%), strB (48.3%) and strA (47.5%) corresponding with resistance phenotypes. Alarmingly, blaCTX was detected in 63.9% (39/61) of chicken isolates. The majority of E. coli isolates from humans (90.6%), beef (81.5%) and chicken (70.5%) belonged to commensal phylogroups (A, B1, C). Using PFGE analysis, 16 out of 24 clusters (66.7%) contained isolates from different sources at a similarity level ≥75%. MLST results assigned E. coli isolates into 25, 19 and 13 sequence types (STs) from chicken, human and beef isolates, respectively. Six shared STs were identified including ST1011, ST156, ST48, ST224 (chicken and beef), ST10 (human and chicken) and ST226 (human and beef). Simpson’s index of diversity was higher for MLST (0.98) than PFGE (0.94). In conclusion, the existence of common genetic determinants among isolates from retail foods and humans in Egypt as well as the circulation of shared STs indicates a possible epidemiological link with potential zoonotic hazards.
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Xu A, Scullen O, Sheen S, Liu Y, Johnson JR, Sommers CH. Inactivation of extraintestinal pathogenic E. coli suspended in ground chicken meat by high pressure processing and identification of virulence factors which may affect resistance to high pressure. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.107070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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